[English] 日本語
Yorodumi
- EMDB-16381: Resting state homomeric GluA2 F231A mutant AMPA receptor in compl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-16381
TitleResting state homomeric GluA2 F231A mutant AMPA receptor in complex with TARP gamma-2
Map data
Sample
  • Complex: Homomeric GluA2 F231A mutant AMPA receptor in complex with TARP gamma 2
    • Protein or peptide: Voltage-dependent calcium channel gamma-2 subunit
    • Protein or peptide: Glutamate receptor 2
  • Ligand: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid
  • Ligand: PALMITIC ACID
  • Ligand: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: water
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 / Trafficking of AMPA receptors / postsynaptic neurotransmitter receptor diffusion trapping / regulation of AMPA receptor activity / channel regulator 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 / Trafficking of AMPA receptors / postsynaptic neurotransmitter receptor diffusion trapping / regulation of AMPA receptor activity / channel regulator activity / membrane hyperpolarization / nervous system process / protein targeting to membrane / voltage-gated calcium channel complex / spine synapse / dendritic spine neck / dendritic spine cytoplasm / dendritic spine head / cellular response to amine stimulus / Activation of AMPA receptors / neurotransmitter receptor localization to postsynaptic specialization membrane / ligand-gated monoatomic cation channel activity / perisynaptic space / neuromuscular junction development / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / AMPA glutamate receptor activity / AMPA glutamate receptor clustering / transmission of nerve impulse / kainate selective glutamate receptor activity / immunoglobulin binding / asymmetric synapse / extracellularly glutamate-gated ion channel activity / AMPA glutamate receptor complex / cellular response to glycine / regulation of receptor recycling / membrane depolarization / ionotropic glutamate receptor complex / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / conditioned place preference / positive regulation of synaptic transmission / regulation of postsynaptic membrane neurotransmitter receptor levels / voltage-gated calcium channel activity / response to fungicide / regulation of synaptic transmission, glutamatergic / positive regulation of synaptic transmission, glutamatergic / extracellular ligand-gated monoatomic ion channel activity / cytoskeletal protein binding / glutamate-gated receptor activity / regulation of long-term synaptic depression / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / glutamate-gated calcium ion channel activity / presynaptic active zone membrane / excitatory synapse / ionotropic glutamate receptor signaling pathway / ionotropic glutamate receptor binding / dendrite membrane / dendrite cytoplasm / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / positive regulation of excitatory postsynaptic potential / hippocampal mossy fiber to CA3 synapse / dendritic shaft / SNARE binding / synaptic membrane / PDZ domain binding / calcium channel regulator activity / synaptic transmission, glutamatergic / protein tetramerization / establishment of protein localization / regulation of membrane potential / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / cerebral cortex development / response to calcium ion / receptor internalization / postsynaptic density membrane / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / terminal bouton / synaptic vesicle / long-term synaptic potentiation / amyloid-beta binding / synaptic vesicle membrane / growth cone / presynapse / signaling receptor activity / presynaptic membrane / scaffold protein binding / dendritic spine / chemical synaptic transmission / perikaryon / postsynaptic membrane / neuron projection / postsynaptic density / external side of plasma membrane / axon / neuronal cell body / synapse / dendrite / protein kinase binding
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 / Ligand-gated ion channel / Ionotropic glutamate receptor, L-glutamate and glycine-binding domain / Ligated ion channel L-glutamate- and glycine-binding site ...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 / 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
Glutamate receptor 2 / Voltage-dependent calcium channel gamma-2 subunit
Similarity search - Component
Biological speciesRattus (rats) / Rattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsZhang D / Ivica J / Krieger JM / Ho H / Yamashita K / Cais O / Greger I
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: Nature / Year: 2023
Title: Structural mobility tunes signalling of the GluA1 AMPA glutamate receptor.
Authors: Danyang Zhang / Josip Ivica / James M Krieger / Hinze Ho / Keitaro Yamashita / Imogen Stockwell / Rozbeh Baradaran / Ondrej Cais / Ingo H Greger /
Abstract: AMPA glutamate receptors (AMPARs), the primary mediators of excitatory neurotransmission in the brain, are either GluA2 subunit-containing and thus Ca-impermeable, or GluA2-lacking and Ca-permeable. ...AMPA glutamate receptors (AMPARs), the primary mediators of excitatory neurotransmission in the brain, are either GluA2 subunit-containing and thus Ca-impermeable, or GluA2-lacking and Ca-permeable. Despite their prominent expression throughout interneurons and glia, their role in long-term potentiation and their involvement in a range of neuropathologies, structural information for GluA2-lacking receptors is currently absent. Here we determine and characterize cryo-electron microscopy structures of the GluA1 homotetramer, fully occupied with TARPγ3 auxiliary subunits (GluA1/γ3). The gating core of both resting and open-state GluA1/γ3 closely resembles GluA2-containing receptors. However, the sequence-diverse N-terminal domains (NTDs) give rise to a highly mobile assembly, enabling domain swapping and subunit re-alignments in the ligand-binding domain tier that are pronounced in desensitized states. These transitions underlie the unique kinetic properties of GluA1. A GluA2 mutant (F231A) increasing NTD dynamics phenocopies this behaviour, and exhibits reduced synaptic responses, reflecting the anchoring function of the AMPAR NTD at the synapse. Together, this work underscores how the subunit-diverse NTDs determine subunit arrangement, gating properties and ultimately synaptic signalling efficiency among AMPAR subtypes.
History
DepositionDec 21, 2022-
Header (metadata) releaseAug 30, 2023-
Map releaseAug 30, 2023-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_16381.png

Downloads & links

-
Map

FileDownload / File: emd_16381.map.gz / Format: CCP4 / Size: 127.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 322 pix.
= 265.972 Å		0.83 Å/pix.
x 322 pix.
= 265.972 Å		0.83 Å/pix.
x 322 pix.
= 265.972 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: 0.009
Minimum - Maximum-0.02632024 - 0.046525665
Average (Standard dev.)0.0001639919 (±0.0012643689)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin636363
Dimensions322322322
Spacing322322322
CellA=B=C: 265.972 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_16381_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_16381_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_16381_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Homomeric GluA2 F231A mutant AMPA receptor in complex with TARP g...

EntireName: Homomeric GluA2 F231A mutant AMPA receptor in complex with TARP gamma 2
Components
  • Complex: Homomeric GluA2 F231A mutant AMPA receptor in complex with TARP gamma 2
    • Protein or peptide: Voltage-dependent calcium channel gamma-2 subunit
    • Protein or peptide: Glutamate receptor 2
  • Ligand: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid
  • Ligand: PALMITIC ACID
  • Ligand: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
  • Ligand: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
  • Ligand: water

-
Supramolecule #1: Homomeric GluA2 F231A mutant AMPA receptor in complex with TARP g...

SupramoleculeName: Homomeric GluA2 F231A mutant AMPA receptor in complex with TARP gamma 2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2, #1
Source (natural)Organism: Rattus (rats)

-
Macromolecule #1: Glutamate receptor 2

MacromoleculeName: Glutamate receptor 2 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 99.880891 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQKIMHISVL LSPVLWGLIF GDYKDDDDKV SSNSIQIGGL FPRGADQEYS AFRVGMVQFS TSEFRLTPHI DNLEVANSFA VTNAFCSQF SRGVYAIFGF YDKKSVNTIT SFCGTLHVSF ITPSFPTDGT HPFVIQMRPD LKGALLSLIE YYQWDKFAYL Y DSDRGLST ...String:
MQKIMHISVL LSPVLWGLIF GDYKDDDDKV SSNSIQIGGL FPRGADQEYS AFRVGMVQFS TSEFRLTPHI DNLEVANSFA VTNAFCSQF SRGVYAIFGF YDKKSVNTIT SFCGTLHVSF ITPSFPTDGT HPFVIQMRPD LKGALLSLIE YYQWDKFAYL Y DSDRGLST LQAVLDSAAE KKWQVTAINV GNINNDKKDE TYRSLFQDLE LKKERRVILD CERDKVNDIV DQVITIGKHV KG YHYIIAN LGFTDGDLLK IQFGGANVSG FQIVDYDDSL VSKFIERWST LEEKEYPGAH TATIKYTSAL TYDAVQVMTE AFR NLRKQR IEISRRGNAG DCLANPAVPW GQGVEIERAL KQVQVEGLSG NIKFDQNGKR INYTINIMEL KTNGPRKIGY WSEV DKMVV TLTELPSGND TSGLENKTVV VTTILESPYV MMKKNHEMLE GNERYEGYCV DLAAEIAKHC GFKYKLTIVG DGKYG ARDA DTKIWNGMVG ELVYGKADIA IAPLTITLVR EEVIDFSKPF MSLGISIMIK KPQKSKPGVF SFLDPLAYEI WMCIVF AYI GVSVVLFLVS RFSPYEWHTE EFEDGRETQS SESTNEFGIF NSLWFSLGAF MRQGCDISPR SLSGRIVGGV WWFFTLI II SSYTANLAAF LTVERMVSPI ESAEDLSKQT EIAYGTLDSG STKEFFRRSK IAVFDKMWTY MRSAEPSVFV RTTAEGVA R VRKSKGKYAY LLESTMNEYI EQRKPCDTMK VGGNLDSKGY GIATPKGSSL GTPVNLAVLK LSEQGVLDKL KNKWWYDKG ECGAKDSGSK EKTSALSLSN VAGVFYILVG GLGLAMLVAL IEFCYKSRAE AKRMKVAKNP QNINPSSSQN SQNFATYKEG YNVYGIESV KI

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: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 35.807555 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLFDRGVQML LTTVGAFAAF SLMTIAVGTD YWLYSRGVCK TKSVSENETS KKNEEVMTHS GLWRTCCLEG NFKGLCKQID HFPEDADYE ADTAEYFLRA VRASSIFPIL SVILLFMGGL CIAASEFYKT RHNIILSAGI FFVSAGLSNI IGIIVYISAN A GDPSKSDS ...String:
GLFDRGVQML LTTVGAFAAF SLMTIAVGTD YWLYSRGVCK TKSVSENETS KKNEEVMTHS GLWRTCCLEG NFKGLCKQID HFPEDADYE ADTAEYFLRA VRASSIFPIL SVILLFMGGL CIAASEFYKT RHNIILSAGI FFVSAGLSNI IGIIVYISAN A GDPSKSDS KKNSYSYGWS FYFGALSFII AEMVGVLAVH MFIDRHKQLR ATARATDYLQ ASAITRIPSY RYRYQRRSRS SS RSTEPSH SRDASPVGVK GFNTLPSTEI SMYTLSRDPL KAATTPTATY NSDRDNSFLQ VHNCIQKDSK DSLHANTANR RTT PV

UniProtKB: Voltage-dependent calcium channel gamma-2 subunit

-
Macromolecule #3: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquino...

MacromoleculeName: {[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid
type: ligand / ID: 3 / Number of copies: 4 / Formula: ZK1
Molecular weightTheoretical: 409.254 Da
Chemical component information

ChemComp-ZK1:
{[7-morpholin-4-yl-2,3-dioxo-6-(trifluoromethyl)-3,4-dihydroquinoxalin-1(2H)-yl]methyl}phosphonic acid / antagonist, medication*YM

-
Macromolecule #4: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 4 / Number of copies: 7 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

-
Macromolecule #5: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate

MacromoleculeName: (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / type: ligand / ID: 5 / Number of copies: 4 / Formula: OLC
Molecular weightTheoretical: 356.54 Da
Chemical component information

ChemComp-OLC:
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate

-
Macromolecule #6: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(tri...

MacromoleculeName: (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate
type: ligand / ID: 6 / Number of copies: 5 / Formula: POV
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-POV:
(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / phospholipid*YM

-
Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 6 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.4000000000000001 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 371741
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

-
Atomic model buiding 1

DetailsServalcat
Output model

PDB-8c1r:
Resting state homomeric GluA2 F231A mutant AMPA receptor in complex with TARP gamma-2

+
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