4K5Y

Crystal structure of human corticotropin-releasing factor receptor 1 (CRF1R) in complex with the antagonist CP-376395

• PDB DOI: https://doi.org/10.2210/pdb4K5Y/pdb

• Classification: MEMBRANE PROTEIN, RECEPTOR
• Organism(s): Homo sapiens, Tequatrovirus T4
• Expression System: Trichoplusia ni
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2013-04-15 Released: 2013-07-17 
• Deposition Author(s): Hollenstein, K., Kean, J., Bortolato, A., Cheng, R.K.Y., Dore, A.S., Jazayeri, A., Cooke, R.M., Weir, M., Marshall, F.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free: 0.265 
• R-Value Work: 0.242 
• R-Value Observed: 0.243 

Starting Models: experimental

Literature

Structure of class B GPCR corticotropin-releasing factor receptor 1.

Hollenstein, K., Kean, J., Bortolato, A., Cheng, R.K., Dore, A.S., Jazayeri, A., Cooke, R.M., Weir, M., Marshall, F.H.

(2013) Nature 499: 438-443

• PubMed: 23863939 
• DOI: https://doi.org/10.1038/nature12357
• Primary Citation of Related Structures:  
  4K5Y


• PubMed Abstract: 
  

  Structural analysis of class B G-protein-coupled receptors (GPCRs), cell-surface proteins that respond to peptide hormones, has been restricted to the amino-terminal extracellular domain, thus providing little understanding of the membrane-spanning signal transduction domain. The corticotropin-releasing factor receptor type 1 is a class B receptor which mediates the response to stress and has been considered a drug target for depression and anxiety. Here we report the crystal structure of the transmembrane domain of the human corticotropin-releasing factor receptor type 1 in complex with the small-molecule antagonist CP-376395. The structure provides detailed insight into the architecture of class B receptors. Atomic details of the interactions of the receptor with the non-peptide ligand that binds deep within the receptor are described. This structure provides a model for all class B GPCRs and may aid in the design of new small-molecule drugs for diseases of brain and metabolism.

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Organizational Affiliation: 

Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City AL7 3AX, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 156.77 kDa 
• Atom Count: 8,823 
• Modelled Residue Count: 1,051 
• Deposited Residue Count: 1,323 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Corticotropin-releasing factor receptor 1, T4-Lysozyme chimeric construct	A, B, C	441	Homo sapiens, Tequatrovirus T4	Mutation(s): 16  Gene Names: CRF1R, CRFR, CRFR1, CRHR, CRHR1, E EC: 3.2.1.17 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P00720 (Enterobacteria phage T4) Explore P00720  Go to UniProtKB:  P00720
Find proteins for P34998 (Homo sapiens) Explore P34998  Go to UniProtKB:  P34998
PHAROS:  P34998 GTEx:  ENSG00000120088
UniProt Groups	P00720P34998

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGW	K [auth B], L [auth B], M [auth B]	(1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate C40 H77 O10 P PAZGBAOHGQRCBP-HGWHEPCSSA-N
OLC	F [auth A], G [auth A], J [auth B]	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate C21 H40 O4 RZRNAYUHWVFMIP-GDCKJWNLSA-N
1Q5	D [auth A], I [auth B], R [auth C]	3,6-dimethyl-N-(pentan-3-yl)-2-(2,4,6-trimethylphenoxy)pyridin-4-amine C21 H30 N2 O VIZBSVDBNLAVAW-UHFFFAOYSA-N
OLA	E [auth A], S [auth C]	OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N
1PE	N [auth B]	PENTAETHYLENE GLYCOL C10 H22 O6 JLFNLZLINWHATN-UHFFFAOYSA-N
SO4	H [auth A], O [auth B], P [auth B], Q [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
1Q5	PDBBind:  4K5Y	Kd: 6.7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.98 Å
• R-Value Free: 0.265 
• R-Value Work: 0.242 
• R-Value Observed: 0.243 
• Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 86.559	α = 90
b = 123.968	β = 90
c = 166.834	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-07-17 
Deposition Author(s): Hollenstein, K., Kean, J., Bortolato, A., Cheng, R.K.Y., Dore, A.S., Jazayeri, A., Cooke, R.M., Weir, M., Marshall, F.H.

Revision History  

• Version 1.0: 2013-07-17
  Type: Initial release
  
• Version 1.1: 2013-10-23
  Changes: Database references
• Version 1.2: 2017-08-09
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary