4OR2 | pdb_00004or2

Human class C G protein-coupled metabotropic glutamate receptor 1 in complex with a negative allosteric modulator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.268 (Depositor), 0.273 (DCC) 
  • R-Value Work: 
    0.227 (Depositor) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4OR2

Ligand Structure Quality Assessment 


This is version 1.7 of the entry. See complete history

Literature

Structure of a class C GPCR metabotropic glutamate receptor 1 bound to an allosteric modulator

Wu, H.Wang, C.Gregory, K.J.Han, G.W.Cho, H.P.Xia, Y.Niswender, C.M.Katritch, V.Meiler, J.Cherezov, V.Conn, P.J.Stevens, R.C.

(2014) Science 344: 58-64

  • DOI: https://doi.org/10.1126/science.1249489
  • Primary Citation Related Structures: 
    4OR2

  • PubMed Abstract: 

    The excitatory neurotransmitter glutamate induces modulatory actions via the metabotropic glutamate receptors (mGlus), which are class C G protein-coupled receptors (GPCRs). We determined the structure of the human mGlu1 receptor seven-transmembrane (7TM) domain bound to a negative allosteric modulator, FITM, at a resolution of 2.8 angstroms. The modulator binding site partially overlaps with the orthosteric binding sites of class A GPCRs but is more restricted than most other GPCRs. We observed a parallel 7TM dimer mediated by cholesterols, which suggests that signaling initiated by glutamate's interaction with the extracellular domain might be mediated via 7TM interactions within the full-length receptor dimer. A combination of crystallography, structure-activity relationships, mutagenesis, and full-length dimer modeling provides insights about the allosteric modulation and activation mechanism of class C GPCRs.


  • Organizational Affiliation
    • Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.

Macromolecule Content 

  • Total Structure Weight: 91.11 kDa 
  • Atom Count: 5,906 
  • Modeled Residue Count: 726 
  • Deposited Residue Count: 778 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Soluble cytochrome b562, Metabotropic glutamate receptor 1
A, B
389Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 3 
Gene Names: cybCGRM1_HUMANGPRC1AGRM1MGLUR1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for Q13255 (Homo sapiens)
Explore Q13255 
Go to UniProtKB:  Q13255
PHAROS:  Q13255
GTEx:  ENSG00000152822 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP0ABE7Q13255
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR

Query on CLR



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth A]
G [auth A]
O [auth B]
D [auth A],
E [auth A],
F [auth A],
G [auth A],
O [auth B],
P [auth B]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
FM9

Query on FM9



Download:Ideal Coordinates CCD File
C [auth A],
K [auth B]
4-fluoro-N-methyl-N-{4-[6-(propan-2-ylamino)pyrimidin-4-yl]-1,3-thiazol-2-yl}benzamide
C18 H18 F N5 O S
WIVGIKIKQHUFOD-UHFFFAOYSA-N
OLC

Query on OLC



Download:Ideal Coordinates CCD File
I [auth A],
J [auth A],
N [auth B]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
OLA

Query on OLA



Download:Ideal Coordinates CCD File
H [auth A]OLEIC ACID
C18 H34 O2
ZQPPMHVWECSIRJ-KTKRTIGZSA-N
PO4

Query on PO4



Download:Ideal Coordinates CCD File
L [auth B],
M [auth B]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.268 (Depositor), 0.273 (DCC) 
  • R-Value Work:  0.227 (Depositor) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.361α = 90
b = 86.552β = 90
c = 168.277γ = 90
Software Package:
Software NamePurpose
Blu-Icedata collection
AutoSolphasing
BUSTERrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2014-03-19
    Type: Initial release
  • Version 1.1: 2014-03-26
    Changes: Structure summary
  • Version 1.2: 2015-02-04
    Changes: Derived calculations
  • Version 1.3: 2015-04-01
    Changes: Database references
  • Version 1.4: 2017-08-16
    Changes: Refinement description, Source and taxonomy
  • Version 1.5: 2017-11-22
    Changes: Refinement description
  • Version 1.6: 2024-04-03
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.7: 2024-11-13
    Changes: Structure summary