5BKG

Cyro-EM structure of human Glycine Receptor alpha2-beta heteromer, glycine bound, (semi)open state

PDB DOI: https://doi.org/10.2210/pdb5BKG/pdb
EM Map EMD-9404: EMDB EMDataResource

Classification: MEMBRANE PROTEIN, SIGNALING PROTEIN
Organism(s): Homo sapiens, Aequorea victoria
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMD

Deposited: 2021-03-19 Released: 2021-09-08
Deposition Author(s): Yu, H., Wang, W.
Funding Organization(s): Welch Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.80 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

Characterization of the subunit composition and structure of adult human glycine receptors

Yu, H., Bai, X.-C., Wang, W.

(2021) Neuron 109: 2707-2716

DOI: https://doi.org/10.1016/j.neuron.2021.08.019

Macromolecule Content

Total Structure Weight: 247.69 kDa
Atom Count: 13,509
Modelled Residue Count: 1,686
Deposited Residue Count: 2,158
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine receptor subunit alpha-2	A, B, C, D	364	Homo sapiens	Mutation(s): 0 Gene Names: GLRA2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P23416 (Homo sapiens) Explore P23416 Go to UniProtKB: P23416
PHAROS: P23416 GTEx: ENSG00000101958
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23416
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: P23416-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine receptor subunit beta,Green fluorescent protein	E	702	Homo sapiens, Aequorea victoria	Mutation(s): 0 Gene Names: GLRB, GFP Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P42212 (Aequorea victoria) Explore P42212 Go to UniProtKB: P42212
Find proteins for P48167 (Homo sapiens) Explore P48167 Go to UniProtKB: P48167
PHAROS: P48167 GTEx: ENSG00000109738
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P42212P48167
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 Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain Q [auth E] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain J [auth B] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth E]	F [auth A] G [auth A] I [auth B] J [auth B] M [auth C] F [auth A], G [auth A], I [auth B], J [auth B], M [auth C], N [auth C], O [auth D], P [auth D], Q [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E]
GLY (Subject of Investigation/LOI) Query on GLY Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B]	H [auth A], K [auth B], L [auth B]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B]