9W6W | pdb_00009w6w

5-CT-bound serotonin 5A (5-HT5A) receptor-Gi protein complex

PDB DOI: https://doi.org/10.2210/pdb9W6W/pdb
EM Map EMD-65707: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Mus musculus, Escherichia coli
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2025-08-05 Released: 2025-11-26
Deposition Author(s): Zhang, X., Xie, L., Chen, P., Yu, J., Tian, X., Wei, J., Shao, Z., Yan, W., Xu, Z.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.13 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 and Functional Basis for Biased Agonism at the 5-hydroxytryptamine 5A Receptor.

Zhang, X., Xie, L., Chen, P., Yu, J., Tian, X., Wang, L., Wei, J., Shao, Z., Yan, W., Xu, Z.

(2025) Mol Biomed 6: 107-107

PubMed: 41222804 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/s43556-025-00359-3
Primary Citation of Related Structures:
9W6W

Organizational Affiliation

Division of Nephrology and Kidney Research Institute, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, China.

Macromolecule Content

Total Structure Weight: 169.73 kDa
Atom Count: 8,793
Modeled Residue Count: 1,126
Deposited Residue Count: 1,523
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]	359	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	B [auth C]	71	Homo sapiens	Mutation(s): 0 Gene Names: GNG2
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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	C [auth A]	354	Homo sapiens	Mutation(s): 4 Gene Names: GNAI1 EC: 3.6.5
UniProt & NIH Common Fund Data Resources
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 Group	P63096
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv16	D [auth E]	258	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,5-hydroxytryptamine receptor 5A	E [auth R]	481	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 0 Gene Names: cybC, HTR5A
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7 Go to UniProtKB: P0ABE7
Find proteins for P47898 (Homo sapiens) Explore P47898 Go to UniProtKB: P47898
PHAROS: P47898 GTEx: ENSG00000157219
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P0ABE7P47898
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8K3 (Subject of Investigation/LOI) Query on 8K3 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]	3-(2-azanylethyl)-1H-indole-5-carboxamide C₁₁ H₁₃ N₃ O WKZLNEWVIAGNAW-UHFFFAOYSA-N		Interactions Focus chain F [auth R] Interactions & Density Focus chain F [auth R]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.13 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-11-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	T2221004
National Natural Science Foundation of China (NSFC)	China	32371288
National Natural Science Foundation of China (NSFC)	China	82404716