9MZM | pdb_00009mzm

CryoEM structure of GluK2 bound to glutamate in the shallow desensitized state, consensus map

PDB DOI: https://doi.org/10.2210/pdb9MZM/pdb
EM Map EMD-48761: EMDB EMDataResource

Classification: STRUCTURAL PROTEIN
Organism(s): Rattus norvegicus
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2025-01-23 Released: 2026-02-04
Deposition Author(s): Chang, P.Z., Nami, T.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.86 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

CryoEM structure of GluK2 bound to glutamate in the shallow desensitized state, consensus map

Chang, P.Z., Nami, T.

To be published.

Macromolecule Content

Total Structure Weight: 417.25 kDa
Atom Count: 24,865
Modeled Residue Count: 3,084
Deposited Residue Count: 3,632
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, kainate 2	A, B, C, D	908	Rattus norvegicus	Mutation(s): 0 Gene Names: Grik2, Glur6
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: 6	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: P42260-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain Z [auth D] SDF format, chain Y [auth D] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain P [auth A] SDF format, chain N [auth A] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain O [auth A] MOL2 format, chain Z [auth D] MOL2 format, chain Y [auth D] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain P [auth A] MOL2 format, chain N [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain O [auth A] mmCIF format, chain Z [auth D] mmCIF format, chain Y [auth D] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain P [auth A] mmCIF format, chain N [auth A] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] N [auth A] O [auth A] P [auth A] AA [auth D], BA [auth D], N [auth A], O [auth A], P [auth A], R [auth B], S [auth B], U [auth C], V [auth C], W [auth C], Y [auth D], Z [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
GLU Query on GLU Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain T [auth B] SDF format, chain Q [auth A] SDF format, chain CA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain T [auth B] MOL2 format, chain Q [auth A] MOL2 format, chain CA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain T [auth B] mmCIF format, chain Q [auth A] mmCIF format, chain CA [auth D]	CA [auth D], Q [auth A], T [auth B], X [auth C]	GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Interactions Focus chain CA [auth D] Focus chain Q [auth A] Focus chain T [auth B] Focus chain X [auth C] Interactions & Density Focus chain CA [auth D] Focus chain Q [auth A] Focus chain T [auth B] Focus chain X [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.86 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-02-04

Deposition Author(s):

Chang, P.Z.

Nami, T.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R35GM147266-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	3R35GM147266-01S1