5XLI

Structure of anti-Angiotensin II type2 receptor antibody (D5711-4A03)

  • Classification: IMMUNE SYSTEM

  • Deposited: 2017-05-10 Released: 2018-07-11 
  • Deposition Author(s): Asada, H., Horita, S., Iwata, S., Hirata, K.
  • Funding Organization(s): Japan Agency for Medical Research and Development; Japan Society for the Promotion of Science 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.696 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of the human angiotensin II type 2 receptor bound to an angiotensin II analog.

Asada, H.Horita, S.Hirata, K.Shiroishi, M.Shiimura, Y.Iwanari, H.Hamakubo, T.Shimamura, T.Nomura, N.Kusano-Arai, O.Uemura, T.Suno, C.Kobayashi, T.Iwata, S.

(2018) Nat. Struct. Mol. Biol. 25: 570-576

  • DOI: 10.1038/s41594-018-0079-8
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Angiotensin II (AngII) plays a central role in regulating human blood pressure, which is mainly mediated by interactions between AngII and the G-protein-coupled receptors (GPCRs) AngII type 1 receptor (AT <sub>1 </sub>R) and AngII type 2 receptor (AT ...

    Angiotensin II (AngII) plays a central role in regulating human blood pressure, which is mainly mediated by interactions between AngII and the G-protein-coupled receptors (GPCRs) AngII type 1 receptor (AT 1 R) and AngII type 2 receptor (AT 2 R). We have solved the crystal structure of human AT 2 R binding the peptide ligand [Sar 1 , Ile 8 ]AngII and its specific antibody at 3.2-Å resolution. [Sar 1 , Ile 8 ]AngII interacts with both the 'core' binding domain, where the small-molecule ligands of AT 1 R and AT 2 R bind, and the 'extended' binding domain, which is equivalent to the allosteric modulator binding site of muscarinic acetylcholine receptor. We generated an antibody fragment to stabilize the extended binding domain that functions as a positive allosteric modulator. We also identified a signature positively charged cluster, which is conserved among peptide-binding receptors, to locate C termini at the bottom of the binding pocket. The reported results should help with designing ligands for angiotensin receptors and possibly to other peptide GPCRs.


    Organizational Affiliation

    School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea.,Japan Science and Technology Agency (JST), Precursory Research for Embryonic Science and Technology (PRESTO), Saitama, Japan.,Japan Agency for Medical Research and Development (AMED), Core Research for Evolutional Science and Technology (CREST), Kyoto, Japan.,From the Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP and scg34@cam.ac.uk.,Department of Molecular Pharmacology and Cell Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), 13125 Berlin, Germany.,State Key Laboratory of Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University , Shanghai, China.,Department of Chemistry, University of Florence, 50019 Sesto Fiorentino (FI), Italy. luigi.messori@unifi.it.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt. Electronic address: ahmed.belal@alexu.edu.eg.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada.,Sanofi-Aventis Pharma Deutschland GmbH, Frankfurt am Main, Germany.,College of Pharmacy, Oregon State University , Corvallis, Oregon 97331, United States.,Department of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853, United States.,Department of Integrative Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Centre National de la Recherche Scientifique, Institut National de la Santé de la Recherche Médicale, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, 67404, France.,Department of Biochemistry and Molecular Biology, Monash University, Clayton, Melbourne, VIC, Australia.,Department of Molecular and Cellular Physiology, Stanford University, Stanford, United States.,Synchrotron Radiation Research Section of Macromolecular Crystallography Laboratory, National Cancer Institute, South Cass Avenue 9700, Argonne, IL 60439, U.S.A. bartosz.sekula@nih.gov.,Department of Chemical Sciences, University of Naples Federico II, 80126 Napoli, Italy. ruffo@unina.it.,National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China; Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201210, China.,Department of Quantitative Biology and Medicine, Research Center for Advanced Science and Technology, University of Tokyo, Tokyo, Japan.,I2BC, SB2SM, CNRS UMR 9198, CEA Saclay, 91191, Gif-sur-Yvette, France.,Charles River , Chesterford Research Park , Saffron Walden CB10 1XL , U.K.,Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel.,Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan. shen@cc.okayama-u.ac.jp.,Department of Cellular and Molecular Medicine, Chosun University School of Medicine, Gwangju, 61452, Republic of Korea. Sunglee@chosun.ac.kr.,Department of Immunology, Juntendo University School of Medicine, Tokyo, 113-8421, Japan.,Faculty of Science, Ibaraki University, Mito, Japan.,The ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC, Australia.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt; Department of Analytical & Pharmaceutical Chemistry, Faculty of Pharmacy & Drug Manufacturing, Pharos University in Alexandria, Egypt.,Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.; Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA.,CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; University of Chinese Academy of Sciences, Beijing, 100049, China.,School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, 5005, Australia.,School of Physical Sciences & Computing, Division of Chemistry, University of Central Lancashire, Preston PR1 2HE, United Kingdom; School of Chemistry, University of Leeds, Leeds, LS2 9JT, United Kingdom.,Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, 38163, United States. wli@uthsc.edu.,Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada.,Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, United States.,Department of Anatomy, University of California San Francisco, San Francisco, CA 94143, USA.,National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China; Center for Precision Medicine Multi-Omics Research, Peking University Health Science Center; State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China.,Department of Pharmacology and Toxicology, Faculty of Medicine and Medical Centre, American University of Beirut, Beirut, Lebanon; Department of Pharmacology and Toxicology, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt. Electronic address: ae88@aub.edu.lb.,Pathology and Laboratory Medicine Service, VA Medical Center at Birmingham, Birmingham, AL, 35294, United States.,Department of Biochemistry & Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece. Electronic address: ddleonidas@bio.uth.gr.,From the Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP and.,Molecular Genetics, Institute of Life Science, Kurume University, Fukuoka, Japan.,Protein Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany; BioSupraMol Core Facility, Freie Universität Berlin, 14195 Berlin, Germany.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan. s.iwata@mfour.med.kyoto-u.ac.jp.,Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.,Department of Chemistry, Texas A&M University , College Station, Texas 77843, United States.,Department of Organic Chemistry, University of Debrecen, POB 400, H-4002 Debrecen, Hungary. Electronic address: somsak.laszlo@science.unideb.hu.,Research Institute for Interdisciplinary Science, Graduate School of Natural Science and Technology, Okayama University, Okayama, 700-8530, Japan.,Department of Biochemistry & Biotechnology, University of Thessaly, Biopolis, 41500 Larissa, Greece.,Department of Neurology and Neurological Sciences, Stanford University, Stanford, United States.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia. ilia.voskoboinik@petermac.org.,Synchrotron Radiation Research Section of Macromolecular Crystallography Laboratory, National Cancer Institute, South Cass Avenue 9700, Argonne, IL 60439, U.S.A.,Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada.,Département de Biochimie, de Microbiologie et de Bio-Informatique, IBIS et PROTEO, Université Laval, Pavillon Charles-Eugène Marchand, Québec, Canada.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.,Structural Biology Program, Memorial Sloan Kettering Cancer Center, New York, United States.,Biotechnology Research Centre, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan.,Graduate School of Pharmaceutical Sciences, Kyushu University, Fukuoka, Japan.,Institute of Molecular Biology and Biophysics, ETH Zurich, Swiss Federal Institute of Technology, 8093 Zurich, Switzerland.,Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.; Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.,Department of Pharmacy, University of Pisa, 56126 Pisa, Italy. tiziano.marzo@unipi.it.,Ion Mobility-Mass Spectrometry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany; Department of Molecular Physics, Fritz Haber Institute of the Max Planck Society, 14195 Berlin, Germany.,Protein Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany.,School of Molecular Sciences, University of Western Australia, Perth, WA, 6009, Australia.,Department of Dermatology, Comprehensive Cancer Center, Cancer Chemoprevention Program, University of Alabama at Birmingham, Birmingham, AL, 35294, United States.,Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India.,National Center for Protein Science Shanghai , Shanghai, China.,Department of Chemical Sciences, University of Naples Federico II, 80126 Napoli, Italy. giarita.ferraro@gmail.com.,Health and Life Sciences, De Montfort University, Gateway House, Leicester, LE1 9BH, United Kingdom.,X-ray Crystallography Facility, National Institute of Immunology, New Delhi 110067, India.,Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20, Nanxincun, Xiangshan, Beijing, 100093, China. shen@cc.okayama-u.ac.jp.,CHDI Management/CHDI Foundation , 6080 Center Drive , Los Angeles , California 90045 , United States.,Department of Chemistry, University of Basel, BPR 1096, Mattenstrasse 24a, 4058 Basel, Switzerland.,Department of Pharmacology and Toxicology, Faculty of Medicine and Medical Centre, American University of Beirut, Beirut, Lebanon.,Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany.,Department of Cellular and Molecular Medicine, Chosun University School of Medicine, Gwangju, 61452, Republic of Korea.,Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel.,Axe Molecular Endocrinology and Nephrology, CHU de Québec Research Center, Department of Molecular Medicine, Laval University, Québec, Canada.,University of Chinese Academy of Sciences, Yuquan Rd, Shijingshan District, Beijing, 100049, China.,RIKEN, SPring-8 Center, Hyogo, Japan. s.iwata@mfour.med.kyoto-u.ac.jp.,Department of Veterans Affairs Medical Center, Memphis, TN, 38104, United States.,Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul 02792, Republic of Korea.,Molecular Biology Institute, University of California, Los Angeles, CA, USA.,Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India ashish_arora@cdri.res.in.,KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea.,Department of Chemistry, University of Pennsylvania, Philadelphia, PA, 19104, United States.,GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, PA 19426, USA.,RIKEN, SPring-8 Center, Hyogo, Japan.,Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, United States.,Howard Hughes Medical Institute, Stanford University, Stanford, United States.,Structural Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany.,Department of Organic Chemistry, University of Debrecen, POB 400, H-4002 Debrecen, Hungary.,Department of Chemistry, University of Washington, 4000 15th Ave NE, Bagley Hall, Seattle, WA, 98195-1700, USA.,Protein Biochemistry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany. Electronic address: chfreund@zedat.fu-berlin.de.,Department of Chemical Sciences, University of Naples Federico II, 80126 Napoli, Italy. antonello.merlino@unina.it.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Alexandria University, Alexandria, 21521, Egypt.,Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, United States.,Department of Chemical Sciences, University of Naples Federico II, 80126 Napoli, Italy. cuccioli@unina.it.,Cancer Cell Death Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Max Planck Institute for Terrestrial Microbiology, D-35043 Marburg, Germany.,College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA.,Department of Photon Science, Stanford University, Stanford, United States.,Astex Pharmaceuticals, 436 Cambridge Science Park, Milton Road, Cambridge CB4 0QA, UK.,Killer Cell Biology Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. ilia.voskoboinik@petermac.org.,National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China.,Department of Medical Biochemistry, Faculty of Medicine, Alexandria University, Egypt.,Killer Cell Biology Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. amelia.brennan@petermac.org.,Department of Cell Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Photosynthesis Research Center, Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, No. 20, Nanxincun, Xiangshan, Beijing, 100093, China.,Department of Crystallography/Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London, UK.,Department of Integrative Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, Centre National de la Recherche Scientifique, Institut National de la Santé de la Recherche Médicale, Université de Strasbourg, 1 rue Laurent Fries, Illkirch, 67404, France. rochel@igbmc.fr.,Department of Environmental Engineering, Chosun University, Gwangju, 61452, Republic of Korea.,National Center for Protein Science Shanghai, State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 201210, China; Shanghai Science Research Center, Chinese Academy of Sciences, Shanghai 201210, China. Electronic address: cong@sibcb.ac.cn.,Microbiology Division, CSIR-Central Drug Research Institute, Lucknow 226031, India.,GlaxoSmithKline, 5 Moore Drive, P.O. Box 13398, Research Triangle Park, NC 27709, USA. Electronic address: david.n.deaton@gsk.com.,Department of Orthopaedic Surgery, University of California, Los Angeles, CA, USA.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia.,Department of Biochemistry, Geisel School of Medicine, Dartmouth College, Hanover, New Hampshire, USA.,Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem tér 1, H-4032 Debrecen, Hungary.,GlaxoSmithKline, 5 Moore Drive, P.O. Box 13398, Research Triangle Park, NC 27709, USA.,Institute for Photonics and Advanced Sensing, The School of Biological Sciences, The University of Adelaide, North Tce, Adelaide, South Australia, 5005, Australia.,Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, 38163, United States.,Department of Biomolecular Sciences, Weizmann Institute of Science, 7610001 Rehovot, Israel; dan.tawfik@weizmann.ac.il Bar-Even@mpimp-golm.mpg.de.,School of Physical Sciences & Computing, Division of Chemistry, University of Central Lancashire, Preston PR1 2HE, United Kingdom. Electronic address: jhayes@uclan.ac.uk.,Physical and Theoretical Chemistry Laboratory, University of Oxford, OX1 3QZ Oxford, United Kingdom.,Molecular Medicine Program, The Hospital for Sick Children, Toronto, ON M5G 0A4, Canada; john.rubinstein@utoronto.ca.,Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine & Pharmacology TMP, Theodor-Stern-Kai 7, 60596, Frankfurt, Germany.,the Cambridge Institute for Medical Research, University of Cambridge, Wellcome Trust/MRC Building, Cambridge CB2 0XY, United Kingdom.,Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Kafrelsheikh University, Kafr El-Sheikh, 33516, Egypt.,CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China. Electronic address: fengyg@qibebt.ac.cn.,Department of Material Science, Graduate School of Science, Osaka City University Sugimoto, Sumiyoshi-ku, Osaka, 558-8585, Japan.,Ion Mobility-Mass Spectrometry, Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany.,Charles River , Leiden 2333 CR , Netherlands.,GlaxoSmithKline, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK.,Killer Cell Biology Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia.,Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, 38163, United States.,Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany; dan.tawfik@weizmann.ac.il Bar-Even@mpimp-golm.mpg.de.,Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Project Group Translational Medicine & Pharmacology TMP, Theodor-Stern-Kai 7, 60596, Frankfurt, Germany; Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt, Theodor-Stern-Kai 7, 60596, Frankfurt, Germany.,Institute of Microbial Technology, Chandigarh, Council of Scientific and Industrial Research, Chandigarh 160 036, India.,Department of Structural Biology, Stanford University, Stanford, United States.,CAS Key Laboratory of Biofuels, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China; Qingdao Engineering Laboratory of Single Cell Oil, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101, China.,Institute of Bioinformatics and Applied Biotechnology, Bangalore, India.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FabL
a, b
213N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FabH
c, d
220N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.696 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.654α = 90.00
b = 150.498β = 93.10
c = 75.322γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and DevelopmentJapanA19170600003
Japan Society for the Promotion of ScienceJapan15J04343
Japan Society for the Promotion of ScienceJapan22590270

Revision History 

  • Version 1.0: 2018-07-11
    Type: Initial release
  • Version 1.1: 2018-07-25
    Type: Data collection, Database references