[English] 日本語
Yorodumi
- EMDB-46872: Resting state 1 of the GluA2-gamma2 complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-46872
TitleResting state 1 of the GluA2-gamma2 complex
Map dataResting state 1 LBD-TMD locally sharpened map
Sample
  • Complex: GluA2-TARPgamma2 Complex
    • Protein or peptide: Isoform Flip of Glutamate receptor 2
    • Protein or peptide: Voltage-dependent calcium channel gamma-2 subunit
Keywordsligand-gated ion channel / ionotropic glutamate receptor / ampa receptor / ion channel / TRANSPORT PROTEIN
Function / homology
Function and homology information


Presynaptic depolarization and calcium channel opening / LGI-ADAM interactions / Trafficking of AMPA receptors / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cerebellar mossy fiber / regulation of AMPA receptor activity / postsynaptic neurotransmitter receptor diffusion trapping / membrane hyperpolarization / nervous system process ...Presynaptic depolarization and calcium channel opening / LGI-ADAM interactions / Trafficking of AMPA receptors / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cerebellar mossy fiber / regulation of AMPA receptor activity / postsynaptic neurotransmitter receptor diffusion trapping / membrane hyperpolarization / nervous system process / protein targeting to membrane / voltage-gated calcium channel complex / neurotransmitter receptor localization to postsynaptic specialization membrane / neuromuscular junction development / spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / transmission of nerve impulse / ligand-gated monoatomic cation channel activity / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / cellular response to glycine / extracellularly glutamate-gated ion channel activity / membrane depolarization / asymmetric synapse / regulation of receptor recycling / regulation of postsynaptic membrane neurotransmitter receptor levels / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / voltage-gated calcium channel activity / glutamate-gated receptor activity / regulation of synaptic transmission, glutamatergic / response to fungicide / cytoskeletal protein binding / presynaptic active zone membrane / ionotropic glutamate receptor binding / dendrite membrane / glutamate-gated calcium ion channel activity / extracellular ligand-gated monoatomic ion channel activity / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite cytoplasm / ionotropic glutamate receptor signaling pathway / SNARE binding / hippocampal mossy fiber to CA3 synapse / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / regulation of membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / protein tetramerization / synaptic membrane / modulation of chemical synaptic transmission / establishment of protein localization / postsynaptic density membrane / terminal bouton / Schaffer collateral - CA1 synapse / cerebral cortex development / receptor internalization / response to calcium ion / synaptic vesicle membrane / synaptic vesicle / signaling receptor activity / presynapse / amyloid-beta binding / presynaptic membrane / growth cone / scaffold protein binding / chemical synaptic transmission / perikaryon / postsynaptic membrane / dendritic spine / postsynaptic density / neuron projection / axon / neuronal cell body / dendrite / synapse / protein-containing complex binding / protein kinase binding / glutamatergic synapse / cell surface / endoplasmic reticulum / protein-containing complex / identical protein binding / membrane / plasma membrane
Similarity search - Function
Voltage-dependent calcium channel, gamma-2 subunit / : / PMP-22/EMP/MP20/Claudin family / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin superfamily / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel ...Voltage-dependent calcium channel, gamma-2 subunit / : / PMP-22/EMP/MP20/Claudin family / Voltage-dependent calcium channel, gamma subunit / PMP-22/EMP/MP20/Claudin superfamily / Ionotropic glutamate receptor, metazoa / Ligated ion channel L-glutamate- and glycine-binding site / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site / Ligand-gated ion channel / : / 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
Voltage-dependent calcium channel gamma-2 subunit / Glutamate receptor 2
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.18 Å
AuthorsKumar Mondal A / Carrillo E / Jayaraman V / Twomey EC
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM154904 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122528 United States
Other privateKinship Foundation 22098168
Other privateDiana Helis Henry Medical Research Foundation 142548
CitationJournal: Nature / Year: 2025
Title: Glutamate gating of AMPA-subtype iGluRs at physiological temperatures.
Authors: Anish Kumar Mondal / Elisa Carrillo / Vasanthi Jayaraman / Edward C Twomey /
Abstract: Ionotropic glutamate receptors (iGluRs) are tetrameric ligand-gated ion channels that mediate most excitatory neurotransmission. iGluRs are gated by glutamate, where on glutamate binding, they open ...Ionotropic glutamate receptors (iGluRs) are tetrameric ligand-gated ion channels that mediate most excitatory neurotransmission. iGluRs are gated by glutamate, where on glutamate binding, they open their ion channels to enable cation influx into postsynaptic neurons, initiating signal transduction. The structural mechanics of how glutamate gating occurs in full-length iGluRs is not well understood. Here, using the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid subtype iGluR (AMPAR), we identify the glutamate-gating mechanism. AMPAR activation by glutamate is augmented at physiological temperatures. By preparing AMPARs for cryogenic-electron microscopy at these temperatures, we captured the glutamate-gating mechanism. Activation by glutamate initiates ion channel opening that involves all ion channel helices hinging away from the pore axis in a motif that is conserved across all iGluRs. Desensitization occurs when the local dimer pairs decouple and enables closure of the ion channel below through restoring the channel hinges and refolding the channel gate. Our findings define how glutamate gates iGluRs, provide foundations for therapeutic design and demonstrate how physiological temperatures can alter iGluR function.
History
DepositionSep 4, 2024-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_46872.png

Downloads & links

-
Map

FileDownload / File: emd_46872.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationResting state 1 LBD-TMD locally sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.97 Å/pix.
x 440 pix.
= 426.8 Å		0.97 Å/pix.
x 440 pix.
= 426.8 Å		0.97 Å/pix.
x 440 pix.
= 426.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.97 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.5486929 - 0.99059016
Average (Standard dev.)0.0006777522 (±0.0127117485)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 426.80002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Resting state 1 LBD-TMD half map

Fileemd_46872_half_map_1.map
AnnotationResting state 1 LBD-TMD half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Resting state 1 LBD-TMD half map

Fileemd_46872_half_map_2.map
AnnotationResting state 1 LBD-TMD half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : GluA2-TARPgamma2 Complex

EntireName: GluA2-TARPgamma2 Complex
Components
  • Complex: GluA2-TARPgamma2 Complex
    • Protein or peptide: Isoform Flip of Glutamate receptor 2
    • Protein or peptide: Voltage-dependent calcium channel gamma-2 subunit

-
Supramolecule #1: GluA2-TARPgamma2 Complex

SupramoleculeName: GluA2-TARPgamma2 Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus norvegicus (Norway rat)

-
Macromolecule #1: Isoform Flip of Glutamate receptor 2

MacromoleculeName: Isoform Flip of Glutamate receptor 2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 47.938141 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EQKTVVVTTI LESPYVMMKK NHEMLEGNER YEGYCVDLAA EIAKHCGFKY KLTIVGDGKY GARDADTKIW NGMVGELVYG KADIAIAPL TITLVREEVI DFSKPFMSLG ISIMIKKPQK SKPGVFSFLD PLAYEIWMCI VFAYIGVSVV LFLVSRFSPY E WHTEEFED ...String:
EQKTVVVTTI LESPYVMMKK NHEMLEGNER YEGYCVDLAA EIAKHCGFKY KLTIVGDGKY GARDADTKIW NGMVGELVYG KADIAIAPL TITLVREEVI DFSKPFMSLG ISIMIKKPQK SKPGVFSFLD PLAYEIWMCI VFAYIGVSVV LFLVSRFSPY E WHTEEFED GRETQSSEST NEFGIFNSLW FSLGAFMQQG CDISPRSLSG RIVGGVWWFF TLIIISSYTA NLAAFLTVER MV SPIESAE DLSKQTEIAY GTLDSGSTKE FFRRSKIAVF DKMWTYMRSA EPSVFVRTTA EGVARVRKSK GKYAYLLEST MNE YIEQRK PCDTMKVGGN LDSKGYGIAT PKGSSLGTPV NLAVLKLSEQ GVLDKLKNKW WYDKGECGAK DSGSKEKTSA LSLS NVAGV FYILVGGLGL AMLVALIEFC YKSRA

UniProtKB: Glutamate receptor 2

-
Macromolecule #2: Voltage-dependent calcium channel gamma-2 subunit

MacromoleculeName: Voltage-dependent calcium channel gamma-2 subunit / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 22.633041 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: RGVQMLLTTV GAFAAFSLMT IAVGTDYWLY SRGVCKTKSV SENETSKKNE EVMTHSGLWR TCCLEGNFKG LCKQIDHFPE DADYEADTA EYFLRAVRAS SIFPILSVIL LFMGGLCIAA SEFYKTRHNI ILSAGIFFVS AGLSNIIGII VYISANAGDP S KSDSKKNS ...String:
RGVQMLLTTV GAFAAFSLMT IAVGTDYWLY SRGVCKTKSV SENETSKKNE EVMTHSGLWR TCCLEGNFKG LCKQIDHFPE DADYEADTA EYFLRAVRAS SIFPILSVIL LFMGGLCIAA SEFYKTRHNI ILSAGIFFVS AGLSNIIGII VYISANAGDP S KSDSKKNS YSYGWSFYFG ALSFIIAEMV GVLAVHMFID RHKQLTG

UniProtKB: Voltage-dependent calcium channel gamma-2 subunit

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration4 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER / Details: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 74785
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

+
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