6WHA | pdb_00006wha

HTR2A bound to 25-CN-NBOH in complex with a mini-Galpha-q protein, beta/gamma subunits and an active-state stabilizing single-chain variable fragment (scFv16) obtained by cryo-electron microscopy (cryoEM)

PDB DOI: https://doi.org/10.2210/pdb6WHA/pdb
EM Map EMD-21669: EMDB EMDataResource

Classification: MEMBRANE PROTEIN/IMMUNE SYSTEM
Organism(s): Escherichia coli, Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2020-04-07 Released: 2020-09-23
Deposition Author(s): Skiniotis, G., Roth, B., Kim, K., Panova, O.
Funding Organization(s): National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA), National Institutes of Health/National Institute of Mental Health (NIH/NIMH)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.36 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structure of a Hallucinogen-Activated Gq-Coupled 5-HT2A Serotonin Receptor

Kim, K., Che, T., Panova, O., Shoichet, B.K., Skiniotis, G., Roth, B.L.

(2020) Cell 182: 1574-1588

DOI: https://doi.org/10.1016/j.cell.2020.08.024

Macromolecule Content

Total Structure Weight: 160.51 kDa
Atom Count: 7,888
Modeled Residue Count: 1,074
Deposited Residue Count: 1,439
Unique protein chains: 5

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Soluble cytochrome b562,5-hydroxytryptamine receptor 2A chimera	A	497	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 0 Gene Names: cybC, HTR2A, HTR2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7 Go to UniProtKB: P0ABE7
Find proteins for P28223 (Homo sapiens) Explore P28223 Go to UniProtKB: P28223
PHAROS: P28223 GTEx: ENSG00000102468
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P28223 P0ABE7
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
G subunit q (Gi2-mini-Gq chimeric)	B	246	Homo sapiens	Mutation(s): 0

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| 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	358	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62873
Sequence Annotations Expand
Reference Sequence

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| 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	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P59768
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
single Fab chain (svFv16)	E	267	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
U0G (Subject of Investigation/LOI) Query on U0G Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	4-(2-{[(2-hydroxyphenyl)methyl]amino}ethyl)-2,5-dimethoxybenzonitrile C₁₈ H₂₀ N₂ O₃ VWEDZTZAXHMZIL-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
U0G	BindingDB: 6WHA	Ki: min: 2.71, max: 5.79 (nM) from 2 assay(s)
U0G	BindingDB: 6WHA	EC50: min: 1.9, max: 137 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.36 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-09-23

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)	United States	R37 DA045657
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	RO1 MH112205