5YE3

Crystal structure of the complex of di-acetylated histone H4 and 2A7D9 Fab fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

JQ1 affects BRD2-dependent and independent transcription regulation without disrupting H4-hyperacetylated chromatin states.

Handoko, L.Kaczkowski, B.Hon, C.C.Lizio, M.Wakamori, M.Matsuda, T.Ito, T.Jeyamohan, P.Sato, Y.Sakamoto, K.Yokoyama, S.Kimura, H.Minoda, A.Umehara, T.

(2018) Epigenetics 13: 410-431

  • DOI: 10.1080/15592294.2018.1469891
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The bromodomain and extra-terminal domain (BET) proteins are promising drug targets for cancer and immune diseases. However, BET inhibition effects have been studied more in the context of bromodomain-containing protein 4 (BRD4) than BRD2, and the BE ...

    The bromodomain and extra-terminal domain (BET) proteins are promising drug targets for cancer and immune diseases. However, BET inhibition effects have been studied more in the context of bromodomain-containing protein 4 (BRD4) than BRD2, and the BET protein association to histone H4-hyperacetylated chromatin is not understood at the genome-wide level. Here, we report transcription start site (TSS)-resolution integrative analyses of ChIP-seq and transcriptome profiles in human non-small cell lung cancer (NSCLC) cell line H23. We show that di-acetylation at K5 and K8 of histone H4 (H4K5acK8ac) co-localizes with H3K27ac and BRD2 in the majority of active enhancers and promoters, where BRD2 has a stronger association with H4K5acK8ac than H3K27ac. Although BET inhibition by JQ1 led to complete reduction of BRD2 binding to chromatin, only local changes of H4K5acK8ac levels were observed, suggesting that recruitment of BRD2 does not influence global histone H4 hyperacetylation levels. This finding supports a model in which recruitment of BET proteins via histone H4 hyperacetylation is predominant over hyperacetylation of histone H4 by BET protein-associated acetyltransferases. In addition, we found that a remarkable number of BRD2-bound genes, including MYC and its downstream target genes, were transcriptionally upregulated upon JQ1 treatment. Using BRD2-enriched sites and transcriptional activity analysis, we identified candidate transcription factors potentially involved in the JQ1 response in BRD2-dependent and -independent manner.


    Organizational Affiliation

    Department of biological and medical physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.,Laboratory of Genetics, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA; Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA. Electronic address: dlyumkis@salk.edu.,Department of Systems Biology for Medicine, School of Basic Medical Sciences, Shanghai Medical College of Fudan University, Shanghai, People's Republic of China.,Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, Universidad Nacional de Córdoba - Consejo Nacional de Investigaciones Científicas y Técnicas (UNC-CONICET)), Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA, Córdoba, Argentina. Electronic address: jromero@fcq.unc.edu.ar.,Structural Genomics Consortium, University of Toronto, Toronto, ON M5G 1L7, Canada.,Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France. pedro.alzari@pasteur.fr marco.bellinzoni@pasteur.fr.,Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy.,German Cancer Consortium, DKTK , 60590 Site Frankfurt/Mainz , DE , Germany.,Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: ysun8@mdanderson.org.,Center for Open Research Resources & Equipment (COR2E) , University of Connecticut , 91 North Eagleville Road , Storrs , Connecticut 06269 , United States.,Instituto Nacional de Enfermedades Virales Humanas "Dr. Julio I. Maiztegui", Monteagudo 251 Pergamino, Buenos Aires, 2700, Argentina.,Department of Biology, Washington University in St Louis, St Louis, MO, 63130, USA.,Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea; Unit on Structural and Chemical Biology of Membrane Proteins, Cell Biology and Neurobiology Branch, National Institute of Child Health and Human Development, National Institutes of Health, 35A Convent Drive, Bethesda, MD 20892, USA.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520-8103.,Department of Neuroscience, The Scripps Research Institute, Jupiter, United States.,Institute for X-Ray Physics, University of Goettingen, 37077 Goettingen, Germany.,Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea.,State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China.,c Cell Biology Center, Institute of Innovative Research , Tokyo Institute of Technology, Yokohama , Kanagawa , Japan.,3Faculty of Health Sciences, Department of Medical Biology, Research group of Host-Microbe Interactions, UiT-The Artic University of Norway, 9037 Tromsø, Norway.,Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA.,Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), US National Institutes of Health (NIH), Bethesda, MD, USA.,Department of Life Sciences, Imperial College, London SW7 2AZ, UK; UMR5305, CNRS/Université Claude Bernard Lyon 1, 69367 Lyon Cedex 7, France. Electronic address: david.hulmes@ibcp.fr.,CBH, KTH-Royal Institute of Technology, SE-10691 Stockholm, Sweden. Electronic address: sophia@kth.se.,6Helmholtz Centre for Infection Research (HZI), Inhoffenstraße 7, 38124 Braunschweig, Germany.,Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.,Chemical Biology and Medicinal Chemistry, and.,Department of Chemistry, Institutes of Biomedical Sciences and Multiscale Research Institute of Complex System, Fudan University, Shanghai, People's Republic of China.,Department of Molecular Medicine, Unit of Immunology and General Pathology, University of Pavia, Pavia, Italy.,Department of Cancer Systems Imaging, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China.,Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany. rficner@uni-goettingen.de.,State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438 Shanghai, China; wenbo.ma@ucr.edu majb@fudan.edu.cn.,Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea; Department of Pharmacology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC 27516, USA.,Experimental Medical Science, Medical Structural Biology, BMC C13, Lund University, SE-221 84 Lund, Sweden.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA. Electronic address: smeroueh@iu.edu.,Unit of Polar Genomics , Korea Polar Research Institute , Incheon 21990 , Republic of Korea.,ESRF - The European Synchrotron, 71 Rue Jules Horowitz, F-38000 Grenoble, France.,Department of Molecular Biology, Faculty of Science, Sciences III, University of Geneva, CH-1211 Geneva 4, Switzerland.,MacCHESS, Cornell University, Ithaca, NY 14853.,Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, UK.,CNR-Institute of Molecular Biology and Pathology, Rome, Italy.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA. Electronic address: margaret.phillips@utsouthwestern.edu.,Department of Chemistry, Indiana University, Bloomington, IN 47405; cedann@indiana.edu dbkearns@indiana.edu.,Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, UK katrin.rittinger@crick.ac.uk.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA. abraham@crystal.harvard.edu.,Department of Botany, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Department of Pharmacology, Yale University, New Haven, CT, USA.,Workgroup Structural Biology of Biosynthetic Enzymes , Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1 , 66123 Saarbrücken , Germany.,School of Molecular Sciences, Arizona State University, Tempe, AZ 85287.,The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany.,Department of Pediatrics, Herman B. Wells Center for Pediatric Research, Indiana University Simon Cancer Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,School of Biological Sciences, 60 Nanyang Drive, Nanyang Technological University, Singapore, 637551, Singapore. julien@ntu.edu.sg.,Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry, RWTH Aachen University Hospital, Pauwelsstrasse 30, D-52074 Aachen, Germany.,The Max-Planck Institute of Biochemistry, Core Facility, Am Klopferspitz 18, 82152 Martinsried, Germany.,Center for Matrix Biology, Vanderbilt University Medical Center, United States.,SER-CAT and Department of Biochemistry and Molecular Biology , University of Georgia , Athens , Georgia 30602 , United States.,Department of Biochemistry and Molecular Genetics, University of Colorado Denver (UCD), Anschutz Medical Campus, Aurora, CO 80045, USA. rui.zhao@ucdenver.edu hong.zhou@ucla.edu.,Institut Pasteur, Unité de Microbiologie Structurale, CNRS UMR 3528 & Université Paris Diderot, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France.,Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), US National Institutes of Health (NIH), Bethesda, MD, USA. wei.yang@nih.gov.,Department of Pharmaceutical Sciences , University of Connecticut , 69 North Eagleville Road , Storrs , Connecticut 06269 , United States.,Laboratory of Molecular Neurobiology and Biophysics, Howard Hughes Medical Institute, The Rockefeller University, New York, United States.,Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, Universidad Nacional de Córdoba - Consejo Nacional de Investigaciones Científicas y Técnicas (UNC-CONICET)), Departamento de Química Biológica Ranwel Caputto, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, X5000HUA, Córdoba, Argentina.,the Departments of Microbiology and Immunology, and Integrative Program for Biological and Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599 and.,Department of Molecular Medicine, The Scripps Research Institute, 130 Scripps Way, Jupiter, FL 33458, USA.,Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany. sjohann1@gwdg.de.,Department of Biosciences and Nutrition and Center for Innovative Medicine, Karolinska Institutet, Blickagången 16, SE-141 83 Huddinge, Sweden.,Department of Molecular Structural Biology, Institute of Microbiology and Genetics, GZMB, Georg-August-University Göttingen, 37077 Göttingen, Germany. pneuman2@gwdg.de.,e PRESTO , Japan Science and Technology Agency (JST) , Kawaguchi, Saitama , Japan.,National Engineering Research Center of Immunological Products, Department of Microbiology and Biochemical Pharmacy, College of Pharmacy, Third Military Medical University, Chongqing, China. Electronic address: Jianggu2012@163.com.,Department of Dermatology , University Medical Center, Eberhard Karls University Tübingen , Liebermeisterstr. 25 , 72076 Tübingen , DE , Germany.,Department of Biosciences, Rice University, Houston, TX, USA.,Institute of Molecular Physiology, Cell and Matrix Biology, Johannes Gutenberg-University Mainz, Johann-Joachim-Becher-Weg 7, D-55128 Mainz, Germany.,Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea.,Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, UK.,Department of Cellular Biology and Pharmacology, Herbert Wertheim College of Medicine , Florida International University , Miami , Florida 33134 , United States.,Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, Indiana 46285, United States.,Vanderbilt University Medical Center, United States.,d RIKEN Structural Biology Laboratory, Yokohama , Kanagawa , Japan.,Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA; Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA.,ENEA CR Frascati, Diagnostics and Metrology Laboratory, FSN-TECFIS-DIM, Frascati, Italy.,Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Biointerface Laboratory, Helmholtz Institute for Biomedical Engineering, RWTH Aachen University Medical Faculty, Pauwelsstrasse 30, D-52074 Aachen, Germany.,From the Departments of Chemistry, redinbo@unc.edu.,Nanyang Institute of Structural Biology, Experimental Medicine Building, 59 Nanyang Drive, Singapore, 636921, Singapore. julien@ntu.edu.sg.,b Division of Structural and Synthetic Biology , RIKEN Center for Life Science Technologies, Yokohama , Kanagawa , Japan.,Department of Cell Biology, Yale University, New Haven, CT, USA. david.calderwood@yale.edu.,Istituto Zooprofilattico dell'Abruzzo e del Molise, Campo Boario, 64100 Teramo, Italy.,Department of Biological Sciences Xi'an Jiaotong-Liverpool University111 Ren'ai Road, Dushu Lake Higher Education Town, Suzhou, 215123, People's Republic of China.,Department of Physics, Simon Fraser University, Canada.,Laboratory of biomolecular NMR spectroscopy, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow, Russia.,School of Biological Sciences, 60 Nanyang Drive, Nanyang Technological University, Singapore, 637551, Singapore.,Department of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel. mlandau@technion.ac.il.,Department of Biochemistry and Molecular Genetics, University of Colorado Denver (UCD), Anschutz Medical Campus, Aurora, CO 80045, USA.,Simon Fraser University, Canada.,The Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany. Electronic address: baumeist@biochem.mpg.de.,Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461; denis.rousseau@einstein.yu.edu.,a Division of Genomic Technologies , RIKEN Center for Life Science Technologies, Yokohama , Kanagawa , Japan.,Structural Biology Brussels, Vrije Universiteit Brussel, Brussels, Belgium.,a Laboratoire d'Expression génétique microbienne, Institut de Biologie Physico-Chimique, IBPC, CNRS , Université Paris Diderot , Paris , France.,Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan.,Department of Neurosurgery, Huashan Hospital, Institutes of Biomedical Sciences, State Key Laboratory of Medical Neurobiology, Shanghai Medical College of Fudan University, Shanghai, People's Republic of China.,Section on Biological Chemistry, National Institute of Dental and Craniofacial Research (NIDCR), US National Institutes of Health, Bethesda, MD, USA.,Department of Medicine, Division of Infectious Diseases, Brigham and Women's Hospital, Boston, MA, 02115, USA. abraham@crystal.harvard.edu.,Biochemistry and Biophysics, and.,Electron Imaging Center for Nanomachines, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA.,b Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologiques, CNRS , Université Paris Descartes , Paris , France.,Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521; wenbo.ma@ucr.edu majb@fudan.edu.cn.,Department of Chemistry , University of Connecticut , 55 North Eagleville Road , Storrs , Connecticut 06269 , United States.,Institut Pasteur, Plateforme de Biophysique Moléculaire, 25 Rue du Docteur Roux, 75724 Paris Cedex 15, France.,Department of Pathology, University of Texas Medical Branch at Galveston, Galveston, TX, 77555, USA.,Structural Genomics Consortium , Johann Wolfgang Goethe University , Buchmann Institute for Molecular Life Sciences, Max-von-Laue-Str. 15 , D-60438 Frankfurt am Main , DE , Germany.,UMR5086, CNRS/Université Claude Bernard Lyon 1, 69367 Lyon Cedex 7, France.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA; Eugene and Marilyn Glick Eye Institute, Department of Ophthalmology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Laboratory of Structural Biology, Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan.,Biotechnology Research Division , Korea Atomic Energy Research Institute (KAERI) , Jeongeup 56212 , Republic of Korea.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA. charles.sindelar@yale.edu.,c Institut de Biologie Physico-Chimique , IBPC, CNRS , Paris , France.,State Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, 200438 Shanghai, China.,Department of Integrative Structural and Computational Biology, The Scripps Research Institute, Jupiter, United States.,Institute for Pharmaceutical Chemistry , Johann Wolfgang Goethe University , Max-von-Laue-Str. 9 , D-60438 Frankfurt am Main , DE , Germany.,Department of Plant Pathology, Nanjing Agriculture University, 210095 Nanjing, China.,Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: jrmarszalek@mdanderson.org.,Laboratory of Molecular and Cell Biology, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA; Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA. Electronic address: patrick@salk.edu.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA. shenb@scripps.edu.,Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016.,Biodesign Center for Applied Structural Discovery, The Biodesign Institute, Arizona State University, Tempe, AZ 85287.,Department of BioHealth Informatics, Indiana University School of Informatics and Computing, Indianapolis, IN 46202, USA.,Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Laboratory of Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA. abraham@crystal.harvard.edu.,Structural and Molecular Microbiology, VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.,Department of Chemistry & Nanoscience , Ewha Womans University , Seoul 03760 , Republic of Korea.,Department of Food Science and Engineering , Ewha Womans University , Seoul 03760 , Republic of Korea.,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.,Department of Drug Design and Optimization , Helmholtz Institute for Pharmaceutical Research Saarland (HIPS) , Campus E8.1 , 66123 Saarbrücken , Germany.,Department of Biology, Indiana University, Bloomington, IN 47405 cedann@indiana.edu dbkearns@indiana.edu.,Program in Immunology, Harvard Medical School, Boston, MA, 02115, USA.,Department of Pharmacy , Pharmaceutical and Medicinal Chemistry, Saarland University , Campus E8.1 , 66123 Saarbrücken , Germany.,Midwest Center for Structural Genomics and Structural Biology Center, Biosciences Division, Argonne National Laboratory, Argonne, IL, USA.,Leicester Tuberculosis Research Group (LTBRG) and Leicester Institute of Structural and Chemical Biology (LISCB), Department of Respiratory Science & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK.,Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Center for Co-Clinical Trials, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Institute of Molecular and Cell Biology, Singapore 138673.,Department of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel.,Department of Molecular and Cellular Biology , University of Connecticut , 91 North Eagleville Road , Storrs , Connecticut 06269 , United States.,Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,School of Molecular Cell Biology & Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel-Aviv, 6997801, Israel.,Institut de Biologie Structurale, Université Grenoble Alpes, Centre National de la Recherche Scientifique (CNRS), Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Grenoble, 38044, France.,Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, United States.,Department of Life Sciences, Imperial College, London SW7 2AZ, UK. Electronic address: e.hohenester@imperial.ac.uk.,Department of Pharmacology, Yale University, New Haven, CT, USA. david.calderwood@yale.edu.,Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.,Laboratory of Genetics, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA; Helmsley Center for Genomic Medicine, Salk Institute for Biological Studies, 10010 N. Torrey Pines Road, La Jolla, CA 92037, USA.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111; philim01@nyulangone.org Jinhua.wu@fccc.edu.,Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA.,Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016; philim01@nyulangone.org Jinhua.wu@fccc.edu.,Technology Center for Protein Sciences, Ministry of Education Key Laboratory of Protein Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China.,The Max-Planck Institute of Biochemistry, Department of Cellular Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany. Electronic address: bracher@biochem.mpg.de.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.,Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103; thomas.pollard@yale.edu.,Natural Products Library Initiative at The Scripps Research Institute, The Scripps Research Institute, Jupiter, FL, USA. shenb@scripps.edu.,Department of Life Science, Dongguk University-Seoul, Ilsandong-gu, Goyang-si, Gyeonggi-do, 10326, Republic of Korea. jylee001@dongguk.edu.,Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea. Electronic address: hscho8@yonsei.ac.kr.,Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA.,Department of Chemistry, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto, 606-8502, Japan. ktakeda@kuchem.kyoto-u.ac.jp.,Department of Medical Biophysics, University of Toronto and Princess Margaret Cancer Centre, 101 College Street, MaRS South Tower, Suite 707, Toronto, ON M5G 1L7, Canada.,Department of Microbiology, Immunology, and Molecular Genetics, UCLA, Los Angeles, CA 90095, USA.,Department of Microbiology, Monash University, Clayton, Australia.,Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York, United States of America.,UMR5305, CNRS/Université Claude Bernard Lyon 1, 69367 Lyon Cedex 7, France.,Department of Physics, Arizona State University, Tempe, AZ 85287.,d Laboratoire de Cristallographie et RMN biologiques , CNRS, Université Paris Descartes , Paris , France.,5Department of Integrative Medical Biology (IMB), Umeå University, SE-90187 Umeå, Sweden.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, United States.,Center for Plant Cell Biology, University of California, Riverside, CA 92521.,Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111.,State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences and School of Medicine, Tsinghua University, Beijing 100084, China. nyan@princeton.edu.,Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.,e Laboratoire de Microbiologie , Université libre de Bruxelles (ULB) , Gosselies , Belgium.,From the Departments of Chemistry.,West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China. Electronic address: lugw@scu.edu.cn.,CBH, KTH-Royal Institute of Technology, SE-10691 Stockholm, Sweden.,Department of Agricultural Biotechnology, Center for Food Safety and Toxicology, Center for Food and Bioconvergence, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea. Electronic address: hanc210@snu.ac.kr.,Department of Cell Biology, Yale University, New Haven, CT 06520-8103.,4Umeå Centre for Molecular Medicine (UCMM), Umeå University, SE-90187 Umeå, Sweden.,Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520-8103.,Department of Molecular Biosciences, University of Kansas, Lawrence, United States.,Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, USA. shenb@scripps.edu.,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.,Department of Physiology and Biophysics, Albert Einstein College of Medicine, Bronx, NY 10461.,Biochemistry Graduate Program, Indiana University, Bloomington, IN 47405.,Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul 120-749, Republic of Korea.,1Department of Molecular Biology and The Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-90187 Umeå, Sweden.,Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,2Department of Chemistry, Umeå University, SE-901 87 Umeå, Sweden.,SLAC National Accelerator Laboratory, Menlo Park, CA 94025.,College of Pharmacy and Graduate School of Pharmaceutical Sciences , Ewha Womans University , Seoul 03760 , Republic of Korea.,Department of Chemistry, Indiana University, Bloomington, IN 47405.,Department of Microbiology and Plant Pathology, University of California, Riverside, CA 92521.,Electron Imaging Center for Nanomachines, University of California, Los Angeles (UCLA), Los Angeles, CA 90095, USA. rui.zhao@ucdenver.edu hong.zhou@ucla.edu.,State Key Laboratory of Genetic Engineering, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, 200438 Shanghai, China.,Hauptman-Woodward Institute and SUNY University of Buffalo, Buffalo, NY 14203.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA, 02115, USA.,Department of Pharmaceutical/Medicinal Chemistry , Eberhard Karls University Tübingen , Auf der Morgenstelle 8 , 72076 Tübingen , DE , Germany.,Department of Life Sciences, Imperial College, London SW7 2AZ, UK.,Leicester Institute for Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 9HN, United Kingdom.,Department of Applied Chemistry, Faculty of Science and Engineering, Waseda University, 3-4-1 Ohkubo, Shinjuku-ku, Tokyo 169-8555, Japan.,West China Hospital Emergency Department (WCHED), State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu, Sichuan, 610041, China; Disaster Medicine Center, Sichuan University, Chengdu, Sichuan, 610041, China.,Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.,Proteolysis Laboratory, Department of Structural Biology, Molecular Biology Institute of Barcelona, CSIC, Barcelona Science Park, Helix Building, c/o Baldiri Reixac 15-21, E-08028 Barcelona, Catalonia, Spain.,University of Science and Technology , Daejeon , Republic of Korea.,Medicine, Vanderbilt University Medical Center, United States.,the Department of Biochemistry, Institute for Protein Design, University of Washington, Seattle, Washington 98195.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
2A7D9 VH CH1 chain
B
211N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
2A7D9 L chain
A
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
di-acetylated histone H4
C
12Homo sapiensMutation(s): 0 
Gene Names: HIST1H4A, HIST1H4B, HIST1H4C, HIST1H4D, HIST1H4E, HIST1H4F, HIST1H4H, HIST1H4I, HIST1H4J, HIST1H4K, HIST1H4L, HIST2H4A, HIST2H4B, HIST4H4 (H4/A, H4FA, H4/I, H4FI, H4/G, H4FG, H4/B, H4FB, H4/J, H4FJ, H4/C, H4FC, H4/H, H4FH, H4/M, H4FM, H4/E, H4FE, H4/D, H4FD, H4/K, H4FK, H4/N, H4F2, H4FN, HIST2H4, H4/O, H4FO)
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
C
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 39.951α = 90.00
b = 85.978β = 90.00
c = 122.849γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-08-22
    Type: Initial release
  • Version 1.1: 2018-09-19
    Type: Data collection, Database references