7XXH

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

PDB DOI: https://doi.org/10.2210/pdb7XXH/pdb
EM Map EMD-33503: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2022-05-30 Released: 2023-06-07
Deposition Author(s): Tan, Q., Li, B., Han, S., Zhao, Q., Wu, B.
Funding Organization(s): National Science Foundation (NSF, China), Ministry of Science and Technology (MoST, China), Chinese Academy of Sciences

Experimental Data Snapshot

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

Starting Model: experimental
View more details

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

PubMed: 37155313 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1093/procel/pwac025
Primary Citation of Related Structures:
7XXH, 7XXI

Organizational Affiliation

CAS Key Laboratory of Receptor Research, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.

Macromolecule Content

Total Structure Weight: 160.6 kDa
Atom Count: 8,847
Modelled Residue Count: 1,158
Deposited Residue Count: 1,430
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
P2Y purinoceptor 1	A [auth R]	413	Homo sapiens	Mutation(s): 0 Gene Names: P2RY1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P47900 (Homo sapiens) Explore P47900 Go to UniProtKB: P47900
PHAROS: P47900 GTEx: ENSG00000169860
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P47900
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(11) subunit alpha	B [auth A]	353	Homo sapiens	Mutation(s): 0 EC: 3.6.5 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P29992 (Homo sapiens) Explore P29992 Go to UniProtKB: P29992
PHAROS: P29992 GTEx: ENSG00000088256
Find proteins for P63096 (Homo sapiens) Explore P63096 Go to UniProtKB: P63096
PHAROS: P63096 GTEx: ENSG00000127955
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P63096P29992
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C [auth B]	346	Homo sapiens	Mutation(s): 0 Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens) Explore P62873 Go to UniProtKB: P62873
PHAROS: P62873 GTEx: ENSG00000078369
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62873
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D [auth G]	71	Homo sapiens	Mutation(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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P59768
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
scfv16	E [auth H]	247	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6AD (Subject of Investigation/LOI) Query on 6AD Download Ideal Coordinates CCD File SDF format, chain F [auth R] MOL2 format, chain F [auth R] mmCIF format, chain F [auth R]	F [auth R]	2-(methylsulfanyl)adenosine 5'-(trihydrogen diphosphate) C₁₁ H₁₇ N₅ O₁₀ P₂ S WLMZTKAZJUWXCB-KQYNXXCUSA-N		Interactions Focus chain F [auth R] Interactions & Density Focus chain F [auth R]

Binding Affinity Annotations
ID	Source	Binding Affinity
6AD	BindingDB: 7XXH	IC50: min: 22, max: 1.00e+4 (nM) from 7 assay(s)
6AD	BindingDB: 7XXH	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

Released Date: 2023-06-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	31825010
National Science Foundation (NSF, China)	China	82121005
Ministry of Science and Technology (MoST, China)	China	2018YFA0507000
Chinese Academy of Sciences	China	XDB37030100
Chinese Academy of Sciences	China	JCYJ-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