9M7H | pdb_00009m7h

Cryo-EM structure of the orphan receptor GPRC5D in ligand free state resolved via the fusion/crosslinking strategy

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.17 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 9M7H

This is version 1.0 of the entry. See complete history. 

Literature

Cryo-EM structure determination of GPCRs with disulfide-crosslinked fusion protein

Han, S.C., Li, M.H.

To be published.

Macromolecule Content 

  • Total Structure Weight: 96.46 kDa 
  • Atom Count: 5,675 
  • Modeled Residue Count: 723 
  • Deposited Residue Count: 869 
  • Unique protein chains: 3

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
G-protein coupled receptor family C group 5 member D379Homo sapiensMutation(s): 0 
Gene Names: GPRC5D
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZD1 (Homo sapiens)
Explore Q9NZD1 
Go to UniProtKB:  Q9NZD1
PHAROS:  Q9NZD1
GTEx:  ENSG00000111291 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NZD1
Sequence Annotations
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Green fluorescent protein196Aequorea victoriaMutation(s): 0 
Gene Names: gfp
UniProt
Find proteins for A0A059PIQ0 (Aequorea victoria)
Explore A0A059PIQ0 
Go to UniProtKB:  A0A059PIQ0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A059PIQ0
Sequence Annotations
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
GFP-clamp E186C294Homo sapiensMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLR
(Subject of Investigation/LOI)

Query on CLR


Download:Ideal Coordinates CCD File
D [auth A]CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CRO
Query on CRO
B
L-PEPTIDE LINKINGC15 H17 N3 O5THR, TYR, GLY

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.17 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.19.2_4158
RECONSTRUCTIONRELION

Structure Validation

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View more in-depth experimental data

Entry History 

& Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2026-09-16
    Type: Initial release