8GC2 | pdb_00008gc2

Domoate-bound GluK2 kainate receptor in partially-open conformation 1

PDB DOI: https://doi.org/10.2210/pdb8GC2/pdb
EM Map EMD-29926: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Rattus norvegicus
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2023-03-01 Released: 2024-03-13
Deposition Author(s): Bogdanovic, N., Tajima, N.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 8GC2

This is version 1.1 of the entry. See complete history.

Literature

Structural basis for kainate receptor activation by a partial agonist

Bogdanovic, N., Tajima, N.

To be published.

Macromolecule Content

Total Structure Weight: 404.55 kDa
Atom Count: 24,342
Modeled Residue Count: 2,993
Deposited Residue Count: 3,500
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, kainate 2	A, B, C, D	875	Rattus norvegicus	Mutation(s): 0 Gene Names: Grik2, Glur6 Membrane Entity: Yes
UniProt
Find proteins for P42260 (Rattus norvegicus) Explore P42260 Go to UniProtKB: P42260
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P42260
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: P42260-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, L	5		N-Glycosylation	Interactions Focus chain E Focus chain L Interactions & Density Focus chain E Focus chain L
Glycosylation Resources
GlyTouCan: G21381MC GlyCosmos: G21381MC GlyGen: G21381MC

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

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	5		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G66753FB GlyCosmos: G66753FB GlyGen: G66753FB

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H, I, K	5		N-Glycosylation	Interactions Focus chain H Focus chain I Focus chain K Interactions & Density Focus chain H Focus chain I Focus chain K
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DOQ (Subject of Investigation/LOI) Query on DOQ Download:Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain R [auth B] SDF format, chain O [auth A] MOL2 format, chain U [auth C] MOL2 format, chain R [auth B] MOL2 format, chain O [auth A] mmCIF format, chain U [auth C] mmCIF format, chain R [auth B] mmCIF format, chain O [auth A]	O [auth A], R [auth B], U [auth C]	(2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-1,3-HEXADIENYL]-3-PYRROLIDINEACETIC ACID C₁₅ H₂₁ N O₆ VZFRNCSOCOPNDB-AOKDLOFSSA-N		Interactions Focus chain O [auth A] Focus chain R [auth B] Focus chain U [auth C] Interactions & Density Focus chain O [auth A] Focus chain R [auth B] Focus chain U [auth C]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A]	M [auth A] N [auth A] P [auth B] Q [auth B] S [auth C] M [auth A], N [auth A], P [auth B], Q [auth B], S [auth C], T [auth C], V [auth D], W [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1.4487
RECONSTRUCTION	RELION	4.0

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-03-13

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R35 GM147266-01

Revision History (Full details and data files)

Version 1.0: 2024-03-13
Type: Initial release
Version 1.1: 2024-10-16
Changes: Data collection, Structure summary

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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.