7XXH

Cryo-EM structure of the purinergic receptor P2Y1R in complex with 2MeSADP and G11


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural insights into signal transduction of the purinergic receptors P2Y1R and P2Y12R.

Li, B.Han, S.Wang, M.Yu, Y.Ma, L.Chu, X.Tan, Q.Zhao, Q.Wu, B.

(2023) Protein Cell 14: 382-386


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
P2Y purinoceptor 1A [auth R]413Homo sapiensMutation(s): 0 
Gene Names: P2RY1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P47900 (Homo sapiens)
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Go to UniProtKB:  P47900
PHAROS:  P47900
GTEx:  ENSG00000169860 
Entity Groups  
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UniProt GroupP47900
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(11) subunit alphaB [auth A]353Homo sapiensMutation(s): 0 
EC: 3.6.5
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P29992 (Homo sapiens)
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Go to UniProtKB:  P29992
PHAROS:  P29992
GTEx:  ENSG00000088256 
Find proteins for P63096 (Homo sapiens)
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Go to UniProtKB:  P63096
PHAROS:  P63096
GTEx:  ENSG00000127955 
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UniProt GroupsP63096P29992
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1C [auth B]346Homo sapiensMutation(s): 0 
Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens)
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PHAROS:  P62873
GTEx:  ENSG00000078369 
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UniProt GroupP62873
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2D [auth G]71Homo sapiensMutation(s): 0 
Gene Names: GNG2
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens)
Explore P59768 
Go to UniProtKB:  P59768
PHAROS:  P59768
GTEx:  ENSG00000186469 
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UniProt GroupP59768
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
scfv16E [auth H]247Homo sapiensMutation(s): 0 
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6AD (Subject of Investigation/LOI)
Query on 6AD

Download Ideal Coordinates CCD File 
F [auth R]2-(methylsulfanyl)adenosine 5'-(trihydrogen diphosphate)
C11 H17 N5 O10 P2 S
WLMZTKAZJUWXCB-KQYNXXCUSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
6AD BindingDB:  7XXH IC50: min: 22, max: 1.00e+4 (nM) from 7 assay(s)
EC50: min: 1.3, max: 1.00e+4 (nM) from 56 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Science Foundation (NSF, China)China31825010
National Science Foundation (NSF, China)China82121005
Ministry of Science and Technology (MoST, China)China2018YFA0507000
Chinese Academy of SciencesChinaXDB37030100
Chinese Academy of SciencesChinaJCYJ-SHFY-2021-008

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-23
    Changes: Data collection, Structure summary