6A44

R1EN(5-227)-ubiquitin fusion


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal Structure Determination of Ubiquitin by Fusion to a Protein That Forms a Highly Porous Crystal Lattice

Maita, N.

(2018) J. Am. Chem. Soc. 140: 13546-13549

  • DOI: 10.1021/jacs.8b07512
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The protein crystallization process requires screening of a large number of conditions using a large quantity of high-purity protein, which makes crystal structure analysis difficult. Thus, the development of easy and versatile protein crystallizatio ...

    The protein crystallization process requires screening of a large number of conditions using a large quantity of high-purity protein, which makes crystal structure analysis difficult. Thus, the development of easy and versatile protein crystallization techniques is both extremely desirable and highly challenging. Here I demonstrate the crystallization and structure determination of ubiquitin by genetic fusion to the highly porous honeycomb lattice of R1EN. I successfully crystallized and collected X-ray data from three R1EN-ubiquitin constructs with various linker lengths under the same conditions as the original R1EN. The crystals diffracted to 1.7-2.4 Å resolution, and the ubiquitin structures were determined with results almost identical to the previously published structure. Moreover, the ubiquitin structure could be solved by molecular replacement using R1EN alone. This method may reduce the effort required for crystallization screening and is applicable to de novo protein structure determination.


    Organizational Affiliation

    Faculty of Science, Nara Women's University, Nara, Japan.,College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, People's Republic of China. Electronic address: zhouwh@nankai.edu.cn.,Laboratory of Biosignaling & Therapeutics, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.,Department of Chemistry and Technologies of Drugs, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy.,Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305.,Institut de Biologie Structurale, Université Grenoble Alpes-CEA-CNRS, Grenoble, France.,Graduate School of Horticulture, Chiba University, Matsudo, Chiba, Japan.,Pohang Accelerator Laboratory, Pohang, Gyeongbuk, Republic of Korea.,VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050 Brussels, Belgium jlauer@mpi-cbg.de wim.versees@vub.be.,Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom. Electronic address: stuart.conway@chem.ox.ac.uk.,Department of Clinical Pathology, University of Melbourne, Australia.,Institute of Bioscience, Universiti Putra Malaysia, UPM Serdang, Selangor Malaysia.,School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom.,Department of Anesthesiology, University of Michigan, Ann Arbor, MI, 48105, USA.,Neuroscience, IMED Biotech Unit , AstraZeneca , Cambridge CB21 6GH , U.K.,Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Mansfield Road, Oxford, OX1 3TA, U.K.,Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.,Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas, 66047.,Henry Wellcome Building for Molecular Physiology, University of Oxford, Oxford, OX3 7BN, UK.,The Gut Health and Food Safety Programme, Quadram Bioscience Institute, NR4 7UA Norwich, United Kingdom.,Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, Japan. ts@chembio.t.u-tokyo.ac.jp.,Department of Radiation Oncology, Perlmutter Cancer Center , NYU Langone Medical Center , New York , New York 10016 , United States.,Epigenetic Regulation of Chromatin Function Group, Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.,Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305.,Department Molecular Oncology and Immunology, B6 Plesmanlaan 121, Amsterdam, 1066CX, The Netherlands.,Pohang Accelerator Laboratory, Pohang, Gyeongbuk, Republic of Korea. jaehyun.park@postech.ac.kr.,Laboratory of Bioinorganic Chemistry, Department of Pharmacy and Biotechnology, University of Bologna, Viale G. Fanin 40, I-40127 Bologna, Italy. stefano.ciurli@unibo.it.,Polgenix Inc., Cleveland, OH 44106, USA.,The Gut Health and Food Safety Programme, Quadram Bioscience Institute, NR4 7UA Norwich, United Kingdom; c.dong@uea.ac.uk nathalie.juge@quadram.ac.uk.,Departments of Biophysics, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas, 75390.,Moscow Institute of Physics and Technology, Dolgoprudniy, Russia.,College of Life Sciences, College of Pharmacy, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, People's Republic of China.,Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany. Electronic address: goerlich@mpibpc.mpg.de.,Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, 112, Taiwan.,Consorzio Interuniversitario di Reattività Chimica e Catalisi (CIRCC) , via Celso Ulpiani 27 , 70126 Bari , Italy.,Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK.,BioMedical Research Centre, University of East Anglia, NR4 7TJ Norwich, United Kingdom.,the Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, and mhk8n@kribb.re.kr.,School of Pharmacy, University of East Anglia, NR4 7TJ Norwich, United Kingdom.,Antibody and Vaccine Group, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK. Electronic address: ann.white@ucb.com.,Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan tendo@cc.kyoto-su.ac.jp.,Max Planck Institute of Biophysics, Frankfurt am Main, Germany.,Cardiovascular and Metabolic Diseases, IMED Biotech Unit , AstraZeneca , 141 57 Huddinge , Sweden.,Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, India.,Henry Wellcome Building for Molecular Physiology, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7LD, U.K.,Boehringer Ingelheim RCV GmbH & Co. KG , Doktor-Boehringer-Gasse 5-11 , 1120 Vienna , Austria.,Fakultät für Biologie, Universität Duisburg-Essen, Essen, Germany.,Department of Chemistry, Graduate School of Science, Nagoya University, Nagoya, Japan.,CRUK/MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Old Road Campus Research Building, Oxford OX3 7DQ, United Kingdom.,Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas.,School of Chemistry and Biochemistry , The University of Western Australia (M313) , 35 Stirling Highway , Crawley , WA 6009 , Australia.,Hamburg Centre for Ultrafast Imaging & Institute for Nanostructure and Solid State Physics, University of Hamburg, 20146 Hamburg, Germany.,Graduate School of Science, Osaka Prefecture University, 1-1 Gakuen-cho, Naka-ku, Sakai, Osaka 599-8531, Japan.,Department of Biology, Faculty of Science, Niigata University, Ikarashi 2-8050, Nishi-ku, Niigata 950-2181, Japan.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China.,Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, UK.,Laboratory for Functional Genomics of Extremophiles, Faculty of Agriculture, Kyushu University, Fukuoka, Japan kawarabayasi.yutaka@nifty.com.,NTU Institute of Structural Biology, Nanyang Technological University, 59 Nanyang Drive, 636921, Singapore.,Division of Cardiovascular Medicine, Radcliffe Department of Medicine, Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford, OX3 7LD, UK.,Japan Science and Technology Agency/Core Research for Evolutional Science and Technology, Kyoto Sangyo University, Kyoto, Japan.,Discovery Safety, Drug Safety and Metabolism, IMED Biotech Unit , AstraZeneca , Waltham , Massachusetts 02451 , United States.,Medicines Discovery Institute , Cardiff University , Main Building, Park Place , Cardiff CF10 3AT , United Kingdom.,Laboratório de Cristalografia de Proteínas, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, Brazil.,Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstraße 108, 01307 Dresden, Germany jlauer@mpi-cbg.de wim.versees@vub.be.,Division of Organic Chemistry, CSIR- National Chemical Laboratory, Pune, India.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China. Electronic address: zhmin07@ahu.edu.cn.,From the Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, bhoh@kaist.ac.kr.,Department of Anesthesiology, Weill Cornell Medical College, New York, United States.,College of Life Sciences, Tianjin University, Tianjin, 300071, People's Republic of China.,MRC-University of Glasgow Centre for Virus Research, Garscube Campus, Glasgow, Scotland, United Kingdom.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan. Electronic address: muto.tsuyoshi.zu@daiichisankyo.co.jp.,Institute of Crystallography, University of Aachen (RWTH), Aachen, Germany.,Department of Biochemistry, Ludwig-Maximilians-Universität München, Munich, Germany.,Institute of Life Science and Natural Resources, Korea University, Seoul, Republic of Korea. structures@korea.ac.kr.,From the Picobiology Institute and tsuki@protein.osaka-u.ac.jp.,Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, United States.,Department of Molecular Biology, University of Geneva, 30 Quai E. Ansermet, 1211 Geneva, Switzerland.,Division of Disease Proteomics, Institute of Advanced Medical Sciences , Tokushima University , 3-18-15 Kuramoto-cho , Tokushima 770-8503 , Japan.,Epigenetics Discovery Performance Unit, GlaxoSmithKline R&D, Stevenage Hertfordshire SG1 2NY, United Kingdom.,Department of Cellular Logistics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany.,Academy of Scientific and Innovative Research (AcSIR), CSIR-National Chemical Laboratory, Pune, India.,York Structural Biology Laboratory , Department of Chemistry , The University of York , YO10 5DD , UK.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany. ivan.dikic@biochem2.de.,VA Tennessee Valley Healthcare System , 1310 24th Avenue S. , Nashville , Tennessee 37212 , United States.,University of Puerto Rico at Humacao, Humacao, PR, USA.,Cayman Chemical Company , 1180 East Ellsworth , Ann Arbor , Michigan 48108 , United States.,Molecular Medicine, Scripps Research, United States.,Department of Pathology, Weill Cornell Medical College, New York, United States.,T-Cell Modulation Group, Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom.,Research Service, Louis Stokes Cleveland VA Medical Center, Cleveland, OH 44106, USA.,Department of Biochemistry & Molecular Biology, University of Melbourne, Australia.,Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100093, China.,Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.,Department of Molecular and Integrative Physiology , University of Michigan Medical School , Ann Arbor , Michigan 48109 , United States.,Oncology Chemistry, IMED Biotech Unit , AstraZeneca , Cambridge CB4 0WG , U.K.,Department of Cell Biochemistry, University of Groningen, Groningen 9747 AG, The Netherlands.,Cancer Immunology Discovery, Pfizer Inc., 230 E. Grand Ave, South San Francisco, CA, 94080, USA. shermanmichael.chin@pfizer.com.,Department of Biochemistry, National Centre of Competence in Research Chemical Biology, University of Geneva, Geneva, Switzerland.,University of Florence, NEUROFARBA Department, Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence, Italy. claudiu.supuran@unifi.it.,Sprint Bioscience , 141 57 Huddinge , Sweden.,Infectious Diseases Discovery , GlaxoSmithKline , 1250 South Collegeville Road , Collegeville , Pennsylvania 19426 , United States.,Antibody and Vaccine Group, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK; Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK.,Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany.,VIB Switch Laboratory, VIB, 3000 Leuven, Belgium.,Cleveland Center for Membrane and Structural Biology, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Chiba, Japan.,From the Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425 olsensk@musc.edu.,Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Singapore.,Center for RNA Biology , University of Rochester School of Medicine and Dentistry , Rochester , New York 14642 , United States.,Department of Structure and Function on Neural Network, Korea Brain Research Institute, Deagu, Republic of Korea.,Department of Botany and Plant Biology, University of Geneva, 30 Quai E. Ansermet, 1211 Geneva, Switzerland.,From the Picobiology Institute and yoshi@sci.u-hyogo.ac.jp.,Protein Core Facility, University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK.,European Synchrotron Radiation Facility, 38043 Grenoble, France.,CRUK Beatson Institute, Garscube Campus, Glasgow, Scotland United Kingdom.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305; kcgarcia@stanford.edu.,Scripps Research, United States.,Charnwood Molecular , Loughborough LE11 5DA , U.K.,Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom.,Department of Hematology and Oncology, Center for Cancer Immune Therapy, Herlev Hospital, University of Copenhagen, Herlev, Denmark.,Department of Biochemistry & Genetics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Australia.,Institute of Biochemistry II, Goethe University Frankfurt - Medical Faculty, University Hospital, Frankfurt am Main, Germany.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, 100193, China. chenzhongzhou@cau.edu.cn.,Dipartimento di Scienze Chimiche , Università di Napoli Federico II, Complesso Universitario di Monte S. Angelo , via Cintia 21 , 80126 Napoli , Italy.,Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.,Hauptman Woodward Medical Research Institute, Suny Buffalo, NY, USA.,Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan.,Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA.,Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Molecular Physiology and Biophysics, Faculty of Medical Sciences, University of Fukui, Fukui, Japan.,Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, United Kingdom.,Department of Molecular Microbiology, Washington University School of Medicine, St Louis, MO 63110, USA.,Cancer Immunology Discovery, Pfizer Inc., 230 E. Grand Ave, South San Francisco, CA, 94080, USA.,BioMedical Research Centre, University of East Anglia, NR4 7TJ Norwich, United Kingdom; c.dong@uea.ac.uk nathalie.juge@quadram.ac.uk.,Laboratory for Functional Genomics of Extremophiles, Faculty of Agriculture, Kyushu University, Fukuoka, Japan.,Institute for Life Sciences, University of Southampton, Southampton SO17 1BJ, UK; Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.,Department of Chemistry , Vanderbilt University , Nashville , Tennessee 37232-0146 , United States.,Meyer Cancer Center, Department of Medicine , Weill Cornell Medical College , New York , New York 10065 , United States.,National Institute of Advanced Industrial Science and Technology (AIST), Bioproduction Research Institute, Ibaraki, Japan.,Department of Biochemistry and Biophysics , University of Rochester School of Medicine and Dentistry , Rochester , New York 14642 , United States.,Department of Biochemistry, National University of Singapore, Singapore.,California Institute for Biomedical Research , 11119 North Torrey Pines Road , La Jolla , California 92037 , United States.,Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Japan.,the Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, and jwhwang@kribb.re.kr.,Immunocore LTD, Oxford, United Kingdom.,Antibody and Vaccine Group, Cancer Sciences Unit, University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK.,From the Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305.,Research Centre for Molecular Cancer Prevention, La Trobe University, Melbourne, Australia.,Department of Physiology and Biophysics, Weill Cornell Medical College, New York, United States.,Japan Science and Technology Agency/Core Research for Evolutional Science and Technology, Nagoya University, Nagoya, Japan.,College of Life Sciences, State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin, 300071, People's Republic of China.,Department of Medicinal Chemistry, Faculty of Pharmaceutical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark.,Department of Molecular Biology and Biochemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada.,Biostructural Mechanism Laboratory, RIKEN SPring-8 Center, Sayo, Japan.,Division of Structural Biology, Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, OX3 7BN, UK.,the Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, and.,Department of Chemistry , Simon Fraser University , Burnaby , British Columbia V5A 1S6 , Canada . Email: dvocadlo@sfu.ca.,Institute of Biochemistry, ETH Zürich, Zürich, Switzerland.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305.,Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ 85721, USA. Electronic address: rebeccapage@email.arizona.edu.,Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia.,Institute for Protein Dynamics, Kyoto Sangyo University, Kyoto, Japan.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China.,State Key Laboratory of Marine Environmental Science, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, People's Republic of China.,Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.,the Department of Food Science and Engineering, Ewha Womans University, Seoul 03760, Korea.,Department of Food Science, National (Taiwan) Ocean University, Keelung, 202, Taiwan.,Protein Structure Laboratory, Del Shankel Structural Biology Center, University of Kansas, Lawrence, KS, 66045.,From the Department of Biochemistry and Molecular Biology and Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina 29425.,Technion - Israel Institute of Technology, Haifa, 3200003, Israel.,Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 3TA, United Kingdom.,the Japan Science and Technology Agency, CREST, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan.,Simons Electron Microscopy Center, New York Structural Biology Center, New York, United States.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China. Electronic address: tangrp99@iccas.ac.cn.,Graduate Division of Nutritional and Environmental Sciences, University of Shizuoka, Shizuoka, Japan.,Department of Chemistry and Biotechnology, Graduate School of Engineering, University of Tokyo, Bunkyo-ku, Tokyo, Japan.,Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, UPM Serdang, Selangor, Malaysia.,Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, Beijing Technology and Business University, Beijing, 100048, China.,Discovery Sciences, IMED Biotech Unit , AstraZeneca , S-43183 Mölndal , Sweden.,Division of Biotechnology, Korea University, Seoul, Republic of Korea. structures@korea.ac.kr.,From the Picobiology Institute and.,Department of Biomedical Engineering, Texas A&M University, College Station, Texas; Department of Materials Science and Engineering, Texas A&M University, College Station, Texas; School of Computational Sciences, Korea Institute for Advanced Study, Seoul, South Korea. Electronic address: hwm@tamu.edu.,Department of Chemistry , The Scripps Research Institute , 10550 North Torrey Pines Road , La Jolla , California 92037 , United States.,VIB-VUB Center for Structural Biology, Pleinlaan 2, 1050 Brussels, Belgium.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, 117543, Singapore.,SAXS/WAXS, Australian Synchrotron, Clayton, Australia.,Max Planck Institute of Biochemistry, Department of Structural Cell Biology, Martinsried, Germany.,Systems Immunity Research Institute, Cardiff University School of Medicine, Cardiff, United Kingdom.,Department of Chemistry , University of Rochester , Rochester , New York 14627 , United States.,Department of Life Science, Graduate School of Life Science, University of Hyogo, 3-2-1 Koto, Kamigori, Akoh, Hyogo 678-1297, muramoto@sci.u-hyogo.ac.jp.,Biotechnology Center, National Chung Hsing University, Taichung City, 402, Taiwan.,Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA, United Kingdom; Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.,Bristol-Myers Squibb, 700 Bay Rd, Redwood City, CA, 94063, USA.,Research Center for Materials Science, Nagoya University, Nagoya, Japan.,Botnar Research Centre, Oxford Biomedical Research Unit, Oxford OX3 7LD, U.K.,Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK. andrew.mcmichael@ndm.ox.ac.uk.,Cancer Immunology Discovery, Pfizer Inc., 230 E. Grand Ave, South San Francisco, CA, 94080, USA. javier.chaparro-riggers@pfizer.com.,Department of Life Science, POSTECH, Pohang, Gyeongbuk, Republic of Korea.,Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom.,Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas. Electronic address: jaehyuncho@tamu.edu.,Structural Genomics Consortium, University of Toronto, Toronto, Ontario, M5G 1L7, Canada.,Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan.,Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Pavia, Italy.,Department of Molecular Biosciences, University of Kansas, Lawrence, Kansas, 66045.,Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, United States; Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109-2216, United States; Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109-2216, United States.,Department of Pediatrics, Washington University School of Medicine, St Louis, MO 63110, USA.,Department of Biomedical Engineering, Texas A&M University, College Station, Texas.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, PB 802, 3000 Leuven, Belgium.,Department of Biochemistry, Weill Cornell Medical College, New York, United States.,the Infection and Immunity Research Laboratory, Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, and.,Nuffield Department of Medicine Research Building, Roosevelt Drive, Nuffield Department of Medicine, University of Oxford, Oxford, OX3 7FZ, UK. geraldine.gillespie@ndm.ox.ac.uk.,Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas, 66047.,Department of Systems Biology , Harvard Medical School , Boston , Massachusetts 02215 , United States.,Institute of Complex Systems (ICS), ICS-6: Structural Biochemistry, Research Centre Juelich, Juelich, Germany.,Institute of Biochemistry II, Goethe University Frankfurt - Medical Faculty, University Hospital, Frankfurt am Main, Germany. ivan.dikic@biochem2.de.,Center for Integrated Protein Sciences Munich, Munich, Germany.,Departments of Microbiology, 5323 Harry Hines Blvd., Dallas, Texas, 75390.,Department of Material and Biological Chemistry, Faculty of Science, Yamagata University, Yamagata, Japan.,Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, Kansas, 66506.,Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, United Kingdom.,Department of Molecular and Integrative Physiology, Department of Internal Medicine, Division of Gastroenterology, and Rogel Cancer Center , University of Michigan , Ann Arbor , Michigan 48109 , United States.,Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Pune, India.,National Synchrotron Light Source-II, Brookhaven National Laboratory, Upton, NY 11973, USA.,Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, OX3 7FZ, UK.,IMCA-CAT, Hauptman-Woodward Medical Research Institute, Argonne, Illinois, 60439.,CSIRO Health and Biosecurity, Adelaide, SA, 5000, Australia.,School of Life Sciences, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Key Laboratory of Human Microenvironment and Precision Medicine of Anhui Higher Education Institutes, Anhui University, 111 Jiulong Road, Hefei, Anhui, 230601, China; Department of Biological and Food Engineering, Bozhou University, 2266 Tangwang Road, Bozhou, Anhui, China.,Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, 97006, USA.,Structural Genomics Consortium, University of Oxford, Headington, OX3 7DQ, U.K.,Asubio Pharma Co., Ltd., 6-4-3 Minatojima-Minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan. Electronic address: murafuji.hidenobu.bj@daiichisankyo.co.jp.,Purdue Institute of Immunology, Inflammation and Infectious Diseases and Department of Biological Sciences, Purdue University, West Lafayette, IN, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA-directed DNA polymerase homolog (R1),Polyubiquitin-C
A
302Homo sapiensBombyx mori
This entity is chimeric
Mutation(s): 2 
Gene Names: UBC,
EC: 2.7.7.49
Find proteins for P0CG48 (Homo sapiens)
Go to Gene View: UBC
Go to UniProtKB:  P0CG48
Find proteins for Q7M4J4 (Bombyx mori)
Go to UniProtKB:  Q7M4J4
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACY
Query on ACY

Download SDF File 
Download CCD File 
A
ACETIC ACID
C2 H4 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.189 
  • Space Group: P 3 2 1
Unit Cell:
Length (Å)Angle (°)
a = 141.801α = 90.00
b = 141.801β = 90.00
c = 38.150γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
MOLREPphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-06-19 
  • Released Date: 2018-10-24 
  • Deposition Author(s): Maita, N.

Funding OrganizationLocationGrant Number
Japan Society for the Promotion of ScienceJapan15K13747

Revision History 

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2018-11-07
    Type: Data collection, Database references