9BU3

Homomeric alpha3 glycine receptor in the presence of 0.1 mM glycine in a desensitized state

PDB DOI: https://doi.org/10.2210/pdb9BU3/pdb
EM Map EMD-44900: 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: 2.80 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

Physiological modulation of alpha3 glycine receptors

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

To be published.

Macromolecule Content

Total Structure Weight: 312.65 kDa
Atom Count: 14,630
Modelled Residue Count: 1,710
Deposited Residue Count: 2,390
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(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 BA [auth B] SDF format, chain DB [auth E] 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 LA [auth C] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain P [auth A] SDF format, chain QA [auth D] SDF format, chain R [auth A] SDF format, chain RA [auth D] SDF format, chain SA [auth D] SDF format, chain TA [auth D] SDF format, chain VA [auth D] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth B] SDF format, chain ZA [auth E] MOL2 format, chain BA [auth B] MOL2 format, chain DB [auth E] 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 LA [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] MOL2 format, chain QA [auth D] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth D] MOL2 format, chain SA [auth D] MOL2 format, chain TA [auth D] MOL2 format, chain VA [auth D] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth E] mmCIF format, chain BA [auth B] mmCIF format, chain DB [auth E] 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 LA [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A] mmCIF format, chain QA [auth D] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth D] mmCIF format, chain SA [auth D] mmCIF format, chain TA [auth D] mmCIF format, chain VA [auth D] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain ZA [auth E]	BA [auth B] DB [auth E] EB [auth E] FB [auth E] GA [auth C] BA [auth B], DB [auth E], EB [auth E], FB [auth E], GA [auth C], GB [auth E], HA [auth C], IA [auth C], JA [auth C], LA [auth C], M [auth A], N [auth A], O [auth A], P [auth A], QA [auth D], R [auth A], RA [auth D], SA [auth D], TA [auth D], VA [auth D], W [auth B], X [auth B], Y [auth B], Z [auth B], ZA [auth E]	[(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 BA [auth B] Focus chain DB [auth E] 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 LA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth D] Focus chain R [auth A] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain VA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Focus chain ZA [auth E] Interactions & Density Focus chain BA [auth B] Focus chain DB [auth E] 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 LA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain QA [auth D] Focus chain R [auth A] Focus chain RA [auth D] Focus chain SA [auth D] Focus chain TA [auth D] Focus chain VA [auth D] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Focus chain ZA [auth E]
PX4 Query on PX4 Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain AB [auth E] SDF format, chain BB [auth E] SDF format, chain CA [auth B] SDF format, chain CB [auth E] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain HB [auth E] SDF format, chain KA [auth C] SDF format, chain MA [auth C] SDF format, chain NA [auth C] SDF format, chain OA [auth C] SDF format, chain Q [auth A] SDF format, chain S [auth A] SDF format, chain T [auth A] SDF format, chain U [auth A] SDF format, chain UA [auth D] SDF format, chain WA [auth D] SDF format, chain XA [auth D] SDF format, chain YA [auth D] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth E] MOL2 format, chain BB [auth E] MOL2 format, chain CA [auth B] MOL2 format, chain CB [auth E] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain HB [auth E] MOL2 format, chain KA [auth C] MOL2 format, chain MA [auth C] MOL2 format, chain NA [auth C] MOL2 format, chain OA [auth C] MOL2 format, chain Q [auth A] MOL2 format, chain S [auth A] MOL2 format, chain T [auth A] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth D] MOL2 format, chain WA [auth D] MOL2 format, chain XA [auth D] MOL2 format, chain YA [auth D] mmCIF format, chain AA [auth B] mmCIF format, chain AB [auth E] mmCIF format, chain BB [auth E] mmCIF format, chain CA [auth B] mmCIF format, chain CB [auth E] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain HB [auth E] mmCIF format, chain KA [auth C] mmCIF format, chain MA [auth C] mmCIF format, chain NA [auth C] mmCIF format, chain OA [auth C] mmCIF format, chain Q [auth A] mmCIF format, chain S [auth A] mmCIF format, chain T [auth A] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth D] mmCIF format, chain WA [auth D] mmCIF format, chain XA [auth D] mmCIF format, chain YA [auth D]	AA [auth B] AB [auth E] BB [auth E] CA [auth B] CB [auth E] AA [auth B], AB [auth E], BB [auth E], CA [auth B], CB [auth E], DA [auth B], EA [auth B], HB [auth E], KA [auth C], MA [auth C], NA [auth C], OA [auth C], Q [auth A], S [auth A], T [auth A], U [auth A], UA [auth D], WA [auth D], XA [auth D], YA [auth D]	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 BB [auth E] Focus chain CA [auth B] Focus chain CB [auth E] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain HB [auth E] Focus chain KA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain Q [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain UA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain YA [auth D] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth E] Focus chain BB [auth E] Focus chain CA [auth B] Focus chain CB [auth E] Focus chain DA [auth B] Focus chain EA [auth B] Focus chain HB [auth E] Focus chain KA [auth C] Focus chain MA [auth C] Focus chain NA [auth C] Focus chain OA [auth C] Focus chain Q [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain UA [auth D] Focus chain WA [auth D] Focus chain XA [auth D] Focus chain YA [auth D]
GLY (Subject of Investigation/LOI) 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: 2.80 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