8HMP

GPR52 with Gs and c17

PDB DOI: https://doi.org/10.2210/pdb8HMP/pdb
EM Map EMD-34902: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda, Spodoptera, Escherichia coli, Trichoplusia ni
Mutation(s): Yes
Membrane Protein: Yes PDBTM

Deposited: 2022-12-05 Released: 2023-06-21
Deposition Author(s): Chen, B., Xu, F.
Funding Organization(s): National Science Foundation (NSF, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.77 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

Allosteric coupling between G-protein binding and extracellular ligand binding sites in GPR52 revealed by 19 F-NMR and cryo-electron microscopy.

Fan, Y., Lin, X., Pan, B., Chen, B., Liu, D., Wuthrich, K., Xu, F.

(2023) MedComm (2020) 4: e260-e260

PubMed: 37051308 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1002/mco2.260
Primary Citation of Related Structures:
8HMP

Organizational Affiliation

iHuman Institute School of Life Science and Technology Shanghai Key Laboratory of High-resolution Electron Microscopy ShanghaiTech University Shanghai China.

Macromolecule Content

Total Structure Weight: 130.58 kDa
Atom Count: 8,319
Modelled Residue Count: 1,045
Deposited Residue Count: 1,158
Unique protein chains: 5

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	A [auth B]	340	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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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	B [auth G]	96	Homo sapiens	Mutation(s): 1 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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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nb35	C [auth N]	149	Homo sapiens	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
G-protein coupled receptor 52	D [auth R]	324	Homo sapiens	Mutation(s): 0 Gene Names: GPR52 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2T5 (Homo sapiens) Explore Q9Y2T5 Go to UniProtKB: Q9Y2T5
PHAROS: Q9Y2T5 GTEx: ENSG00000203737
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9Y2T5
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Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short	E [auth A]	249	Homo sapiens	Mutation(s): 6 Gene Names: GNAS, GNAS1, GSP Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P63092 (Homo sapiens) Explore P63092 Go to UniProtKB: P63092
PHAROS: P63092 GTEx: ENSG00000087460
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P63092
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EN6 (Subject of Investigation/LOI) Query on EN6 Download Ideal Coordinates CCD File SDF format, chain F [auth R] MOL2 format, chain F [auth R]	F [auth R]	N-(2-hydroxyethyl)-5-(hydroxymethyl)-3-methyl-1-[2-[[3-(trifluoromethyl)phenyl]methyl]-1-benzothiophen-7-yl]pyrazole-4-carboxamide C₂₄ H₂₂ F₃ N₃ O₃ S VJMRKWPMFQGIPI-UHFFFAOYSA-N		Interactions Focus chain F [auth R] Interactions & Density Focus chain F [auth R]