[English] 日本語
Yorodumi
- EMDB-53109: The composite map of of the AMPAR complex GluA3- TARP gamma2 in t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-53109
TitleThe composite map of of the AMPAR complex GluA3- TARP gamma2 in the apo state.
Map dataComposite map of the AMPAR complex GluA3-TARP gamma 2 in the apo state.
Sample
  • Complex: homomeric AMPAR complex GluA3 in tandem with the auxiliary subunit TARP gamma2
    • Protein or peptide: Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium channel gamma-2 subunit
KeywordsAMPAR / ion channels / neurotransmission / MEMBRANE PROTEIN
Function / homology
Function and homology information


Presynaptic depolarization and calcium channel opening / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cerebellar mossy fiber / LGI-ADAM interactions / postsynaptic neurotransmitter receptor diffusion trapping / Trafficking of AMPA receptors / channel regulator activity / regulation of AMPA receptor activity / membrane hyperpolarization ...Presynaptic depolarization and calcium channel opening / eye blink reflex / positive regulation of protein localization to basolateral plasma membrane / cerebellar mossy fiber / LGI-ADAM interactions / postsynaptic neurotransmitter receptor diffusion trapping / Trafficking of AMPA receptors / channel regulator activity / regulation of AMPA receptor activity / membrane hyperpolarization / nervous system process / Synaptic adhesion-like molecules / protein targeting to membrane / voltage-gated calcium channel complex / neurotransmitter receptor localization to postsynaptic specialization membrane / protein heterotetramerization / neuromuscular junction development / parallel fiber to Purkinje cell synapse / Activation of AMPA receptors / AMPA glutamate receptor activity / transmission of nerve impulse / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / membrane depolarization / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / synaptic cleft / regulation of postsynaptic membrane neurotransmitter receptor levels / voltage-gated calcium channel activity / response to fungicide / glutamate-gated receptor activity / ionotropic glutamate receptor binding / presynaptic active zone membrane / somatodendritic compartment / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / calcium channel regulator activity / positive regulation of synaptic transmission, glutamatergic / hippocampal mossy fiber to CA3 synapse / dendritic shaft / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / modulation of chemical synaptic transmission / postsynaptic density membrane / terminal bouton / Schaffer collateral - CA1 synapse / long-term synaptic potentiation / response to calcium ion / amyloid-beta binding / presynaptic membrane / protein homotetramerization / perikaryon / dendritic spine / postsynaptic membrane / postsynaptic density / neuronal cell body / dendrite / glutamatergic synapse / cell surface / protein-containing complex / 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
Glutamate receptor 3 / Voltage-dependent calcium channel gamma-2 subunit
Similarity search - Component
Biological speciesRattus (rat) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsPokharna A / Krieger J / Greger I / Ho H / Yamashita K / Cais O
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust223194/Z/21/Z United Kingdom
Medical Research Council (MRC, United Kingdom)MC_U105174197 United Kingdom
CitationJournal: To Be Published
Title: The NTD dimer and the interfacing LBD region of the AMPAR complex GluA3- TARP gamma2 in the apo state.
Authors: Pokharna A / Krieger J / Greger I
History
DepositionMar 11, 2025-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_53109.png

Downloads & links

-
Map

FileDownload / File: emd_53109.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map of the AMPAR complex GluA3-TARP gamma 2 in the apo state.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 422.912 Å		0.83 Å/pix.
x 512 pix.
= 422.912 Å		0.83 Å/pix.
x 512 pix.
= 422.912 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 9.0
Minimum - Maximum-0.7656952 - 66.083619999999996
Average (Standard dev.)1.7437553 (±1.3089122)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 422.912 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: Low-resolution consensus map of the AMPAR complex GluA3-TARP...

Fileemd_53109_additional_1.map
AnnotationLow-resolution consensus map of the AMPAR complex GluA3-TARP gamma 2 in the apo state corresponding to the composite map.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : homomeric AMPAR complex GluA3 in tandem with the auxiliary subuni...

EntireName: homomeric AMPAR complex GluA3 in tandem with the auxiliary subunit TARP gamma2
Components
  • Complex: homomeric AMPAR complex GluA3 in tandem with the auxiliary subunit TARP gamma2
    • Protein or peptide: Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium channel gamma-2 subunit

-
Supramolecule #1: homomeric AMPAR complex GluA3 in tandem with the auxiliary subuni...

SupramoleculeName: homomeric AMPAR complex GluA3 in tandem with the auxiliary subunit TARP gamma2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Rattus (rat)

-
Macromolecule #1: Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium ch...

MacromoleculeName: Isoform Flip of Glutamate receptor 3,Voltage-dependent calcium channel gamma-2 subunit
type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 131.711859 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FPNTISIGGL FMRNTVQEHS AFRFAVQLYN TNQNTTEKPF HLNYHVDHLD SSNSFSVTNA FCSQFSRGVY AIFGFYDQMS MNTLTSFCG ALHTSFVTPS FPTDADVQFV IQMRPALKGA ILSLLSYYKW EKFVYLYDTE RGFSVLQAIM EAAVQNNWQV T ARSVGNIK ...String:
FPNTISIGGL FMRNTVQEHS AFRFAVQLYN TNQNTTEKPF HLNYHVDHLD SSNSFSVTNA FCSQFSRGVY AIFGFYDQMS MNTLTSFCG ALHTSFVTPS FPTDADVQFV IQMRPALKGA ILSLLSYYKW EKFVYLYDTE RGFSVLQAIM EAAVQNNWQV T ARSVGNIK DVQEFRRIIE EMDRRQEKRY LIDCEVERIN TILEQVVILG KHSRGYHYML ANLGFTDILL ERVMHGGANI TG FQIVNNE NPMVQQFIQR WVRLDEREFP EAKNAPLKYT SALTHDAILV IAEAFRYLRR QRVDVSRRGS AGDCLANPAV PWS QGIDIE RALKMVQVQG MTGNIQFDTY GRRTNYTIDV YEMKVSGSRK AGYWNEYERF VPFSDQQISN DSSSSENRTI VVTT ILESP YVMYKKNHEQ LEGNERYEGY CVDLAYEIAK HVRIKYKLSI VGDGKYGARD PETKIWNGMV GELVYGRADI AVAPL TITL VREEVIDFSK PFMSLGISIM IKKPQKSKPG VFSFLDPLAY EIWMCIVFAY IGVSVVLFLV SRFSPYEWHL EDNNEE PRD PQSPPDPPNE FGIFNSLWFS LGAFMQQGCD ISPRSLSGRI VGGVWWFFTL IIISSYTANL AAFLTVERMV SPIESAE DL AKQTEIAYGT LDSGSTKEFF RRSKIAVYEK MWSYMKSAEP SVFTKTTADG VARVRKSKGK FAFLLESTMN EYIEQRKP C DTMKVGGNLD SKGYGVATPK GSALGTPVNL AVLKLSEQGI LDKLKNKWWY DKGECGAKDS GSKDKTSALS LSNVAGVFY ILVGGLGLAM MVALIEFCYK SRAESKRMKL TKNTQNFKPA PAGGSGSGGL FDRGVQMLLT TVGAFAAFSL MTIAVGTDYW LYSRGVCKT KSVSENETSK KNEEVMTHSG LWRTCCLEGN FKGLCKQIDH FPEDADYEAD TAEYFLRAVR ASSIFPILSV I LLFMGGLC IAASEFYKTR HNIILSAGIF FVSAGLSNII GIIVYISANA GDPSKSDSKK NSYSYGWSFY FGALSFIIAE MV GVLAVHM FIDRHKQLRA TARATDYLQA SAITRIPSYR YRYQRRSRSS SRSTEPSHSR DASPVGVKGF NTLPSTEISM YTL SRDPLK AATTPTATYN SDRDNSFLQV HNCIQKDSKD SLHANTANRR TTPV

UniProtKB: Glutamate receptor 3, Voltage-dependent calcium channel gamma-2 subunit

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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 / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: OTHER / Number images used: 1184304
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
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