3N7P | pdb_00003n7p

Crystal structure of the ectodomain complex of the CGRP receptor, a Class-B GPCR, reveals the site of drug antagonism


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.241 (Depositor), 0.272 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 
    0.215 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3N7P

This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of the Ectodomain Complex of the CGRP Receptor, a Class-B GPCR, Reveals the Site of Drug Antagonism.

Ter Haar, E.Koth, C.M.Abdul-Manan, N.Swenson, L.Coll, J.T.Lippke, J.A.Lepre, C.A.Garcia-Guzman, M.Moore, J.M.

(2010) Structure 18: 1083-1093

  • DOI: https://doi.org/10.1016/j.str.2010.05.014
  • Primary Citation Related Structures: 
    3N7P, 3N7R, 3N7S

  • PubMed Abstract: 

    Dysregulation of the calcitonin gene-related peptide (CGRP), a potent vasodilator, is directly implicated in the pathogenesis of migraine. CGRP binds to and signals through the CGRP receptor (CGRP-R), a heterodimer containing the calcitonin receptor-like receptor (CLR), a class B GPCR, and RAMP1, a receptor activity-modifying protein. We have solved the crystal structure of the CLR/RAMP1 N-terminal ectodomain heterodimer, revealing how RAMPs bind to and potentially modulate the activities of the CLR GPCR subfamily. We also report the structures of CLR/RAMP1 in complex with the clinical receptor antagonists olcegepant (BIBN4096BS) and telcagepant (MK0974). Both drugs act by blocking access to the peptide-binding cleft at the interface of CLR and RAMP1. These structures illustrate, for the first time, how small molecules bind to and modulate the activity of a class B GPCR, and highlight the challenges of designing potent receptor antagonists for the treatment of migraine and other class B GPCR-related diseases.


  • Organizational Affiliation
    • Vertex Pharmaceuticals Incorporated, 130 Waverly Street, Cambridge, MA 02139, USA.

Macromolecule Content 

  • Total Structure Weight: 99.84 kDa 
  • Atom Count: 5,529 
  • Modeled Residue Count: 703 
  • Deposited Residue Count: 844 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Calcitonin gene-related peptide type 1 receptorA,
B,
C,
G [auth J]
115Homo sapiensMutation(s): 0 
Gene Names: CALCRLCALRL_HUMANCGRPR
UniProt & NIH Common Fund Data Resources
Find proteins for Q16602 (Homo sapiens)
Explore Q16602 
Go to UniProtKB:  Q16602
PHAROS:  Q16602
GTEx:  ENSG00000064989 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16602
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Receptor activity-modifying protein 1D,
E,
F,
H [auth R]
96Homo sapiensMutation(s): 0 
Gene Names: RAMP1RAMP1_HUMAN
UniProt & NIH Common Fund Data Resources
Find proteins for O60894 (Homo sapiens)
Explore O60894 
Go to UniProtKB:  O60894
PHAROS:  O60894
GTEx:  ENSG00000132329 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60894
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
K [auth A]
L [auth B]
M [auth B]
I [auth A],
J [auth A],
K [auth A],
L [auth B],
M [auth B],
N [auth B],
O [auth D],
P [auth D],
Q [auth D],
R [auth E],
S [auth E],
T [auth J],
U [auth J],
V [auth R],
W [auth R],
X [auth R]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A,
B,
C,
G [auth J]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.241 (Depositor), 0.272 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.249 (DCC) 
  • R-Value Observed: 0.215 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118α = 90
b = 118β = 90
c = 225.4γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Released Date: 2010-09-15 
  • Deposition Author(s): Ter Haar, E.

Revision History  (Full details and data files)

  • Version 1.0: 2010-09-15
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description
  • Version 1.3: 2024-11-06
    Changes: Data collection, Database references, Derived calculations, Structure summary