9EE5 | pdb_00009ee5

Cryo-EM structure of the ONO2550289-bound prostaglandin D2 receptor (DP1)-bRIL-Fab complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural insights into mechanism of activation and deactivation of prostaglandin receptors

Davoudinasab, B.Han, G.W.Cherezov, V.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
anti-BRIL Fab Heavy ChainA [auth H]229Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
anti-Fab Nanobody synthetic constructB [auth K]123synthetic constructMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
anti-BRIL Fab Light ChainC [auth L]214synthetic constructMutation(s): 0 
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Prostaglandin D2 receptor,Soluble cytochrome b562D [auth A]495Homo sapiensMutation(s): 6 
Gene Names: PTGDRcybC
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli)
Explore P0ABE7 
Go to UniProtKB:  P0ABE7
Find proteins for Q13258 (Homo sapiens)
Explore Q13258 
Go to UniProtKB:  Q13258
PHAROS:  Q13258
GTEx:  ENSG00000168229 
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UniProt GroupsQ13258P0ABE7
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BIL (Subject of Investigation/LOI)
Query on A1BIL

Download Ideal Coordinates CCD File 
E [auth A][2-chloro-5-(2,6-dimethyl-4-{[(2S)-4-methyl-3,4-dihydro-2H-1,4-benzoxazin-2-yl]methoxy}benzamido)phenyl]acetic acid
C27 H27 Cl N2 O5
KHJQYLXBPSJLGG-NRFANRHFSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.89 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC4.7.0

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM127086

Revision History  (Full details and data files)

  • Version 1.0: 2025-09-03
    Type: Initial release