9KVH | pdb_00009kvh

A Cryo_EM structure of 5_HT1A complex with TMT

PDB DOI: https://doi.org/10.2210/pdb9KVH/pdb
EM Map EMD-62594: EMDB EMDataResource

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

Deposited: 2024-12-05 Released: 2025-12-03
Deposition Author(s): Yuan, Q., Li, S.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.59 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

A Cryo_EM structure of 5_HT1A complex with TMT

Yuan, Q., Li, S.

To be published.

Macromolecule Content

Total Structure Weight: 158.05 kDa
Atom Count: 8,923
Modeled Residue Count: 1,125
Deposited Residue Count: 1,414
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) subunit alpha-1	A	354	Homo sapiens	Mutation(s): 0 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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	344	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
SCFV16	C [auth E]	247	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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(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
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
5-hydroxytryptamine receptor 1A	E [auth R]	398	Homo sapiens	Mutation(s): 0 Gene Names: HTR1A, ADRB2RL1, ADRBRL1
UniProt & NIH Common Fund Data Resources
Find proteins for P08908 (Homo sapiens) Explore P08908 Go to UniProtKB: P08908
PHAROS: P08908 GTEx: ENSG00000178394
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P08908
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
J40 (Subject of Investigation/LOI) Query on J40 Download Ideal Coordinates CCD File SDF format, chain G [auth R] MOL2 format, chain G [auth R] mmCIF format, chain G [auth R]	G [auth R]	[(2R)-1-[oxidanyl-[(2R,3R,5S,6R)-2,3,5,6-tetrakis(oxidanyl)-4-phosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-3-tetradecanoyloxy-propan-2-yl] (5E,8E)-hexadeca-5,8,11,14-tetraenoate C₃₉ H₆₈ O₁₆ P₂ KFDYJTVTHSTWNE-UDQXHECVSA-N		Interactions Focus chain G [auth R] Interactions & Density Focus chain G [auth R]
CHO (Subject of Investigation/LOI) Query on CHO Download Ideal Coordinates CCD File SDF format, chain H [auth R] MOL2 format, chain H [auth R] mmCIF format, chain H [auth R]	H [auth R]	GLYCOCHENODEOXYCHOLIC ACID C₂₆ H₄₃ N O₅ GHCZAUBVMUEKKP-GYPHWSFCSA-N		Interactions Focus chain H [auth R] Interactions & Density Focus chain H [auth R]
CLR (Subject of Investigation/LOI) Query on CLR Download Ideal Coordinates CCD File SDF format, chain I [auth R] MOL2 format, chain I [auth R] mmCIF format, chain I [auth R]	I [auth R]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain I [auth R] Interactions & Density Focus chain I [auth R]
A1EG9 (Subject of Investigation/LOI) Query on A1EG9 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]	Cinobufotenine C₁₃ H₁₉ N₂ O LTBMTFANUCBSEL-UHFFFAOYSA-N		Interactions Focus chain F [auth R] Interactions & Density Focus chain F [auth R]