[English] 日本語
Yorodumi
- PDB-9osi: The intact LBD state of GluK2/K5 with alpha-amino-3-hydroxy-5-met... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9osi
TitleThe intact LBD state of GluK2/K5 with alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)
Components
  • Glutamate receptor ionotropic, kainate 2
  • Glutamate receptor ionotropic, kainate 5,Green fluorescent protein chimera
KeywordsSIGNALING PROTEIN / Kainate receptor / ionotropic glutamate receptor / membrane protein / ligand-gated ion channel
Function / homology
Function and homology information


regulation of synaptic vesicle fusion to presynaptic active zone membrane / protein retention in ER lumen / mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / Activation of Ca-permeable Kainate Receptor / kainate selective glutamate receptor complex / regulation of short-term neuronal synaptic plasticity / glutamate receptor activity / ubiquitin conjugating enzyme binding ...regulation of synaptic vesicle fusion to presynaptic active zone membrane / protein retention in ER lumen / mossy fiber rosette / detection of cold stimulus involved in thermoception / Activation of Na-permeable kainate receptors / Activation of Ca-permeable Kainate Receptor / kainate selective glutamate receptor complex / regulation of short-term neuronal synaptic plasticity / glutamate receptor activity / ubiquitin conjugating enzyme binding / negative regulation of synaptic transmission, glutamatergic / regulation of JNK cascade / inhibitory postsynaptic potential / receptor clustering / kainate selective glutamate receptor activity / modulation of excitatory postsynaptic potential / extracellularly glutamate-gated ion channel activity / ionotropic glutamate receptor complex / positive regulation of synaptic transmission / behavioral fear response / neuronal action potential / glutamate-gated receptor activity / glutamate-gated calcium ion channel activity / establishment of localization in cell / presynaptic modulation of chemical synaptic transmission / dendrite cytoplasm / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / bioluminescence / hippocampal mossy fiber to CA3 synapse / SNARE binding / generation of precursor metabolites and energy / PDZ domain binding / synaptic transmission, glutamatergic / excitatory postsynaptic potential / cellular response to glucose stimulus / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / intracellular protein transport / SH3 domain binding / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / modulation of chemical synaptic transmission / intracellular calcium ion homeostasis / terminal bouton / positive regulation of neuron apoptotic process / neuron apoptotic process / presynaptic membrane / scaffold protein binding / chemical synaptic transmission / negative regulation of neuron apoptotic process / perikaryon / postsynaptic membrane / postsynaptic density / axon / neuronal cell body / ubiquitin protein ligase binding / synapse / dendrite / glutamatergic synapse / endoplasmic reticulum / nucleoplasm / membrane / identical protein binding / plasma membrane
Similarity search - Function
Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : ...Green fluorescent protein, GFP / Green fluorescent protein-related / Green fluorescent protein / Green fluorescent protein / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / : / Ionotropic glutamate receptor / Eukaryotic homologues of bacterial periplasmic substrate binding proteins. / Receptor, ligand binding region / Receptor family ligand binding region / Periplasmic binding protein-like I
Similarity search - Domain/homology
Green fluorescent protein / Glutamate receptor ionotropic, kainate 2 / Glutamate receptor ionotropic, kainate 5
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Aequorea victoria (jellyfish)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.95 Å
AuthorsKhanra, N.K. / Meyerson, J.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1 R35 GM142662 United States
CitationJournal: Nat Commun / Year: 2026
Title: Structures of partially occupied hetero-tetramers provide insight into kainate receptor activation and desensitization.
Authors: Nandish K Khanra / Alexa Strauss / Laura Moreno Wasielewski / Sophie Lenze / Joel Meyerson / Andreas Reiner / Joshua Levitz /
Abstract: Kainate receptors (KARs) are critical mediators and modulators of synaptic transmission which undergo rapid activation and desensitization upon binding of the neurotransmitter glutamate. Under ...Kainate receptors (KARs) are critical mediators and modulators of synaptic transmission which undergo rapid activation and desensitization upon binding of the neurotransmitter glutamate. Under various physiological and pharmacological conditions agonist binding likely occurs to only a subset of subunits within these tetrameric receptors, motivating an analysis of the functional and conformational effects of partial versus complete ligand occupancy. Here we report cryo-EM structures of the GluK2/GluK5 hetero-tetramer under partially-occupied conditions using 5-iodowillardiine and AMPA as GluK5-selective agonists. High-resolution pre-active state structures containing closed/open ligand binding domain (LBD) dimers with intact interfaces reveal gating-associated interface reshaping, inter-dimer motions, and pore-linker repositioning in response to asymmetric agonist binding. Interfacial LBD mutations to a central cluster formed by the GluK5 subunits and to an inter-dimer interface between GluK2 and GluK5 subunits, highlight the roles of interactions between LBD dimers in controlling receptor function, including the distinct slow deactivation of GluK5-containing receptors. Finally, the absence or presence of intact, partially, and fully ruptured LBD interfaces under different ligand conditions allows us to propose a revised model of stepwise ionotropic glutamate receptor activation and desensitization.
History
DepositionMay 24, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2026Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Additional map / Part number: 2 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 6, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glutamate receptor ionotropic, kainate 5,Green fluorescent protein chimera
B: Glutamate receptor ionotropic, kainate 2
C: Glutamate receptor ionotropic, kainate 5,Green fluorescent protein chimera
D: Glutamate receptor ionotropic, kainate 2


Theoretical massNumber of molelcules
Total (without water)459,3174
Polymers459,3174
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

-
Components

#1: Protein Glutamate receptor ionotropic, kainate 5,Green fluorescent protein chimera / GluK5 / Glutamate receptor KA-2 / KA2


Mass: 123676.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Glutamate receptor ionotropic, kainate 5 with Green fluorescent protein at the C-terminal
Source: (gene. exp.) Rattus norvegicus (Norway rat), (gene. exp.) Aequorea victoria (jellyfish)
Gene: Grik5, GFP / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q63273, UniProt: P42212
#2: Protein Glutamate receptor ionotropic, kainate 2 / GluK2 / Glutamate receptor 6 / GluR6


Mass: 105981.617 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Glutamate receptor ionotropic, kainate 2 / Source: (gene. exp.) Rattus norvegicus (Norway rat) / Cell line: HEK293S GnTI- / Gene: Grik2, Glur6 / Production host: Homo sapiens (human) / References: UniProt: P42260
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: The intact LBD state of GluK2/K5 with alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.458802 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Rattus norvegicus (Norway rat)10116
31Aequorea victoria (jellyfish)6100
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8 / Details: 20 mM Tris, 300 mM NaCl, 0.35 mM DDM, pH 8.0
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMTris2-Amino-2-(hydroxymethyl)propane-1,3-diol1
2300 mMNaClNaCl1
30.35 mMDDMn-Dodecyl-beta-D-Maltopyranoside1
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Functionalized with PEG-thiol / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: UltrAuFoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 51.28 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

EM software
IDNameCategory
1RELIONparticle selection
2Leginonimage acquisition
4CTFFINDCTF correction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7403033
3D reconstructionResolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 189632 / Symmetry type: POINT

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more