9BP0 | pdb_00009bp0

Cryo-EM structure of human heteromeric Glycine Receptor alpha3S346E-beta with glycine

PDB DOI: https://doi.org/10.2210/pdb9BP0/pdb
EM Map EMD-44756: EMDB EMDataResource

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

Deposited: 2024-05-06 Released: 2025-05-14
Deposition Author(s): Liu, X., Wang, W.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.67 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Cryo-EM structure of human heteromeric Glycine Receptor alpha3S346E-beta with glycine

Liu, X., Wang, W.

To be published.

Macromolecule Content

Total Structure Weight: 273.91 kDa
Atom Count: 13,743
Modeled Residue Count: 1,704
Deposited Residue Count: 2,368
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine receptor subunit alpha-3	A, B, C, D	422	Homo sapiens	Mutation(s): 0 Gene Names: GLRA3
UniProt & NIH Common Fund Data Resources
Find proteins for O75311 (Homo sapiens) Explore O75311 Go to UniProtKB: O75311
PHAROS: O75311 GTEx: ENSG00000145451
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O75311
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: O75311-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine receptor subunit beta,Green fluorescent protein	E	680	Homo sapiens	Mutation(s): 0 Gene Names: GLRB, MMB69_26960
UniProt & NIH Common Fund Data Resources
Find proteins for P48167 (Homo sapiens) Explore P48167 Go to UniProtKB: P48167
PHAROS: P48167 GTEx: ENSG00000109738
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P48167
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain E	Go to GlyGen: P48167-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain M [auth E] SDF format, chain K [auth D] SDF format, chain J [auth C] SDF format, chain H [auth B] SDF format, chain F [auth A] MOL2 format, chain M [auth E] MOL2 format, chain K [auth D] MOL2 format, chain J [auth C] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] mmCIF format, chain M [auth E] mmCIF format, chain K [auth D] mmCIF format, chain J [auth C] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A]	F [auth A], H [auth B], J [auth C], K [auth D], M [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain M [auth E] Interactions & Density Focus chain F [auth A] Focus chain H [auth B] Focus chain J [auth C] Focus chain K [auth D] Focus chain M [auth E]
GLY (Subject of Investigation/LOI) Query on GLY Download:Ideal Coordinates CCD File SDF format, chain N [auth E] SDF format, chain L [auth D] SDF format, chain I [auth B] SDF format, chain G [auth A] MOL2 format, chain N [auth E] MOL2 format, chain L [auth D] MOL2 format, chain I [auth B] MOL2 format, chain G [auth A] mmCIF format, chain N [auth E] mmCIF format, chain L [auth D] mmCIF format, chain I [auth B] mmCIF format, chain G [auth A]	G [auth A], I [auth B], L [auth D], N [auth E]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth D] Focus chain N [auth E] Interactions & Density Focus chain G [auth A] Focus chain I [auth B] Focus chain L [auth D] Focus chain N [auth E]