6N4Y

Metabotropic Glutamate Receptor 5 Extracellular Domain with Nb43


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.262 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural insights into the activation of metabotropic glutamate receptors.

Koehl, A.Hu, H.Feng, D.Sun, B.Zhang, Y.Robertson, M.J.Chu, M.Kobilka, T.S.Laermans, T.Steyaert, J.Tarrasch, J.Dutta, S.Fonseca, R.Weis, W.I.Mathiesen, J.M.Skiniotis, G.Kobilka, B.K.

(2019) Nature 566: 79-84

  • DOI: 10.1038/s41586-019-0881-4
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Metabotropic glutamate receptors are family C G-protein-coupled receptors. They form obligate dimers and possess extracellular ligand-binding Venus flytrap domains, which are linked by cysteine-rich domains to their 7-transmembrane domains. Spectrosc ...

    Metabotropic glutamate receptors are family C G-protein-coupled receptors. They form obligate dimers and possess extracellular ligand-binding Venus flytrap domains, which are linked by cysteine-rich domains to their 7-transmembrane domains. Spectroscopic studies show that signalling is a dynamic process, in which large-scale conformational changes underlie the transmission of signals from the extracellular Venus flytraps to the G protein-coupling domains-the 7-transmembrane domains-in the membrane. Here, using a combination of X-ray crystallography, cryo-electron microscopy and signalling studies, we present a structural framework for the activation mechanism of metabotropic glutamate receptor subtype 5. Our results show that agonist binding at the Venus flytraps leads to a compaction of the intersubunit dimer interface, thereby bringing the cysteine-rich domains into close proximity. Interactions between the cysteine-rich domains and the second extracellular loops of the receptor enable the rigid-body repositioning of the 7-transmembrane domains, which come into contact with each other to initiate signalling.


    Organizational Affiliation

    California Institute for Quantitative Biosciences, University of California, Berkeley, United States.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: nathanael_gray@dfci.harvard.edu.,College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China. Electronic address: weifei_c@nwsuaf.edu.cn.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. laub@mit.edu.,Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France. andre.zapun@ibs.fr.,Hefei National Laboratory for Physical Science at the Microscale, School of Life Sciences, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230027, China.,Mitchell Cancer Institute, The University of South Alabama, Mobile, Alabama.,From the Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.,Department of Chemistry and Biochemistry, University of California Los Angeles, Los Angeles, CA 90095, USA.,Howard Hughes Medical Institute, University of California, Berkeley, United States.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. yiorgo@stanford.edu.,Department of Biotechnology , The University of Tokyo , 1-1-1 Yayoi , Bunkyo-ku, Tokyo 113-8657 , Japan.,Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.,College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China; LBPA, ENS de Cachan, Université Paris-Saclay, Centre National de la Recherche Scientifique, 61 Avenue du Président Wilson, 94235, Cachan, France. Electronic address: xxi01@ens-cachan.fr.,Centre for Bacterial Cell Biology, Institute for Cell and Molecular Bioscience, Newcastle University, Newcastle Upon Tyne, NE2 4AX, United Kingdom.,David Geffen School of Medicine, University of California Los Angeles and Greater West Los Angeles Health Care System, Los Angeles, CA 90095, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA. kyle.l.brown@vanderbilt.edu.,College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China.,the Department of Neuroscience, Mayo Clinic College of Medicine, Jacksonville, Florida 32224.,Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. jmm@sund.ku.dk.,Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,From the Departments of Biological Chemistry and Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA-DOE Institute, UCLA, Los Angeles, California 90095 and.,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.,York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK.,IBMC - Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar, Porto, Portugal.,Department of Molecular and Cell Biology, University of California, Berkeley, United States.,High Magnet Field Laboratory, Chinese Academy of Science, 50 Shushanhu Road, Hefei, Anhui 230031, China.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Electronic address: peter_sorger@hms.harvard.edu.,Aspirnaut Summer research program, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA. yiorgo@stanford.edu.,Biosciences Division, SLAC National Accelerator Laboratory, Stanford University, Stanford, CA, USA.,VIB-VUB Center for Structural Biology, VIB, Brussels, Belgium.,Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA.,Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.,Veterans Affairs Hospital, Nashville, TN, 37232, USA.,School of Biological Sciences , Nanyang Technological University , 50 Nanyang Drive , Singapore 637551.,DuPont Nutrition and Health, 3329 Agriculture Dr, Madison, WI, 53716, USA.,Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Leadership Alliance, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, Wales, United Kingdom.,Northeastern Collaborative Access Team, Argonne National Laboratory, Lemont, IL, 60439, USA.,Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada; Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.,Bioinformatics Institute , ASTAR (Agency for Science, Technology and Research) , 30 Biopolis Street, #07-01 Matrix , Singapore 138671 . Email: chandra@bii.a-star.edu.sg ; Tel: +65 6478 8273.,Centre Hospitalier Universitaire de Québec Research Center, Université Laval, Québec City, QC, G1V 4G2, Canada.,Félix d'Hérelle Reference Center for Bacterial Viruses, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada. sylvain.moineau@bcm.ulaval.ca.,Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China.,the Molecular Biophysics and Integrated Bioimaging Division, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and.,Koch Institute for Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA.,Department of Chemistry , University of Nevada, Reno , 1664 North Virginia Street , Reno , Nevada 89557 , United States.,From the Departments of Biological Chemistry and Chemistry and Biochemistry, Howard Hughes Medical Institute, UCLA-DOE Institute, UCLA, Los Angeles, California 90095 and david@mbi.ucla.edu.,ConfometRx, Santa Clara, CA, USA. kobilka@stanford.edu.,James Cook University, Cairns, Australia.,Membrane Biochemistry and Biophysics, Department of Chemistry, Faculty of Science, Utrecht University, Utrecht, 3584, The Netherlands.,The University of New South Wales, Faculty of Medicine, St Vincent's Clinical School, Darlinghurst, Sydney, NSW, 2010, Australia.,California NanoSystems Institute, University California Los Angeles, Los Angeles, CA 90095, USA.,Departments of Biochemistry and Radiation Oncology, The University of Texas Southwestern Medical Center at Dallas, Dallas, TX 75390, USA.,Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA. laub@mit.edu.,Division of Molecular Biotherapy, Cancer Chemotherapy Center , Japanese Foundation for Cancer Research , 3-8-31 Ariake , Koto-ku, Tokyo 135-8850 , Japan.,Architecture et Fonction des Macromolécules Biologiques, Aix-Marseille Université, Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France.,Departamento de Química, Universidade Nova de Lisboa, Caparica, 2829-516, Portugal.,Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.,i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,The Pirbright Institute, Pirbright, Woking, United Kingdom.,The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK.,Department of Biological Sciences , National University of Singapore , 14 Science Drive 4 , Singapore 117543.,Université Paris Descartes, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques UMR 8601 CNRS, Sorbonne Paris Cité (USPC), Paris, 75006, France.,Life Sciences Institute and Department of Biological Chemistry, University of Michigan Medical School, Ann Arbor, MI, USA.,Dahlem Centre of Plant Sciences, Department of Plant Physiology and Biochemistry, Freie Universität Berlin, Königin-Luise-Straße 12-16, 14195, Berlin, Germany.,Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China. Electronic address: qma@qdio.ac.cn.,Chemical Kinomics Research Center, Korea Institute of Science and Technology (KIST), 5 Hwarangro 14-gil, Seongbuk-gu, Seoul 02792, Republic of Korea; KU-KIST Graduate School of Converging Science and Technology, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea.,DuPont Nutrition and Health, BP 10, 86220, Dangé-Saint-Romain, France.,p53 Laboratory , ASTAR (Agency for Science, Technology and Research) , 8A Biomedical Grove, #06-04/05, Neuros/Immunos , Singapore 138648 . Email: cjbrown@p53lab.a-star.edu.sg ; Tel: +65 6478 8273.,Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, 1432, Norway.,Université Grenoble Alpes, CNRS, CEA, IBS UMR 5075, 38044, Grenoble, France.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA.,Architecture et Fonction des Macromolécules Biologiques, Centre National de la Recherche Scientifique (CNRS), Campus de Luminy, Case 932, 13288, Marseille Cedex 09, France.,ConfometRx, Santa Clara, CA, USA.,Center for Environmental Health Sciences MIT, Massachusetts Institute of Technology, Cambridge, MA, USA.,Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA. kyle.l.brown@vanderbilt.edu.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal.,Ipsen Bioscience , 650 East Kendall Street , Cambridge , MA 02142 , USA.,Département de biochimie, de microbiologie, et de bioinformatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada.,Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA.,School of Veterinary Sciences, University of Bristol, Bristol, United Kingdom.,Department of Agrifood Production and Environmental Sciences, University of Florence, Florence, Italy.,Immunology Division, Garvan Institute of Medical Research, 384 Victoria Road, Darlinghurst, Sydney, NSW, 2010, Australia. d.langley@garvan.org.au.,Structural Biology Brussels, Vrije Universiteit Brussel (VUB), Brussels, Belgium.,Division of Plant Biology, Department of Biosciences, University of Helsinki, FIN-00014, Helsinki, Finland.,NDBio Therapeutics Inc., Incheon 21984, Republic of Korea.,Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232-2372, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Center for Structural Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Ipsen Innovation , 5, Avenue du Canada , Les Ulis , France 91940 . Email: sergeauvin@gmail.com ; Tel: +33 160 922481.,Department of Microbiology, Immunology, & Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA.,Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany; Buchmann Institute for Life Sciences (BMLS) and Structural Genomics Consortium Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany; German Cancer Network (DKTK), Frankfurt Site, 60438 Frankfurt am Main, Germany.,Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853, USA.,Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK.,Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India.,Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA. kobilka@stanford.edu.,the Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224, radisky.evette@mayo.edu.,Center for Matrix Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA.,Département de biochimie, de microbiologie, et de bioinformatique, Faculté des sciences et de génie, Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, G1V 0A6, Canada. sylvain.moineau@bcm.ulaval.ca.,Univ. Lyon, ENS de Lyon, Univ. Claude Bernard, CNRS UMR 5239, INSERM U1210, LBMC, 46 allée d'Italie Site Jacques Monod, F-69007, Lyon, France.,RIKEN Program for Drug Discovery and Medical Technology Platforms , 2-1 Hirosawa , Wako , Saitama 351-0198 , Japan.,From the Avram and Stella Goldstein-Goren Department of Biotechnology Engineering and the National Institute of Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel, papo@bgu.ac.il.,the Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida 32224.,National Magnetic Resonance Facility at Madison , University of Wisconsin-Madison , 433 Babcock Drive , Madison , Wisconsin 53706 , United States.,Center for Structural Biology, Vanderbilt University Medical Center, Nashville, TN, 37232-2372, USA. kyle.l.brown@vanderbilt.edu.,the Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel.,the National Institute for Biotechnology in the Negev (NIBN), Beer-Sheva 84105, Israel.,Systems Immunity Research Institute, Cardiff University, Cardiff, Wales, United Kingdom.,Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI 48109, USA. Electronic address: nkoropat@umich.edu.,Farncombe Family Digestive Health Research Institute, McMaster University. Department of Medicine, Faculty of Health Sciences, McMaster University, Hamilton, ON, L8S 4K1, Canada.,Institute of Pharmaceutical Chemistry, Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany; Buchmann Institute for Life Sciences (BMLS) and Structural Genomics Consortium Goethe-University Frankfurt, Max von Lauestr. 9, 60438 Frankfurt am Main, Germany.,Broad Institute of Harvard and MIT, Cambridge, MA, USA.,Immunology Division, Garvan Institute of Medical Research, 384 Victoria Road, Darlinghurst, Sydney, NSW, 2010, Australia.,Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC V6T 1Z4, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Metabotropic glutamate receptor 5
A, B, C, D
596Homo sapiensMutation(s): 0 
Gene Names: GRM5 (GPRC1E, MGLUR5)
Find proteins for P41594 (Homo sapiens)
Go to Gene View: GRM5
Go to UniProtKB:  P41594
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nanobody 43
E, F, G, H
123N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
B, C, D
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
A, B, C, D
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
B, C, D
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.262 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 95.528α = 90.00
b = 158.389β = 101.93
c = 111.963γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS092695
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesNS028471

Revision History 

  • Version 1.0: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-02-06
    Type: Data collection, Database references
  • Version 1.2: 2019-02-20
    Type: Data collection, Database references
  • Version 1.3: 2019-12-18
    Type: Author supporting evidence, Data collection