6DB8

Structural basis for promiscuous binding and activation of fluorogenic dyes by DIR2s RNA aptamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86541 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.219 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural basis for activation of fluorogenic dyes by an RNA aptamer lacking a G-quadruplex motif.

Shelke, S.A.Shao, Y.Laski, A.Koirala, D.Weissman, B.P.Fuller, J.R.Tan, X.Constantin, T.P.Waggoner, A.S.Bruchez, M.P.Armitage, B.A.Piccirilli, J.A.

(2018) Nat Commun 9: 4542-4542

  • DOI: 10.1038/s41467-018-06942-3
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The DIR2s RNA aptamer, a second-generation, in-vitro selected binder to dimethylindole red (DIR), activates the fluorescence of cyanine dyes, DIR and oxazole thiazole blue (OTB), allowing detection of two well-resolved emission colors. Using Fab BL3- ...

    The DIR2s RNA aptamer, a second-generation, in-vitro selected binder to dimethylindole red (DIR), activates the fluorescence of cyanine dyes, DIR and oxazole thiazole blue (OTB), allowing detection of two well-resolved emission colors. Using Fab BL3-6 and its cognate hairpin as a crystallization module, we solved the crystal structures of both the apo and OTB-SO 3 bound forms of DIR2s at 2.0 Å and 1.8 Å resolution, respectively. DIR2s adopts a compact, tuning fork-like architecture comprised of a helix and two short stem-loops oriented in parallel to create the ligand binding site through tertiary interactions. The OTB-SO 3 fluorophore binds in a planar conformation to a claw-like structure formed by a purine base-triple, which provides a stacking platform for OTB-SO 3, and an unpaired nucleotide, which partially caps the binding site from the top. The absence of a G-quartet or base tetrad makes the DIR2s aptamer unique among fluorogenic RNAs with known 3D structure.


    Organizational Affiliation

    School of Biological Sciences, The University of Auckland, Auckland, New Zealand.,Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland.,Institute for Integrative Biology of the Cell, CEA, CNRS, Univ Paris-Sud and Université Paris-Saclay, Gif-sur-Yvette, France.,Department of Biochemistry & Biophysics, Stockholm University, Stockholm, Sweden.,School of Medicine, Deakin University, Geelong, VIC 3217, Australia.,Institute for Protein Design, University of Washington, Seattle, WA, USA. emarcos82@gmail.com.,Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390.,Vector Biology Unit, Max Planck Institute for Infection Biology, Berlin, Germany.,State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, P.R. China.,High Pressure and Synchrotron Radiation Physics Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India.,Department of Life Sciences, National Central University, Taoyuan, 32001, Taiwan. chinyuchen@cc.ncu.edu.tw.,Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland. Electronic address: ramesh.pillai@unige.ch.,From the Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 and William.Royer@umassmed.edu.,Food Technology Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, India.,Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Medical Neurobiology, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China. wywen@fudan.edu.cn.,Department of Chemistry, York Structural Biology Laboratory , University of York , Heslington, York YO10 5DD , United Kingdom.,German Research Center for Environmental Health, Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Zentrum München, 85764, Neuherberg, Germany; Chair of Experimental Genetics, Technical University Munich, 85350, Freising-Weihenstephan, Germany; German Center for Diabetes Research (DZD), 85764, Neuherberg, Germany.,Drug Resistance & Membrane Proteins Laboratory, UMR 5086 CNRS-UCBL1, IBCP, 69367, Lyon, France.,Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, CA 90095.,Department of Experimental Medical Science, Lund University, Lund, Sweden.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555.,Department of Applied Biology and Chemical Technology, Central Laboratory of Institute of Molecular Technology for Drug Discovery and Synthesis, The Hong Kong Polytechnic University, Hung Hom, Hong Hong, China.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, New York.,Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea.,Protein Diffraction Group, Experimental Facility Division, National Synchrotron Radiation Research Center, Hsinchu, 30076, Taiwan.,Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK.,Department of Molecular Biosciences, University of Texas at Austin, Austin, TX 78712, USA.,Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.,NCE Discovery (Domainex Ltd) , Chesterford Research Park, Little Chesterford , Saffron Walden , Essex CB10 1XL , U.K.,Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom, and.,Malopolska Centre of Biotechnology, Jagiellonian University, 30-387 Cracow, Poland.,CNRS, IMoPA, Université de Lorraine, Nancy, F-54000, France. xavier.manival@univ-lorraine.fr.,Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Kumamoto 862-0973, Japan; Priority Organization for Innovation and Excellence, Kumamoto University, Kumamoto 862-0973, Japan.,School of Life Science and Technology, ShanghaiTech University, 100 Haike Road, Shanghai 201210, P.R. China.,Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Department of Life Sciences, National Central University, Taoyuan, 32001, Taiwan.,Institute of Structural and Molecular Biology, Birkbeck College, University of London, Malet Street, London, United Kingdom.,Department of Biochemistry, University of Washington, Seattle, WA, USA. emarcos82@gmail.com.,Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC 3800, Australia.,Depertment of Biochemistry, Faculty of Medicine, Osaka Medical College, Osaka, Japan.,Evotec, Milton, United Kingdom.,Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.,Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russian Federation.,Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín, CP1650 San Martín, Argentina.,Department of Chemistry, Chonnam National University, Gwangju, 61186, Republic of Korea. jsunkim@chonnam.ac.kr.,School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea.,Department of Molecular Genetics, German Institute of Human Nutrition, Potsdam-Rehbruecke, Arthur-Scheunert-Allee, Nuthetal, Germany.,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland. Electronic address: allain@mol.biol.ethz.ch.,European Molecular Biology Laboratory, Grenoble Outstation, 71 Avenue des Martyrs, 38042 Grenoble, France.,Faculty of Chemistry, Jagiellonian University, 30-387 Cracow, Poland.,Groningen Enzyme and Cofactor Collection (GECCO), University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands.,Foundation for Applied Molecular Evolution and the Westheimer Institute of Science & Technology, Alachua, FL 32615, USA.,Ingénierie Moléculaire et Physiopathologie Articulaire, Centre National de la Recherche Scientifique Unité Mixte de Recherche 7365, Université de Lorraine, Biopôle de l'Université de Lorraine, Vandoeuvre-les-Nancy Cedex, France.,Department of Biochemistry, University of Washington, Seattle, WA, USA.,Groningen Enzyme and Cofactor Collection (GECCO), University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands. m.w.fraaije@rug.nl.,Structural Biology Brussels, Vrije Universiteit Brussels, 1050 Brussels, Belgium.,Institute of Biostructures and Bioimaging (IBB), National Research Council & Interuniversity Research Centre on Bioactive Peptides (CIRPEB), Via Mezzocannone 16, 80134 Naples, Italy. Electronic address: marilisa.leone@cnr.it.,Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Medical Neurobiology, Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, 200032, China.,Hybrigenics Services, Paris, 75014, France.,From the Departments of Antibody Discovery and Protein Engineering.,Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany.,IGF, CNRS, Université de Montpellier, Montpellier, 34090, France.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN Leiden, the Netherlands.,Institute of Immunology, University Medical Center Ulm, Ulm, Germany.,School of Pharmacy, University of Pittsburgh, Pittsburgh, PA, 15261.,Department of Chemical and Biological Engineering; University of Wisconsin-Madison; 1415 Engineering Drive; Madison, WI, 53706.,Proteomics & Mass Spectrometry Laboratory, ISPAAM, National Research Council, Via Argine 1085, 80147 Naples, Italy.,Beryllium Discovery, Bedford, Massachusetts, United States of America.,GM/CA, Advanced Photon Source, Argonne National Laboratory, Argonne, IL 60439.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA. Electronic address: wilson@scripps.edu.,Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Midatech Pharma Plc, Milton, United Kingdom.,Department of Chemistry , University of Eastern Finland , 80101 Joensuu , Finland.,Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158.,Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ 07030; yi-lu@illinois.edu yong.zhang@stevens.edu moennelo@ohsu.edu.,From the Departments of Structural Biology and.,MRC Laboratory of Molecular Biology, Cambridge, UK.,Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medical College, New York, New York.,Department of Molecular Biology, Science III, University of Geneva, 30 Quai Ernest-Ansermet, CH-1211 Geneva 4, Switzerland.,Institute of Biochemistry, Graz University of Technology, Graz, Austria.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Aapistie 7A, Oulu, Finland.,Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA. hiroshi.matsuo@nih.gov.,Temasek Life Sciences Laboratory, Department of Biological Sciences, National University of Singapore, Singapore, 117604, Singapore. caiyu@tll.org.sg.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, Archimedesweg 6, 2333 CN Leiden, the Netherlands; Department of Neurology, Amsterdam Neuroscience, Academic Medical Center, Meidreefberg 9, 1105 AZ Amsterdam, the Netherlands; Department of Epidemiology, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA 02115, USA.,CNRS, IMoPA, Université de Lorraine, Nancy, F-54000, France.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110; svirgin@vir.bio fremont@wustl.edu.,Janssen Prevention Center, Janssen Pharmaceutical Companies of Johnson & Johnson, 3210 Merryfield Row, San Diego, CA 92121, USA.,Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, 01655, USA.,School of Biochemistry, Devi Ahilya University, Indore, India.,Jagiellonian University, Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics, Gronostajowa 2, 30-387 Kraków, Poland. Electronic address: lewinski@chemia.uj.edu.pl.,Jagiellonian University, Institute of Zoology and Biomedical Research, Department of Cell Biology and Imaging, Gronostajowa 9, 30-387 Kraków, Poland. Electronic address: artur.biela@uj.edu.pl.,Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada.,Department of Physiological Chemistry, University of Veterinary Medicine Hannover, Hannover, Germany.,Graduate School of Science, Osaka City University, Osaka, Japan.,Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105.,From the Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104 augen-pioszak@ouhsc.edu.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110.,Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, 21702, USA.,Section of Structural Biology, Department of Medicine, Imperial College London, London, United Kingdom.,Laboratory of Physical Chemistry, ETH Zürich, Zürich, Switzerland.,Department of Biological Chemistry, University of California at Los Angeles, Los Angeles, California.,BioBank, First Affiliated Hospital, School of Medicine, Xi'an Jiaotong University, Shaanxi Sheng 710061, China.,From the Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil, andre.ambrosio@lnbio.cnpem.br.,Park Place Research Ltd , Unit 5/6 Willowbrook Technology Park, Llandogo Road, St. Mellons , Cardiff CF3 0EF , U.K.,Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania. Electronic address: matulis@ibt.lt.,Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, 3010, Australia.,Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Vilnius, Lithuania.,IGMM, CNRS, Université de Montpellier, Montpellier, 34293, France. edouard.bertrand@igmm.cnrs.fr.,ED515, Paris Sorbonne Université, 75006 Paris, France.,Department of Biological Sciences, University of Bergen, Thormøhlens gate 53, Bergen, 5006, Norway.,Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA.,Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland, 4111, Australia.,Department of Biochemistry and Groupe de Recherche Axé sur la Structure des Protéines , McGill University , Montreal , QC H3G 0B1 , Canada.,College of Pharmaceutical Sciences , Zhejiang University of Technology , Hangzhou 310014 , P. R. China.,Signalling in Apicomplexan Parasites Laboratory, The Francis Crick Institute, NW1 1AT London United Kingdom.,iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2781-901, Portugal.,From the Departments of Antibody Discovery and Protein Engineering, dallacquaw@medimmune.com.,Department of Computer Science, Florida State University, Tallahassee, FL 32306-4530, United States.,CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic.,Institute for Pharmaceutical Chemistry, Philipps University Marburg, 35032, Marburg, Germany. Electronic address: marchais@staff.uni-marburg.de.,Institute of Tropical Medicine and German Center for Infection Research, Partner Site Tübingen, University of Tübingen, Tübingen, Germany.,Departments of Chemistry and Global Health , University of Washington , 36 Bagley Hall, 400 15th Avenue NE , Seattle , Washington 98195 , United States.,From the Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104.,Viral Mutation Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute at Frederick, Frederick, MD, 21702, USA.,Department of Structural Biology, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Kumamoto 862-0973, Japan.,Department of Pharmacology, University of Texas, Southwestern Medical Center, Dallas, TX 75390.,Institute for Frontier Materials, Deakin University, Geelong, VIC 3217, Australia.,Department of Chemistry, Umeå University, Umeå, Sweden.,Jagiellonian University, Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics, Gronostajowa 2, 30-387 Kraków, Poland. Electronic address: loch@chemia.uj.edu.pl.,Department of Internal Medicine, Faculty of Medicine and Health Sciences, Ghent University, 9000 Ghent, Belgium.,Department of Biochemistry & Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Department of Biochemistry, University of Washington, Seattle, WA, USA. dabaker@uw.edu.,Institute of Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland, Hofackerstrasses 30, 4132 Muttenz, Switzerland. Electronic address: georg.lipps@fhnw.ch.,Leicester Institute of Structural and Chemical Biology, University of Leicester, Leicester, United Kingdom.,the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025.,Jagiellonian University, Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics, Gronostajowa 2, 30-387 Kraków, Poland. Electronic address: lipowska@chemia.uj.edu.pl.,Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO 63110.,The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, UiT The Arctic University of Norway, Tromsø, 9037, Norway.,Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, SW7 2AZ London, United Kingdom; s.j.matthews@imperial.ac.uk s.r.wig@imperial.ac.uk.,State Key Laboratory of Bioorganic and Natural Products Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 345 Lingling Road, Shanghai, 200032, China.,Pharmaceutical and Medicinal Chemistry, Saarland University, Campus C23, 66123, Saarbrücken, Germany.,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia.,Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158; rkaback@mednet.ucla.edu stroud@msg.ucsf.edu.,Institute for Protein Design, University of Washington, Seattle, WA, USA.,Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom, and eddjames@soton.ac.uk.,Department of Biothermodynamics and Drug Design, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania.,From the Departments of Antibody Discovery and Protein Engineering, oganesyanv@medimmune.com.,Unité Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528, CNRS, 75015 Paris, France.,Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea.,the Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom.,Research Center for Applied Sciences, Academia Sinica, Taipei, 11529, Taiwan.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390.,Bioactive Molecules and Medicinal Chemistry, EA 4446, Faculty of Pharmacy - ISPB, University Lyon 1, 69373, Lyon, France; Drug Resistance & Membrane Proteins Laboratory, UMR 5086 CNRS-UCBL1, IBCP, 69367, Lyon, France.,State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300071, China.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA. jpicciri@uchicago.edu.,CRBM, University of Montpellier, CNRS, 1919 Route de Mende, Montpellier, 34090, France.,Department of Physiology, University of California, Los Angeles, CA 90095.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801; yi-lu@illinois.edu yong.zhang@stevens.edu moennelo@ohsu.edu.,College of Medicine, Kyungpook National University, Daegu, 41940, Republic of Korea.,Biosuperiors, MedImmune, Gaithersburg, Maryland 20878.,the School of Electrical and Computer Engineering, University of Campinas, São Paulo 13083-852, Brazil, and.,Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee 38105 charles.rock@stjude.org.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390.,Firebird Biomolecular Sciences LLC, Alachua, FL 32615, USA.,UCB Celltech, Slough, United Kingdom.,Department of Microbiology and Immunology, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma 73104.,Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK.,Health Science Research Facility 130, 149 Beaumont Avenue, Department of Molecular Physiology & Biophysics, University of Vermont, Burlington, VT 05405, United States.,Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801.,The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee; Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Department of Physics and Astronomy, University of Tennessee, Knoxville, Tennessee; Shull Wollan Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee.,Laboratory of Cell Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States.,Section of Microbiology and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, United Kingdom.,The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee; Joint Institute for Biological Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Biology and Soft Matter Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee. Electronic address: heberlefa@ornl.gov.,Department of Microbiology and Immunology, University of Otago, 9016 Dunedin, New Zealand.,Division of Life Science, State Key Laboratory of Molecular Neuroscience, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China.,Institute for Pharmaceutical Chemistry, Philipps University Marburg, 35032, Marburg, Germany.,Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA. Electronic address: snowren@berkeley.edu.,Pure MHC LLC, Austin, Texas 78229, and.,Departments of Biochemistry and Immunology, University of Toronto, Toronto, ON, Canada.,Temasek Life Sciences Laboratory, Department of Biological Sciences, National University of Singapore, Singapore, 117604, Singapore.,Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, United States.,Department of Microbiology & Immunology , Columbia University Irving Medical Center , 701 West 168th Street, HHSC 1502 , New York , New York 10032 , United States.,Bioactive Molecules and Medicinal Chemistry, EA 4446, Faculty of Pharmacy - ISPB, University Lyon 1, 69373, Lyon, France.,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland.,Division of Infectious Diseases, Department of Medicine , Columbia University Irving Medical Center , PH8-W, 630 West 168th Street, PH 8-West , New York , New York 10032 , United States.,From the Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil, sandra.dias@lnbio.cnpem.br.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany.,California NanoSystems Institute, University of California at Los Angeles, Los Angeles, California.,Jagiellonian University, Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics, Gronostajowa 2, 30-387 Kraków, Poland. Electronic address: monika.siuda@doctoral.uj.edu.pl.,Infinitus (China) Co. Ltd. , Guangzhou 510663 , P. R. China.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.,Department of Otorhinolaryngology, Klinikum der Universität München, Munich, Germany.,B Cell Immunology, German Cancer Research Institute, Heidelberg, Germany.,Univ. Grenoble Alpes, CEA, CNRS, IBS, F-38000 Grenoble, France. anne.volbeda@ibs.fr.,Department of Protein - DNA Interactions, Institute of Biotechnology, Vilnius University, Saulėtekio al. 7, Vilnius LT-10257, Lithuania.,State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China. Electronic address: jtzheng@sjtu.edu.cn.,Department of Pharmacology , Stony Brook University , Stony Brook , New York 11794 , United States.,Uni Research, Center for Applied Biotechnology, Thormøhlens gate 55, Bergen, 5006, Norway.,Institute of Structural and Molecular Biology , University College London , Gower Street , London WC1E 6BT , U.K.,The Wolfson Institute for Biomedical Research , University College London , Gower Street , London WC1E 6BT , U.K.,Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, SW7 2AZ London, United Kingdom.,Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands. m.w.fraaije@rug.nl.,Department of Applied Life Science, Faculty of Biotechnology and Life Science, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan.,Department of Biochemistry and Molecular Cell Biology, Cornell University, Ithaca, New York. Electronic address: rad82@cornell.edu.,From the Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts 01605 and.,the Carlson School of Chemistry and Biochemistry, Clark University, Worcester, Massachusetts 01610.,Molecular Enzymology Group, University of Groningen, Nijenborgh 4, 9747AG, Groningen, The Netherlands.,Structural Biology Lab, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Ferrata 9, 27100, Pavia, Italy. andrea.mattevi@unipv.it.,Structural Biology Lab, Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Via Ferrata 9, 27100, Pavia, Italy.,Department of Clinical Microbiology and Immunology, Sackler School of Medicine, Tel Aviv University, 69978 Tel Aviv, Israel.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.,Department of Biomedical Engineering, Oregon Health and Science University, Portland, United States.,Center for Biological Sequence Analysis, Department of Bio and Health Informatics, The Technical University of Denmark, 2800 Lyngby, Denmark.,Institute of Biophysics, Consiglio Nazionale delle Ricerche, Genova, Italy.,Institute of Biostructures and Bioimaging (IBB), National Research Council & Interuniversity Research Centre on Bioactive Peptides (CIRPEB), Via Mezzocannone 16, 80134 Naples, Italy.,Experimental Molecular Biophysics, Institute of Physics, Freie Universität Berlin, 14195 Berlin, Germany.,Division of Environmental & Biomolecular Systems, Oregon Health & Science University, Portland, OR 97239.,Equipe labélisée Ligue Nationale Contre le Cancer, 34293, Montpellier, France. edouard.bertrand@igmm.cnrs.fr.,Faculty of Chemistry and Chemical Technology , University of Ljubljana , Večna pot 113 , SI-1000 Ljubljana , Slovenia.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India.,Department of Herbal Medicine Resources, College of Environmental and Bioresource Sciences, Chonbuk National University, Iksan 54596, Republic of Korea.,Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801.,Department of Structural Biology, Genentech, Inc., South San Francisco, United States.,Institute of Molecular Biophysics, Kasha Laboratory, Florida State University, Tallahassee, FL 32306-4380, United States. Electronic address: taylor@bio.fsu.edu.,VIB-VUB Center for Structural Biology, VIB, 1050 Brussels, Belgium.,Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, NJ 07030.,Equipe labélisée Ligue Nationale Contre le Cancer, 34293, Montpellier, France.,Department of Biochemistry , University of Texas Southwestern Medical Center , 5323 Harry Hines Blvd , Dallas , Texas 75390 , United States.,Department of Biophysics , University of Texas Southwestern Medical Center , 5323 Harry Hines Blvd , Dallas , Texas 75390 , United States.,Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110.,Graduate School of Science and Technology, Kumamoto University, 2-39-1 Kurokami, Kumamoto 860-8555, Japan.,Latvian Biomedical Research and Study Center, Riga, Latvia.,Department of Chemistry, National Tsing Hua University, Hsinchu, 30013, Taiwan.,Pohang Accelerator Laboratory, Pohang, Gyeongbuk, 37673, Republic of Korea.,Program in Molecular Medicine, The Hospital for Sick Children Research Institute, Toronto, ON, Canada. h.wardemann@dkfz.de jean-philippe.julien@sickkids.ca.,Institute of Molecular Biophysics, Kasha Laboratory, Florida State University, Tallahassee, FL 32306-4380, United States.,Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA. Electronic address: jimhurley@berkeley.edu.,INRA, CNRS, Centre des Sciences du Goût et de l'Alimentation, Université de Bourgogne-Franche Comté, Dijon, France.,From the Centre for Biological Sciences, Faculty of Natural & Environmental Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom.,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland. Electronic address: boudet.julien@gmail.com.,Sanofi, Strasbourg, France.,Department of Biochemistry, College of Natural Sciences, Kangwon National University, Chuncheon, 24341, Republic of Korea.,The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, CB2 0XY Cambridge, United Kingdom.,Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, TX 75390; dan.rosenbaum@utsouthwestern.edu.,Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,The Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, CB2 0QH Cambridge, United Kingdom.,Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.,MRC Laboratory of Molecular Biology, Cambridge, UK. jyl@mrc-lmb.cam.ac.,Centre for Cardiovascular Biology and Medicine, Division of Medicine , University College London , 5 University Street , London WC1E 6JJ , U.K.,Department of Chemistry , National Taiwan University , 10617 Taipei , Taiwan R.O.C.,Department of Chemistry, The University of Chicago, Chicago, IL, 60637, USA. jpicciri@uchicago.edu.,Department of Applied Life Science, Faculty of Biotechnology and Life Science, Sojo University, 4-22-1 Ikeda, Kumamoto 860-0082, Japan. Electronic address: hira@life.sojo-u.ac.jp.,Sanaria, Rockville, MD, USA.,Division of Environmental & Biomolecular Systems, Oregon Health & Science University, Portland, OR 97239; yi-lu@illinois.edu yong.zhang@stevens.edu moennelo@ohsu.edu.,The Laboratory of Malaria and Vector Research, NIAID, National Institutes of Health, Rockville, Maryland, 20852, USA. jandersen@nih.gov.,Institute of Biological Chemistry, Academia Sinica, Taipei, 11529, Taiwan.,Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, California 92037.,Jagiellonian University, Faculty of Chemistry, Department of Crystal Chemistry and Crystal Physics, Gronostajowa 2, 30-387 Kraków, Poland; Jerzy Haber Institute of Catalysis and Surface Chemistry, Polish Academy of Sciences, Niezapominajek 8, 30-239 Kraków, Poland. Electronic address: kurpiews@chemia.uj.edu.pl.,Department of Biochemistry, University of Oxford, Oxford, UK.,From the Laboratório Nacional de Biociências, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil.,Department of Pharmacology, University of Texas, Southwestern Medical Center, Dallas, TX 75390; Michael.Reese@UTSouthwestern.edu.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801.,From the Division for Cell Biology and dzajonc@lji.org.,Center for Biomedical Research Support , University of Texas , Austin , Texas 78712 , United States.,Institute of Chemistry and Bioanalytics, University of Applied Sciences Northwestern Switzerland, Hofackerstrasses 30, 4132 Muttenz, Switzerland.,CNRS, INSERM, IBSLOR, Université de Lorraine, Nancy, F-54000, France.,Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University), Ministry of Education, Wuhan University School of Pharmaceutical Sciences, 185 Donghu Road., Wuhan, 430071, China.,Institute for Research in Biomedicine (IRB Barcelona), Barcelona Institute of Science and Technology, Barcelona, Spain. emarcos82@gmail.com.,Department of Physiology, University of California, Los Angeles, CA 90095; rkaback@mednet.ucla.edu stroud@msg.ucsf.edu.,Institute of Structural and Molecular Biology, Division of Biosciences, University College London, London, United Kingdom.,Cyrus Biotechnology, Seattle, WA, USA.,Department of Biochemistry; University of Wisconsin-Madison; 440 Henry Mall; Madison, WI, 53706.,Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States.,Molecular Physiology and Biophysics Section, Porter Neuroscience Research Center, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, United States.,a Department of Biotherapeutic and Medicinal Sciences , Biogen , Cambridge , MA , USA.,Department of Computer Science, Genome Center, University of California, Davis, CA 94520.,Shaanxi Key Laboratory of Natural Products & Chemical Biology, College of Chemistry and Pharmacy, Northwest A&F University, 3 Taicheng Road, Yangling, 712100, Shaanxi, China.,Slovenian NMR Center , National Institute of Chemistry , Hajdrihova 19 , SI-1000 Ljubljana , Slovenia.,Amazon, Seattle, WA, USA.,Division of Chemical Biology & Medicinal Chemistry, College of Pharmacy , University of Texas , Austin , Texas 78712 , United States.,Centre for Cancer Immunology, University of Southampton Faculty of Medicine, University Hospital Southampton, Southampton SO16 6YD, United Kingdom.,From the Division for Cell Biology and.,Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24341, Republic of Korea; Institute of Bioscience and Biotechnology, Kangwon National University, Chuncheon, 24341, Republic of Korea. Electronic address: sungil@kangwon.ac.kr.,The Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, CB2 0XY Cambridge, United Kingdom; walker@mrc-mbu.cam.ac.uk.,MRC Laboratory of Molecular Biology, Cambridge, United Kingdom.,Molecular Biology Institute, University of California, Los Angeles, CA 90095.,Shubnikov Institute of Crystallography, Federal Scientific Research Centre `Crystallography and Photonics' of Russian Academy of Sciences, Leninsky Prospekt 59, Moscow 119333, Russian Federation.,EN-FIST Center of Excellence , Trg OF 13 , SI-1000 Ljubljana , Slovenia.,Department of Microbiology, Immunology & Molecular Genetics, University of California at Los Angeles, Los Angeles, California.,Unité Dynamique Structurale des Macromolécules, Institut Pasteur, UMR 3528, CNRS, 75015 Paris, France; marc.delarue@pasteur.fr.,B Cell Immunology, German Cancer Research Institute, Heidelberg, Germany. h.wardemann@dkfz.de jean-philippe.julien@sickkids.ca.,Department of Biopharmaceutics, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto 862-0973, Japan.,Laboratoire de Spectrométrie de Masse BioOrganique, Université de Strasbourg, CNRS, IPHC UMR 7178, Strasbourg, 67000, France.,German Research Center for Environmental Health, Institute of Experimental Genetics, Genome Analysis Center, Helmholtz Zentrum München, 85764, Neuherberg, Germany.,Analytical Sciences, and.,School of Life Sciences (KNU Creative BioResearch Group), KNU Institute for Microorganisms, Kyungpook National University, Daegu, 41566, Republic of Korea. Electronic address: kkim@knu.ac.kr.,Departments of Molecular Biology and Biochemistry, Pharmaceutical Sciences, and Chemistry , University of California, Irvine , Irvine , California 92697-3900 , United States.,Department of Chemistry and Biochemistry, University of California, Santa Cruz, Santa Cruz, CA, USA.,Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA.,Center for Molecular Microscopy, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, United States.,Chair for Molecular Cell Physiology & Endocrinology, Faculty of Biology, Technical University Dresden, 01062, Dresden, Germany.,IGMM, CNRS, Université de Montpellier, Montpellier, 34293, France.,Monash Institute of Pharmaceutical Sciences, Monash University, Melbourne, VIC 3052, Australia.,Department of Radiotherapy (The M-Lab Group), GROW - School for Oncology and Developmental Biology, Maastricht Comprehensive Cancer Centre, Maastricht University Medical Centre, Maastricht, The Netherlands.,Department of Pathology, Amsterdam Neuroscience, VU University Medical Center, de Boelelaan 1117, 1081 HV Amsterdam, the Netherlands.,Institute for Protein Design, University of Washington, Seattle, WA, USA. dabaker@uw.edu.,Vollum Institute, Oregon Health and Science University, Portland, United States.,Unité Récepteurs-Canaux, Institut Pasteur, UMR 3571, CNRS, 75015 Paris, France.,Vertex, Milton, United Kingdom.,Department of Physiology , UT Southwestern Medical Center at Dallas , 5323 Harry Hines Boulevard , Dallas 75390 , Texas , United States.,the Laboratório Nacional de Nanotecnologia, Centro Nacional de Pesquisa em Energia e Materiais, Campinas, São Paulo 13083-970, Brazil.,Department of Chemistry , University of California Irvine , Irvine , California 92697-2025 , United States.,Infection and Immunity Program, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia; Fasseli.Coulibaly@monash.edu.,School of Pharmaceutical Sciences , Sun Yat-sen University , Guangzhou 510006 , P. R. China.,Molecular Biosensor and Imaging Center, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Biomedical Manufacturing, CSIRO, 343 Royal Parade, Parkville, VIC 3052, Australia.,Department of Chemical Engineering; Pennsylvania State University; 158 Fenske Laboratory; University Park, PA, 16802.,Department of Gene Vectors, Helmholtz Center for Environmental Health, Munich, Germany.,University of Florence, NEUROFARBA Department, Sezione di Farmaceutica e Nutraceutica, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), Italy.,School of Biomedical Sciences, Chung Shan Medical University, No.110, Sec.1, Chien-Kuo N. Rd., Taichung City, Taiwan; Department of Medical Research, Chung Shan Medical University Hospital, No.110, Sec.1, Chien-Kuo N. Rd, Taichung City, Taiwan. Electronic address: cyhuang@csmu.edu.tw.,The Laboratory of Malaria and Vector Research, NIAID, National Institutes of Health, Rockville, Maryland, 20852, USA.,Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin, Germany.,SOLEIL Synchrotron, L'Orme de Merisiers, Saint-Aubin, Gif-sur-Yvette, France.,Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.,Parasites and Microbes Programme , Wellcome Sanger Institute , Hinxton, Cambridgeshire CB10 1SA , U.K.,Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, PA, 15213, USA.,Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark.,Department of Biochemistry , University of Texas Health Science Center , San Antonio , Texas 78229-3900 , United States.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA; Beijing Synchrotron Radiation Facility, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, People's Republic of China.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Av. da República, Oeiras, 2780-157, Portugal.,Department of Biochemistry & Molecular Biology, Oregon Health and Science University, Portland, United States.,Department of Computer Science, University of California, Santa Cruz, Santa Cruz, CA, USA.,Center of Life Sciences , Skolkovo Institute of Science and Technology , Skolkovo, Nobel str. 3 , 143026 Moscow , Russia.,The OCU Advanced Research Institute for Natural Science and Technology, Osaka City University, Osaka, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fab-Heavy chain
H
232N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fab-Light chain
L
212N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (60-MER)R60synthetic construct
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
G4A
Query on G4A

Download SDF File 
Download CCD File 
R
2-[(Z)-(3-methyl-1,3-benzoxazol-2(3H)-ylidene)methyl]-3-(3-sulfopropyl)-1,3-benzothiazol-3-ium
C19 H19 N2 O4 S2
AHPYSIGATYXERL-UHFFFAOYSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86541 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.219 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 109.158α = 90.00
b = 118.442β = 90.00
c = 119.310γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Cootmodel building
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research InstituteUnited StatesR01AI081987

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release