9BU2

Homomeric alpha3 glycine receptor in the presence of 1 mM glycine at pH 6.4 in a desensitized state

PDB DOI: https://doi.org/10.2210/pdb9BU2/pdb
EM Map EMD-44899: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera aff. frugiperda 1 BOLD-2017
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2024-05-16 Released: 2024-11-13
Deposition Author(s): Kindig, K., Gibbs, E., Chakrapani, S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/Office of the Director

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.87 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

Homomeric alpha3 glycine receptor in the presence of 1 mM glycine at pH 6.4 in a desensitized state.

Kindig, K., Gibbs, E., Chakrapani, S.

To be published.

Macromolecule Content

Total Structure Weight: 312.65 kDa
Atom Count: 14,795
Modelled Residue Count: 1,730
Deposited Residue Count: 2,390
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine receptor subunit alpha-3	A, B, C, D, E	478	Homo sapiens	Mutation(s): 0 Gene Names: GLRA3 Membrane Entity: Yes
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O75311
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E	Go to GlyGen: O75311-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, G, H, I, J	2		N-Glycosylation	Interactions Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Interactions & Density Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PIO Query on PIO Download Ideal Coordinates CCD File SDF format, chain CB [auth E] SDF format, chain DB [auth E] SDF format, chain EA [auth B] SDF format, chain EB [auth E] SDF format, chain FB [auth E] SDF format, chain GA [auth C] SDF format, chain GB [auth E] SDF format, chain HA [auth C] SDF format, chain IA [auth C] SDF format, chain JA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain P [auth A] SDF format, chain QA [auth D] SDF format, chain RA [auth D] SDF format, chain SA [auth D] SDF format, chain TA [auth D] SDF format, chain U [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain YA [auth D] SDF format, chain Z [auth B] MOL2 format, chain CB [auth E] MOL2 format, chain DB [auth E] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth E] MOL2 format, chain FB [auth E] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth E] MOL2 format, chain HA [auth C] MOL2 format, chain IA [auth C] MOL2 format, chain JA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain U [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth D] MOL2 format, chain Z [auth B] mmCIF format, chain CB [auth E] mmCIF format, chain DB [auth E] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth E] mmCIF format, chain FB [auth E] mmCIF format, chain GA [auth C] mmCIF format, chain GB [auth E] mmCIF format, chain HA [auth C] mmCIF format, chain IA [auth C] mmCIF format, chain JA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth C] mmCIF format, chain P [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain RA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain TA [auth D] mmCIF format, chain U [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain YA [auth D] mmCIF format, chain Z [auth B]	CB [auth E] DB [auth E] EA [auth B] EB [auth E] FB [auth E] CB [auth E], DB [auth E], EA [auth B], EB [auth E], FB [auth E], GA [auth C], GB [auth E], HA [auth C], IA [auth C], JA [auth C], M [auth A], N [auth A], O [auth A], OA [auth C], P [auth A], QA [auth D], RA [auth D], SA [auth D], TA [auth D], U [auth A], W [auth B], X [auth B], Y [auth B], YA [auth D], Z [auth B]	[(2R)-2-octanoyloxy-3-[oxidanyl-[(1R,2R,3S,4R,5R,6S)-2,3,6-tris(oxidanyl)-4,5-diphosphonooxy-cyclohexyl]oxy-phosphoryl]oxy-propyl] octanoate C₂₅ H₄₉ O₁₉ P₃ XLNCEHRXXWQMPK-MJUMVPIBSA-N		Interactions Focus chain CB [auth E] Focus chain DB [auth E] Focus chain EA [auth B] Focus chain EB [auth E] Focus chain FB [auth E] Focus chain GA [auth C] Focus chain GB [auth E] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain U [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B] Interactions & Density Focus chain CB [auth E] Focus chain DB [auth E] Focus chain EA [auth B] Focus chain EB [auth E] Focus chain FB [auth E] Focus chain GA [auth C] Focus chain GB [auth E] Focus chain HA [auth C] Focus chain IA [auth C] Focus chain JA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain OA [auth C] Focus chain P [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain U [auth A] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain YA [auth D] Focus chain Z [auth B]
PX4 Query on PX4 Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth E] SDF format, chain BA [auth B] SDF format, chain BB [auth E] SDF format, chain CA [auth B] SDF format, chain DA [auth B] SDF format, chain HB [auth E] SDF format, chain KA [auth C] SDF format, chain LA [auth C] SDF format, chain MA [auth C] SDF format, chain NA [auth C] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain UA [auth D] SDF format, chain VA [auth D] SDF format, chain WA [auth D] SDF format, chain XA [auth D] SDF format, chain ZA [auth E] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth E] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth E] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth B] MOL2 format, chain HB [auth E] MOL2 format, chain KA [auth C] MOL2 format, chain LA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain UA [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain XA [auth D] MOL2 format, chain ZA [auth E] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth E] mmCIF format, chain BA [auth B] mmCIF format, chain BB [auth E] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth B] mmCIF format, chain HB [auth E] mmCIF format, chain KA [auth C] mmCIF format, chain LA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain UA [auth D] mmCIF format, chain VA [auth D] mmCIF format, chain WA [auth D] mmCIF format, chain XA [auth D] mmCIF format, chain ZA [auth E]	AA [auth B] AB [auth E] BA [auth B] BB [auth E] CA [auth B] AA [auth B], AB [auth E], BA [auth B], BB [auth E], CA [auth B], DA [auth B], HB [auth E], KA [auth C], LA [auth C], MA [auth C], NA [auth C], Q [auth A], R [auth A], S [auth A], T [auth A], UA [auth D], VA [auth D], WA [auth D], XA [auth D], ZA [auth E]	1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₃₆ H₇₃ N O₈ P CITHEXJVPOWHKC-UUWRZZSWSA-O		Interactions Focus chain AA [auth B] Focus chain AB [auth E] Focus chain BA [auth B] Focus chain BB [auth E] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain HB [auth E] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain ZA [auth E] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth E] Focus chain BA [auth B] Focus chain BB [auth E] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain HB [auth E] Focus chain KA [auth C] Focus chain LA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain UA [auth D] Focus chain VA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain ZA [auth E]
GLY Query on GLY Download Ideal Coordinates CCD File SDF format, chain FA [auth C] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain PA [auth D] SDF format, chain V [auth B] MOL2 format, chain FA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain PA [auth D] MOL2 format, chain V [auth B] mmCIF format, chain FA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain PA [auth D] mmCIF format, chain V [auth B]	FA [auth C], K [auth A], L [auth A], PA [auth D], V [auth B]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain FA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain PA [auth D] Focus chain V [auth B] Interactions & Density Focus chain FA [auth C] Focus chain K [auth A] Focus chain L [auth A] Focus chain PA [auth D] Focus chain V [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.87 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2024-11-13

Deposition Author(s):

Kindig, K.

Gibbs, E.

Chakrapani, S.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM131216
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35GM134896
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	3R01GM108921-03S1
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM108921-5S1
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	3R01GM131216-1S1
National Institutes of Health/Office of the Director	United States	1S10OD032437