6HXM

Structure of the citryl-CoA lyase core module of human ATP citrate lyase in complex with citrate and CoASH in space group C2221


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of ATP citrate lyase and the origin of citrate synthase in the Krebs cycle.

Verschueren, K.H.G.Blanchet, C.Felix, J.Dansercoer, A.De Vos, D.Bloch, Y.Van Beeumen, J.Svergun, D.Gutsche, I.Savvides, S.N.Verstraete, K.

(2019) Nature 568: 571-575

  • DOI: 10.1038/s41586-019-1095-5
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Across different kingdoms of life, ATP citrate lyase (ACLY, also known as ACL) catalyses the ATP-dependent and coenzyme A (CoA)-dependent conversion of citrate, a metabolic product of the Krebs cycle, to oxaloacetate and the high-energy biosynthetic ...

    Across different kingdoms of life, ATP citrate lyase (ACLY, also known as ACL) catalyses the ATP-dependent and coenzyme A (CoA)-dependent conversion of citrate, a metabolic product of the Krebs cycle, to oxaloacetate and the high-energy biosynthetic precursor acetyl-CoA 1 . The latter fuels pivotal biochemical reactions such as the synthesis of fatty acids, cholesterol and acetylcholine 2 , and the acetylation of histones and proteins 3,4 . In autotrophic prokaryotes, ACLY is a hallmark enzyme of the reverse Krebs cycle (also known as the reductive tricarboxylic acid cycle), which fixates two molecules of carbon dioxide in acetyl-CoA 5,6 . In humans, ACLY links carbohydrate and lipid metabolism and is strongly expressed in liver and adipose tissue 1 and in cholinergic neurons 2,7 . The structural basis of the function of ACLY remains unknown. Here we report high-resolution crystal structures of bacterial, archaeal and human ACLY, and use distinct substrate-bound states to link the conformational plasticity of ACLY to its multistep catalytic itinerary. Such detailed insights will provide the framework for targeting human ACLY in cancer 8-11 and hyperlipidaemia 12,13 . Our structural studies also unmask a fundamental evolutionary relationship that links citrate synthase, the first enzyme of the oxidative Krebs cycle, to an ancestral tetrameric citryl-CoA lyase module that operates in the reverse Krebs cycle. This molecular transition marked a key step in the evolution of metabolism on Earth.


    Organizational Affiliation

    Graduate School of Science and Molecular Chirality Research Center, Chiba University, Inage, Chiba, Japan.,Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, 1275 York Avenue, New York, NY 10065, USA. Electronic address: limac@mskcc.org.,Medicinal Chemistry & Drug Discovery, Department of Pharmacology , University of Oxford , Mansfield Road , Oxford OX1 3QT , U.K.,Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.,Japan Science and Technology Agency (JST) and Japan Agency for Medical Research and Development (AMED), Core Research for Evolutional Science and Technology (CREST), Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. kobayashi.takuya.4r@kyoto-u.ac.jp.,Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan. narita.akihiro@f.mbox.nagoya-u.ac.jp.,Department of Cellular and Molecular Medicine, School of Medicine, and Section of Molecular Biology, Division of Biological Sciences, UC San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA.,Graduate School of Biosphere Science , Hiroshima University , Kagamiyama 1-4-4, Higashi-Hiroshima , Hiroshima , 739-8528 , Japan.,Unit for Structural Biology, VIB Center for Inflammation Research, Ghent, Belgium. kenneth.verstraete@ugent.be.,Institute of Biophysics and Physical Biochemistry, University of Regensburg, 93040 Regensburg, Germany.,Institute of Human Virology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, USA. Electronic address: marzena.pazgier@usuhs.edu.,Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK.,Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, NY 10461, USA. Electronic address: steven.porcelli@einstein.yu.edu.,Bioorganic Chemistry Group, Instituto de Tecnologia Química Biológica, Universidade Nova de Lisboa, 2780-157 Oeiras, Portugal.,Saverna Therapeutics AG , Pumpmattenweg 3 , CH-4105 Biel-Benken , Switzerland.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, United States.,Center for Biochemistry, Medical Faculty, Center for Molecular Medicine Cologne (CMMC), Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany.,SPARC BioCentre, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Radboud Institute for Molecular Life Sciences, Department of Pediatrics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525, GA, Nijmegen, The Netherlands.,State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia. Electronic address: stanislav.gobec@ffa.uni-lj.si.,Max-Planck-Institute for Biophysics Frankfurt, Max-von-Laue-Str. 3, 60438, Frankfurt, Germany. ulrich.ermler@biophys.mpg.de.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore.,Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil. Electronic address: mario.murakami@ctbe.cnpem.br.,Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, United States.,Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland.,Center for Translational Medicine, the First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China. Electronic address: zhaole2@mail.xjtu.edu.cn.,Institute of Human Virology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, USA.,Cluster of Excellence Macromolecular Complexes, Goethe-University, Max von Laue Str. 9, 60438, Frankfurt am Main, Germany.,School of Biological Sciences , University of Essex , Wivenhoe Park , Colchester , Essex CO4 3SQ , UK . Email: mahough@essex.ac.uk.,Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore; Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,PhD Program in Experimental Biology and Biomedicine (PDBEB), Institute for Interdisciplinary Research (IIIUC), University of Coimbra, 3030-789 Coimbra, Portugal.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.,Boehringer Ingelheim Pharma GmbH & Co KG, Biberach, Germany.,Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA.,Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02139, USA.,Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon, 305-701, Korea.,Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA. adha@ufl.edu.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.,Centre for Biomolecular Magnetic Resonance, Institute for Biophysical Chemistry, Goethe University, Max von Laue Str. 9, 60438, Frankfurt am Main, Germany.,Department of Biochemistry & Molecular Biology, Colorado State University, Fort Collins, CO 80523, USA.,Institute for Interdisciplinary Research (IIIC), University of Coimbra, 3030-789 Coimbra, Portugal.,The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium. kenneth.verstraete@ugent.be.,Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal.,Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. r.suno@mfour.med.kyoto-u.ac.jp.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030.,Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging at the University of Melbourne, Melbourne, Australia.,Boehringer Ingelheim RCV GmbH & Co KG, Vienna, Austria.,Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, 4200-135 Porto, Portugal.,Department of Chemistry, The University of Connecticut, Storrs, CT 06269-3060, USA.,Biochemistry Department, Indian Institute of Science, Bangalore 560012, India.,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.,Food Technology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, Maharashtra 400085, India and snjam@barc.gov.in.,Cell Biology Program, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA.,Novartis Institutes for BioMedical Research (NIBR), Novartis Pharma AG , Forum 1, Novartis Campus, Fabrikstrasse 2 , CH-4056 Basel , Switzerland.,Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Korea.,Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal.,Department of Microbiology & Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia.,IPC Drug Discovery Platform , Institut Paoli-Calmettes , 232 Boulevard de Sainte-Marguerite , 13009 Marseille , France.,Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Tri-Institutional Training Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil; Graduate Program in Functional and Molecular Biology, Institute of Biology, University of Campinas, Campinas, SP, Brazil.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK. radu@mrc-lmb.cam.ac.uk.,Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil.,Bioverativ, a Sanofi company, Waltham, MA; and.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India.,School of Biochemistry, Devi Ahilya University, Indore 452001, India.,Section of Microbiology, Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London, SW7 2AZ, UK. s.helaine@imperial.ac.uk.,Department of Molecular Imaging and Therapy, Beckman Research Institute of the City of Hope, Duarte, CA, USA.,School of Life Sciences, University of Sussex, Brighton, BN1 9QG, UK.,Harry Perkins Institute of Medical Research, Centre for Medical Research, QEII Medical Centre and School of Molecular Sciences, The University of Western Australia, Nedlands, Western Australia, Australia.,Unit for Structural Biology, VIB Center for Inflammation Research, Ghent, Belgium.,Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea.,Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA. bruner@chem.ufl.edu.,National Institute for Research in Tuberculosis, Chennai 600031, India.,Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development, 340 Kingsland Street, Nutley 07110, United States. Electronic address: ftapia@cc.hawaii.edu.,Biophysics, Department of Physics, University of Kaiserslautern, Erwin-Schrödinger-Straße 46, 67663, Kaiserslautern, Germany.,Department of Biochemistry & Biophysics, Center for RNA Biology, and Center for AIDS Research, University of Rochester School of Medicine & Dentistry, Rochester, NY 14642, USA.,Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030.,Department of Life Sciences, Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London, SW7 2AZ, UK.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Structure and Function of Proteins, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany.,Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA. ss1@nih.gov.,Biolojic Design, Ltd., 12 Hamada Street, Rehovot 7670314, Israel.,Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia.,Program in Cellular and Molecular Medicine, Children's Hospital Boston, Boston, United States.,Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX 77030; mestes@bcm.edu.,Section of Microbiology, Medical Research Council Centre for Molecular Bacteriology and Infection, Imperial College London, Armstrong Road, London, SW7 2AZ, UK.,Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, USA. hjin@illinois.edu.,Faculty of Health and Welfare, Tokai Gakuin University, Nakakirino-cyo 5-68, Kakamigahara, Gifu, 504-8511, Japan.,Children's Hospital Boston, Boston, MA.,Biochemistry Department, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.,College of Medicine, Department of Biochemistry and Molecular Biology , University of Florida , Gainesville , Florida 32610 , United States.,Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland. ban@mol.biol.ethz.ch.,Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.,Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia. Electronic address: jerome.lenours@monash.edu.,Antibody Discovery and Protein Engineering, MedImmune, Granta Park, Cambridge CB21 6GH, UK.,Center for Neuroscience and Cell Biology (CNC), University of Coimbra, 3004-504 Coimbra, Portugal; ppereira@ibmc.up.pt numenius@cnc.uc.pt.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK. radu@mrc-lmb.cam.ac.uk.,Laboratoire de Chemoinformatique, CNRS UMR7140 , 1 rue Blaise Pascal , 67000 Strasbourg , France.,Brazilian Bioethanol Science and Technology Laboratory (CTBE), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, SP, Brazil. Electronic address: priscila.giuseppe@ctbe.cnpem.br.,the Guangdong Zhongsheng Pharmaceutical Co., Ltd., Dongguan, Guangdong 523325, China.,The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada. Electronic address: sachdev.sidhu@utoronto.ca.,Department of Biochemistry, McGill University, Montreal, QC, Canada; Corbin Therapeutics, Montreal, QC, Canada.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, USA.,Department of Chemistry, The University of Connecticut, Storrs, CT 06269-3060, USA. Electronic address: amy.howell@uconn.edu.,From the State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China and.,Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Department of Biochemistry, McGill University, Montreal, QC, Canada.,Microbiology, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Biogen Inc, Cambridge, MA.,Department of Medical Life Systems, Faculty of Life and Medical Sciences, Doshisha University, 1-3 Miyakodani, Tatara, Kyotanabe, Kyoto, 610-0394, Japan.,Unit for Structural Biology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.,Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON M5G 1X5, Canada.,Max-Planck-Institute for Biophysics Frankfurt, Max-von-Laue-Str. 3, 60438, Frankfurt, Germany.,Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia.,Dalton Mass Spectrometry Laboratory, Institute of Chemistry, University of Campinas, Campinas, SP, Brazil.,Centre for Biological Sciences, B85 Life Sciences Building M55, University of Southampton, Southampton SO17 1BJ, UK. Electronic address: j.m.werner@soton.ac.uk.,Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.,NIH West Coast Metabolomics Center, UC Davis Genome Center, University of California Davis, Davis, CA, 95616, USA.,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, 92093.,Biochemistry, Faculty of Chemistry, University of Kaiserslautern, Erwin-Schrödinger-Straße 52, 67663, Kaiserslautern, Germany.,Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology (PRESTO), Kawaguchi, Saitama, Japan.,Toyota Physical and Chemical Research Institute, 41-1, Yokomichi, Nagakute, Aichi, 480-1192, Japan.,Cancer Metabolism and Signaling Networks Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA.,Research Center for Ultra-High Voltage Electron Microscopy, Osaka University, 7-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan.,Institute for Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, BIOSS Centre for Biological Signalling Studies, University of Freiburg, Stefan-Meier-Str. 17, 79104, Freiburg im Breisgau, Germany.,The Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada.,From the State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China and chenlijuan125@163.com.,Institute of Biochemistry II, Medical School, Goethe University, Max von Laue Str. 9, 60438, Frankfurt am Main, Germany.,Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA. kwmiller@mgh.harvard.edu.,Department of Organic Chemistry , Lobachevsky State University of Nizhni Novgorod , 23 Gagarin Avenue , 603950 Nizhni Novgorod , Russia.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA.,Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720.,Sprint Bioscience AB , Hälsovägen 7 , SE-141 57 Huddinge , Sweden.,CRCM, CNRS, Inserm, Institut Paoli-Calmettes , Aix-Marseille University , 13009 Marseille , France.,From the High Pressure and Synchrotron Radiation Physics Division and ravimakde@rrcat.gov.in.,European Molecular Biology Laboratory (EMBL), Hamburg Outstation c/o DESY, Hamburg, Germany.,Centre for Biological Sciences, B85 Life Sciences Building M55, University of Southampton, Southampton SO17 1BJ, UK.,National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.,Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstraße 17, 38106, Braunschweig, Germany. U.Rau@tu-bs.de.,Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA. koss@bsd.uchicago.edu.,Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, 4200-135 Porto, Portugal; ppereira@ibmc.up.pt numenius@cnc.uc.pt.,Microbiology, Faculty of Biology, University of Freiburg, Schänzlestrasse 1, 79104, Freiburg, Germany. matthias.boll@biologie.uni-freiburg.de.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK. dlaverty@mrc-lmb.cam.ac.uk.,Key Laboratory of Fermentation Engineering, Ministry of Education, College of Bioengineering, Hubei University of Technology, Wuhan, China; Institute of Human Virology, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, USA.,AstraZeneca R&D, Darwin Building Cambridge Science Park, Milton Road, Cambridge CB4 0WG, UK.,Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Korea.,Cluster of Excellence Macromolecular Complexes, Goethe-University, Max von Laue Str. 9, 60438, Frankfurt am Main, Germany. ulrich.brandt@radboudumc.nl.,Hoffmann-La Roche Ltd., pRED, Pharma Research & Early Development, 340 Kingsland Street, Nutley 07110, United States.,University of Grenoble Alpes, CNRS, CEA, CNRS, IBS, Grenoble, France.,Biolojic Design, Ltd., 12 Hamada Street, Rehovot 7670314, Israel; The Goodman Faculty of Life Sciences, Nanotechnology Building, Bar Ilan University, Ramat Gan 52900, Israel. Electronic address: yanay@ofranlab.org.,State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China.,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.,Institute of Advanced Energy and Graduate School of Energy Science, Kyoto University, Uji, Kyoto, Japan.,University Grenoble Alpes, IBS, F-38044, Grenoble, France; CNRS, IBS, F-38044, Grenoble, France; CEA, IBS, F-38044, Grenoble, France.,Department of Chemistry and Chemical Biology, Northeastern University, Boston, United States.,Institut de Recherche Biomédicale des Armées, 91223, Brétigny sur Orge, France.,Protein Metabolism Medical Research Center and Department of Biomedical Sciences, College of Medicine, Seoul National University, Seoul, 03080, Republic of Korea. yok5@snu.ac.kr.,Center for Biochemistry, Medical Faculty, Center for Molecular Medicine Cologne (CMMC), Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne 50931, Germany. Electronic address: raimund.wagener@uni-koeln.de.,Department of Medicine, Gastroenterology and Hepatology, Baylor College of Medicine, Houston, TX 77030.,Department of Biotechnology, Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, Spielmannstraße 17, 38106, Braunschweig, Germany.,Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, NY 10461, USA; Millennium Institute on Immunology and Immunotherapy, Programa de Inmunologia, Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile.,Computational Biochemistry, University of Bayreuth, Universitätsstrasse 30, NW I, 95447, Bayreuth, Germany.,David Van Andel Advanced Cryo-Electron Microscopy Suite, Van Andel Research Institute, Grand Rapids, MI, USA.,RIKEN, SPring-8 Center, Hyogo, Japan.,University of Chinese Academy of Sciences, Beijing, China.,Institute of Biochemistry I, Medical School, Goethe University, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany.,From the High Pressure and Synchrotron Radiation Physics Division and.,Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606, USA.,Department of Chemistry and Biochemistry , Eastern Oregon University , La Grande , Oregon 97850 , USA . Email: candrew@eou.edu.,Department of Cell Biology and Medical Chemistry, Graduate School of Medicine, Kyoto University, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan. kobayashi.takuya.4r@kyoto-u.ac.jp.,Department of Life Sciences, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.,Integrated Molecular Plant Physiology Research, Department of Biology, University of Antwerp, Antwerp, Belgium.,Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA. ss1@nih.gov.,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium.,MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, UK.,Koch Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.,Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Howard Hughes Medical Institute, 1275 York Avenue, New York, NY 10065, USA.,Key Laboratory of Receptor Research, VARI-SIMM Center, Center for Structure and Function of Drug Targets, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China. eric.xu@vai.org.,Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, USA. hjin@illinois.edu.,Radboud Institute for Molecular Life Sciences, Department of Pediatrics, Radboud University Medical Center, Geert Grooteplein-Zuid 10, 6525, GA, Nijmegen, The Netherlands. ulrich.brandt@radboudumc.nl.,Department of Biology, University of Konstanz, 78457 Konstanz, Germany; Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool, L69 7ZB, UK. Electronic address: olga.mayans@uni-konstanz.de.,Structural Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Boston Biochem, a Bio-Techne Brand, 840 Memorial Drive, Cambridge, MA 02139, USA.,SPARC BioCentre, Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; Cell Biology Program, The Hospital for Sick Children, 686 Bay Street, Toronto, ON M5G 0A4, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada.,Department of Biology, University of Konstanz, 78457 Konstanz, Germany.,Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia; Australian Research Council Centre of Excellence for Advanced Molecular Imaging, Monash University, Clayton, VIC 3800, Australia; Institute of Infection and Immunity, Cardiff University, School of Medicine, Heath Park, Cardiff CF14 4XN, UK.,Japan Science and Technology Agency, Research Acceleration Program, Membrane Protein Crystallography Project, Konoe-cho, Yoshida, Sakyo-ku, Kyoto, Japan.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois, USA. koss@bsd.uchicago.edu.,Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, MI, USA. eric.xu@vai.org.,Department of Chemistry, University of California, San Diego, La Jolla, California, 92093.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA.,Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California, 92093.,Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA.,Structural Biology Research Center, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, 464-8601, Japan.,Protech Inc., Yongeon 103 Daehangno, Jongno-gu, Seoul, 110-799, Republic of Korea. yok5@snu.ac.kr.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560012, India. Electronic address: mrn@iisc.ac.in.,Center for Cancer and Cell Biology, Innovation and Integration Program, Van Andel Research Institute, Grand Rapids, MI, USA.,Department of Physiology, Perelman School of Medicine, University of Pennsylvania, 728 Clinical Research Building, 415 Curie Boulevard, Philadelphia, PA 19104-6085, USA.,Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, 49503, USA.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, 80045, USA. tatiana.kutateladze@ucdenver.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ATP-citrate synthase
A, B
270Homo sapiensMutation(s): 0 
Gene Names: ACLY
EC: 2.3.3.8
Find proteins for P53396 (Homo sapiens)
Go to Gene View: ACLY
Go to UniProtKB:  P53396
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
COA
Query on COA

Download SDF File 
Download CCD File 
A, B
COENZYME A
C21 H36 N7 O16 P3 S
RGJOEKWQDUBAIZ-IBOSZNHHSA-N
 Ligand Interaction
FLC
Query on FLC

Download SDF File 
Download CCD File 
A, B
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.178 
  • R-Value Work: 0.167 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 82.829α = 90.00
b = 111.192β = 90.00
c = 143.372γ = 90.00
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
PHASERphasing
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Research Foundation - FlandersBelgium1524918N

Revision History 

  • Version 1.0: 2019-04-10
    Type: Initial release
  • Version 1.1: 2019-04-17
    Type: Data collection, Database references
  • Version 1.2: 2019-05-08
    Type: Data collection, Database references