9MZI | pdb_00009mzi

CryoEM structure of GluK2 bound to glutamate in the deep desensitized state 3

PDB DOI: https://doi.org/10.2210/pdb9MZI/pdb
EM Map EMD-48757: 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: 3.83 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

CryoEM structure of GluK2 bound to glutamate in the deep desensitized state 3

Chang, P.Z., Nami, T.

To be published.

Macromolecule Content

Total Structure Weight: 420.1 kDa
Atom Count: 24,582
Modeled Residue Count: 3,037
Deposited Residue Count: 3,632
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42260
Glycosylation
Glycosylation Sites: 8	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: P42260-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, H, N, R	3		N-Glycosylation	Interactions Focus chain E Focus chain H Focus chain N Focus chain R Interactions & Density Focus chain E Focus chain H Focus chain N Focus chain R

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	3		N-Glycosylation	Interactions Focus chain F Interactions & Density Focus chain F

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, I, J, L, M G, I, J, L, M, P, Q	2		N-Glycosylation	Interactions Focus chain G Focus chain I Focus chain J Focus chain L Focus chain M Focus chain P Focus chain Q Interactions & Density Focus chain G Focus chain I Focus chain J Focus chain L Focus chain M Focus chain P Focus chain Q

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	K	2		N-Glycosylation	Interactions Focus chain K Interactions & Density Focus chain K

Entity ID: 6
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	O	3		N-Glycosylation	Interactions Focus chain O Interactions & Density Focus chain O

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain EA [auth D] SDF format, chain S [auth A] SDF format, chain U [auth A] SDF format, chain W [auth B] SDF format, chain X [auth B] SDF format, chain Y [auth B] SDF format, chain Z [auth C] SDF format, chain V [auth B] SDF format, chain T [auth A] MOL2 format, chain AA [auth C] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain EA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain U [auth A] MOL2 format, chain W [auth B] MOL2 format, chain X [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain Z [auth C] MOL2 format, chain V [auth B] MOL2 format, chain T [auth A] mmCIF format, chain AA [auth C] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain DA [auth D] mmCIF format, chain EA [auth D] mmCIF format, chain S [auth A] mmCIF format, chain U [auth A] mmCIF format, chain W [auth B] mmCIF format, chain X [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain Z [auth C] mmCIF format, chain V [auth B] mmCIF format, chain T [auth A]	AA [auth C] BA [auth D] CA [auth D] DA [auth D] EA [auth D] AA [auth C], BA [auth D], CA [auth D], DA [auth D], EA [auth D], S [auth A], T [auth A], U [auth A], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth C] Interactions & Density Focus chain AA [auth C] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] Focus chain EA [auth D] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.83 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

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

Revision History (Full details and data files)

Version 1.0: 2026-02-04
Type: Initial release

Prepare Data

Validate Data

Deposit Data

Help and Resources

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CryoEM structure of GluK2 bound to glutamate in the deep desensitized state 3

CryoEM structure of GluK2 bound to glutamate in the deep desensitized state 3

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

Entity ID: 3

Entity ID: 4

Entity ID: 5

Entity ID: 6

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)

9MZI | pdb_00009mzi