7TU9 | pdb_00007tu9

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 OPM PDBTM mpstruc

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

Validation slider image for 7TU9

This is version 1.2 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
Modeled Residue Count: 1,709
Deposited Residue Count: 2,423
Unique protein chains: 2

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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

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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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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 V [auth C] SDF format, chain Q [auth D] SDF format, chain P [auth D] SDF format, chain O [auth D] SDF format, chain JA [auth E] SDF format, chain J [auth A] SDF format, chain IA [auth E] SDF format, chain HA [auth E] SDF format, chain G [auth A] SDF format, chain AA [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain P [auth D] MOL2 format, chain O [auth D] MOL2 format, chain JA [auth E] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth E] MOL2 format, chain HA [auth E] MOL2 format, chain G [auth A] MOL2 format, chain AA [auth B] mmCIF format, chain V [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain P [auth D] mmCIF format, chain O [auth D] mmCIF format, chain JA [auth E] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth E] mmCIF format, chain HA [auth E] mmCIF format, chain G [auth A] mmCIF format, chain AA [auth B]	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 Y [auth B] SDF format, chain U [auth C] SDF format, chain R [auth C] SDF format, chain N [auth D] SDF format, chain M [auth D] SDF format, chain H [auth A] SDF format, chain EA [auth E] SDF format, chain DA [auth E] SDF format, chain CA [auth B] SDF format, chain BA [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain U [auth C] MOL2 format, chain R [auth C] MOL2 format, chain N [auth D] MOL2 format, chain M [auth D] MOL2 format, chain H [auth A] MOL2 format, chain EA [auth E] MOL2 format, chain DA [auth E] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain U [auth C] mmCIF format, chain R [auth C] mmCIF format, chain N [auth D] mmCIF format, chain M [auth D] mmCIF format, chain H [auth A] mmCIF format, chain EA [auth E] mmCIF format, chain DA [auth E] mmCIF format, chain CA [auth B] mmCIF format, chain BA [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 X [auth B] SDF format, chain W [auth B] SDF format, chain T [auth C] SDF format, chain L [auth D] SDF format, chain I [auth A] MOL2 format, chain X [auth B] MOL2 format, chain W [auth B] MOL2 format, chain T [auth C] MOL2 format, chain L [auth D] MOL2 format, chain I [auth A] mmCIF format, chain X [auth B] mmCIF format, chain W [auth B] mmCIF format, chain T [auth C] mmCIF format, chain L [auth D] mmCIF format, chain I [auth A]	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 Z [auth B] SDF format, chain S [auth C] SDF format, chain K [auth D] SDF format, chain GA [auth E] SDF format, chain FA [auth E] SDF format, chain F [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain S [auth C] MOL2 format, chain K [auth D] MOL2 format, chain GA [auth E] MOL2 format, chain FA [auth E] MOL2 format, chain F [auth A] mmCIF format, chain Z [auth B] mmCIF format, chain S [auth C] mmCIF format, chain K [auth D] mmCIF format, chain GA [auth E] mmCIF format, chain FA [auth E] mmCIF format, chain F [auth A]	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)

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.00 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC	3.3.1

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-03-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R35GM134896

Revision History (Full details and data files)

Version 1.0: 2023-03-22
Type: Initial release
Version 1.1: 2024-10-23
Changes: Data collection, Structure summary
Version 1.2: 2025-05-14
Changes: Data collection

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.