7TU9

Alpha1/BetaB Heteromeric Glycine Receptor in Strychnine-Bound State

PDB DOI: https://doi.org/10.2210/pdb7TU9/pdb
EM Map EMD-26130: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Danio rerio
Expression System: Spodoptera aff. frugiperda 1 BOLD-2017
Mutation(s): No
Membrane Protein: Yes OPMPDBTMmpstruc

Deposited: 2022-02-02 Released: 2023-03-22
Deposition Author(s): Gibbs, E., Kumar, A., Chakrapani, S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.00 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

Conformational transitions and allosteric modulation in a heteromeric glycine receptor

Gibbs, E., Klemm, E., Seiferth, D., Kumar, A., Ilca, S.L., Biggin, P.C., Chakrapani, S.

(2023) Nat Commun 14: 1363

DOI: https://doi.org/10.1038/s41467-023-37106-7

Macromolecule Content

Total Structure Weight: 293.23 kDa
Atom Count: 14,315
Modelled Residue Count: 1,709
Deposited Residue Count: 2,423
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 alphaZ1	A, B [auth D], C, D [auth B]	458	Danio rerio	Mutation(s): 0 Gene Names: glra1 Membrane Entity: Yes
UniProt
Find proteins for O93430 (Danio rerio) Explore O93430 Go to UniProtKB: O93430
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O93430
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B [auth D] Focus chain C Focus chain D [auth B]
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 beta subunit 2	E	591	Danio rerio	Mutation(s): 0 Gene Names: glrbb, glrb2 Membrane Entity: Yes
UniProt
Find proteins for Q6DC22 (Danio rerio) Explore Q6DC22 Go to UniProtKB: Q6DC22
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6DC22
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain E
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PIO Query on PIO Download Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain G [auth A] SDF format, chain HA [auth E] SDF format, chain IA [auth E] SDF format, chain J [auth A] SDF format, chain JA [auth E] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain Q [auth D] SDF format, chain V [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain HA [auth E] MOL2 format, chain IA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth E] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth D] MOL2 format, chain V [auth C] mmCIF format, chain AA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain HA [auth E] mmCIF format, chain IA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth E] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain Q [auth D] mmCIF format, chain V [auth C]	AA [auth B] G [auth A] HA [auth E] IA [auth E] J [auth A] AA [auth B], G [auth A], HA [auth E], IA [auth E], J [auth A], JA [auth E], O [auth D], P [auth D], Q [auth D], V [auth C]	[(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 AA [auth B] Focus chain G [auth A] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain V [auth C] Interactions & Density Focus chain AA [auth B] Focus chain G [auth A] Focus chain HA [auth E] Focus chain IA [auth E] Focus chain J [auth A] Focus chain JA [auth E] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth D] Focus chain V [auth C]
PX4 Query on PX4 Download Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain DA [auth E] SDF format, chain EA [auth E] SDF format, chain H [auth A] SDF format, chain M [auth D] SDF format, chain N [auth D] SDF format, chain R [auth C] SDF format, chain U [auth C] SDF format, chain Y [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain DA [auth E] MOL2 format, chain EA [auth E] MOL2 format, chain H [auth A] MOL2 format, chain M [auth D] MOL2 format, chain N [auth D] MOL2 format, chain R [auth C] MOL2 format, chain U [auth C] MOL2 format, chain Y [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain DA [auth E] mmCIF format, chain EA [auth E] mmCIF format, chain H [auth A] mmCIF format, chain M [auth D] mmCIF format, chain N [auth D] mmCIF format, chain R [auth C] mmCIF format, chain U [auth C] mmCIF format, chain Y [auth B]	BA [auth B] CA [auth B] DA [auth E] EA [auth E] H [auth A] BA [auth B], CA [auth B], DA [auth E], EA [auth E], H [auth A], M [auth D], N [auth D], R [auth C], U [auth C], Y [auth B]	1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHOCHOLINE C₃₆ H₇₃ N O₈ P CITHEXJVPOWHKC-UUWRZZSWSA-O		Interactions Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain H [auth A] Focus chain M [auth D] Focus chain N [auth D] Focus chain R [auth C] Focus chain U [auth C] Focus chain Y [auth B] Interactions & Density Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth E] Focus chain EA [auth E] Focus chain H [auth A] Focus chain M [auth D] Focus chain N [auth D] Focus chain R [auth C] Focus chain U [auth C] Focus chain Y [auth B]
SY9 (Subject of Investigation/LOI) Query on SY9 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth D] SDF format, chain T [auth C] SDF format, chain W [auth B] SDF format, chain X [auth B] MOL2 format, chain I [auth A] MOL2 format, chain L [auth D] MOL2 format, chain T [auth C] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] mmCIF format, chain I [auth A] mmCIF format, chain L [auth D] mmCIF format, chain T [auth C] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B]	I [auth A], L [auth D], T [auth C], W [auth B], X [auth B]	STRYCHNINE C₂₁ H₂₂ N₂ O₂ QMGVPVSNSZLJIA-FVWCLLPLSA-N		Interactions Focus chain I [auth A] Focus chain L [auth D] Focus chain T [auth C] Focus chain W [auth B] Focus chain X [auth B] Interactions & Density Focus chain I [auth A] Focus chain L [auth D] Focus chain T [auth C] Focus chain W [auth B] Focus chain X [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain FA [auth E] SDF format, chain GA [auth E] SDF format, chain K [auth D] SDF format, chain S [auth C] SDF format, chain Z [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth E] MOL2 format, chain GA [auth E] MOL2 format, chain K [auth D] MOL2 format, chain S [auth C] MOL2 format, chain Z [auth B] mmCIF format, chain F [auth A] mmCIF format, chain FA [auth E] mmCIF format, chain GA [auth E] mmCIF format, chain K [auth D] mmCIF format, chain S [auth C] mmCIF format, chain Z [auth B]	F [auth A] FA [auth E] GA [auth E] K [auth D] S [auth C] F [auth A], FA [auth E], GA [auth E], K [auth D], S [auth C], Z [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain K [auth D] Focus chain S [auth C] Focus chain Z [auth B] Interactions & Density Focus chain F [auth A] Focus chain FA [auth E] Focus chain GA [auth E] Focus chain K [auth D] Focus chain S [auth C] Focus chain Z [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
SY9	BindingDB: 7TU9	Ki: min: 5, max: 123 (nM) from 3 assay(s)
SY9	BindingDB: 7TU9	IC50: min: 27, max: 513 (nM) from 13 assay(s)