4Z9G | pdb_00004z9g

Crystal structure of human corticotropin-releasing factor receptor 1 (CRF1R) in complex with the antagonist CP-376395 in a hexagonal setting with translational non-crystallographic symmetry

PDB DOI: https://doi.org/10.2210/pdb4Z9G/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens, Enterobacteria phage RB51
Expression System: Trichoplusia ni
Mutation(s): Yes
Membrane Protein: Yes OPM PDBTM MemProtMD

Deposited: 2015-04-10 Released: 2016-06-29
Deposition Author(s): Dore, A.S., Bortolato, A., Hollenstein, K., Cheng, R.K.Y., Read, R.J., Marshall, F.H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.18 Å
R-Value Free:
0.289 (Depositor), 0.304 (DCC)
R-Value Work:
0.244 (Depositor), 0.260 (DCC)
R-Value Observed:
0.247 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Decoding Corticotropin-Releasing Factor Receptor Type 1 Crystal Structures.

Dore, A.S., Bortolato, A., Hollenstein, K., Cheng, R.K.Y., Read, R.J., Marshall, F.H.

(2017) Curr Mol Pharmacol 10: 334-344

PubMed: 28183242 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.2174/1874467210666170110114727
Primary Citation Related Structures:
4Z9G

PubMed Abstract:
The structural analysis of class B G protein-coupled receptors (GPCR), cell surface proteins responding to peptide hormones, has until recently been restricted to the extracellular domain (ECD). Corticotropin-releasing factor receptor type 1 (CRF1R) is a class B receptor mediating stress response and also considered a drug target for depression and anxiety. Here we report the crystal structure of the transmembrane domain of human CRF1R in complex with the small-molecule antagonist CP-376395 in a hexagonal setting with translational non-crystallographic symmetry. Molecular dynamics and metadynamics simulations on this novel structure and the existing TMD structure for CRF1R provides insight as to how the small molecule ligand gains access to the induced-fit allosteric binding site with implications for the observed selectivity against CRF2R. Furthermore, molecular dynamics simulations performed using a full-length receptor model point to key interactions between the ECD and extracellular loop 3 of the TMD providing insight into the full inactive state of multidomain class B GPCRs.

Organizational Affiliation

Heptares Therapeutics Ltd, BioPark, Broadwater Road, Welwyn Garden City, Herts, AL7 3AX. United Kingdom.

Macromolecule Content

Total Structure Weight: 156.02 kDa
Atom Count: 10,244
Modeled Residue Count: 1,239
Deposited Residue Count: 1,329
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Corticotropin-releasing factor receptor 1,Lysozyme,Corticotropin-releasing factor receptor 1	A, B, C	443	Homo sapiens, Enterobacteria phage RB51	Mutation(s): 13 Gene Names: CRHR1, CRFR, CRFR1, CRHR, e, RB51ORF131 EC: 3.2.1.17 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for C3V2B5 (Enterobacteria phage RB51) Explore C3V2B5 Go to UniProtKB: C3V2B5
Find proteins for P34998 (Homo sapiens) Explore P34998 Go to UniProtKB: P34998
PHAROS: P34998 GTEx: ENSG00000120088
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	C3V2B5 P34998
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1Q5 Query on 1Q5 Download:Ideal Coordinates CCD File SDF format, chain R [auth C] SDF format, chain M [auth B] SDF format, chain G [auth A] MOL2 format, chain R [auth C] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] mmCIF format, chain R [auth C] mmCIF format, chain M [auth B] mmCIF format, chain G [auth A]	G [auth A], M [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		Interactions Focus chain G [auth A] Focus chain M [auth B] Focus chain R [auth C] Interactions & Density Focus chain G [auth A] Focus chain M [auth B] Focus chain R [auth C]
OLA Query on OLA Download:Ideal Coordinates CCD File SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain O [auth C] SDF format, chain N [auth C] SDF format, chain L [auth B] SDF format, chain K [auth B] SDF format, chain J [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain O [auth C] MOL2 format, chain N [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth B] MOL2 format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain O [auth C] mmCIF format, chain N [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth B] mmCIF format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] J [auth B] K [auth B] D [auth A], E [auth A], F [auth A], J [auth B], K [auth B], L [auth B], N [auth C], O [auth C], P [auth C], Q [auth C]	OLEIC ACID C₁₈ H₃₄ O₂ ZQPPMHVWECSIRJ-KTKRTIGZSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain J [auth B] Focus chain K [auth B] Focus chain L [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain P [auth C] Focus chain Q [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain I [auth A] SDF format, chain H [auth A] MOL2 format, chain S [auth C] MOL2 format, chain I [auth A] MOL2 format, chain H [auth A] mmCIF format, chain S [auth C] mmCIF format, chain I [auth A] mmCIF format, chain H [auth A]	H [auth A], I [auth A], S [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain S [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain S [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
1Q5	BindingDB: 4Z9G	IC50: 5.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.18 Å
R-Value Free: 0.289 (Depositor), 0.304 (DCC)
R-Value Work: 0.244 (Depositor), 0.260 (DCC)
R-Value Observed: 0.247 (Depositor)

Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 189.359	α = 90
b = 189.359	β = 90
c = 88.575	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-06-29

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2016-06-29
Type: Initial release
Version 1.1: 2017-12-06
Changes: Database references
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Refinement description
Version 1.3: 2024-11-13
Changes: Structure summary