[English] 日本語
Yorodumi
- EMDB-8090: Cryo-EM structure of GluA2/3 AMPA receptor heterotetramer (model I) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-8090
TitleCryo-EM structure of GluA2/3 AMPA receptor heterotetramer (model I)
Map dataNone
Sample
  • Complex: AMPA GluA2/3 heterotetramer
    • Protein or peptide: Glutamate receptor 2GRIA2
    • Protein or peptide: Glutamate receptor 3
Function / homology
Function and homology information


chemical synaptic transmission, postsynaptic / Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space ...chemical synaptic transmission, postsynaptic / Trafficking of AMPA receptors / Synaptic adhesion-like molecules / parallel fiber to Purkinje cell synapse / spine synapse / dendritic spine neck / dendritic spine head / Activation of AMPA receptors / response to lithium ion / perisynaptic space / cellular response to glycine / AMPA glutamate receptor activity / Trafficking of GluR2-containing AMPA receptors / immunoglobulin binding / AMPA glutamate receptor complex / kainate selective glutamate receptor activity / ionotropic glutamate receptor complex / extracellularly glutamate-gated ion channel activity / asymmetric synapse / regulation of receptor recycling / Unblocking of NMDA receptors, glutamate binding and activation / glutamate receptor binding / regulation of postsynaptic membrane potential / synaptic cleft / positive regulation of synaptic transmission / glutamate-gated receptor activity / presynaptic active zone membrane / response to fungicide / regulation of synaptic transmission, glutamatergic / cellular response to brain-derived neurotrophic factor stimulus / somatodendritic compartment / dendrite membrane / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / ionotropic glutamate receptor binding / ionotropic glutamate receptor signaling pathway / dendrite cytoplasm / cytoskeletal protein binding / monoatomic ion transmembrane transport / SNARE binding / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic membrane / synaptic transmission, glutamatergic / PDZ domain binding / postsynaptic density membrane / protein tetramerization / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / establishment of protein localization / terminal bouton / receptor internalization / synaptic vesicle membrane / cerebral cortex development / synaptic vesicle / presynapse / signaling receptor activity / presynaptic membrane / amyloid-beta binding / growth cone / perikaryon / chemical synaptic transmission / postsynaptic membrane / scaffold protein binding / dendritic spine / postsynaptic density / neuron projection / axon / dendrite / neuronal cell body / glutamatergic synapse / synapse / protein-containing complex binding / endoplasmic reticulum membrane / protein kinase binding / cell surface / endoplasmic reticulum / protein-containing complex / membrane / identical protein binding / plasma membrane
Similarity search - Function
Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / 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. ...Bacterial extracellular solute-binding proteins, family 3 / Solute-binding protein family 3/N-terminal domain of MltF / 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 / Glutamate receptor 3
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.25 Å
AuthorsHerguedas B / Garcia-Nafria J / Fernandez-Leiro R / Greger IH
CitationJournal: Science / Year: 2016
Title: Structure and organization of heteromeric AMPA-type glutamate receptors.
Authors: Beatriz Herguedas / Javier García-Nafría / Ondrej Cais / Rafael Fernández-Leiro / James Krieger / Hinze Ho / Ingo H Greger /
Abstract: AMPA-type glutamate receptors (AMPARs), which are central mediators of rapid neurotransmission and synaptic plasticity, predominantly exist as heteromers of the subunits GluA1 to GluA4. Here we ...AMPA-type glutamate receptors (AMPARs), which are central mediators of rapid neurotransmission and synaptic plasticity, predominantly exist as heteromers of the subunits GluA1 to GluA4. Here we report the first AMPAR heteromer structures, which deviate substantially from existing GluA2 homomer structures. Crystal structures of the GluA2/3 and GluA2/4 N-terminal domains reveal a novel compact conformation with an alternating arrangement of the four subunits around a central axis. This organization is confirmed by cysteine cross-linking in full-length receptors, and it permitted us to determine the structure of an intact GluA2/3 receptor by cryogenic electron microscopy. Two models in the ligand-free state, at resolutions of 8.25 and 10.3 angstroms, exhibit substantial vertical compression and close associations between domain layers, reminiscent of N-methyl-D-aspartate receptors. Model 1 resembles a resting state and model 2 a desensitized state, thus providing snapshots of gating transitions in the nominal absence of ligand. Our data reveal organizational features of heteromeric AMPARs and provide a framework to decipher AMPAR architecture and signaling.
History
DepositionFeb 24, 2016-
Header (metadata) releaseMar 16, 2016-
Map releaseMar 16, 2016-
UpdateOct 11, 2017-
Current statusOct 11, 2017Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.068
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.068
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5ide
  • Surface level: 0.068
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8090.png

Downloads & links

-
Map

FileDownload / File: emd_8090.map.gz / Format: CCP4 / Size: 16.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Voxel sizeX=Y=Z: 1.76 Å
Density
Contour LevelBy AUTHOR: 0.068 / Movie #1: 0.068
Minimum - Maximum-0.2742643 - 0.27836835
Average (Standard dev.)0.0017951204 (±0.012236778)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions164164164
Spacing164164164
CellA=B=C: 288.63998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.761.761.76
M x/y/z164164164
origin x/y/z0.0000.0000.000
length x/y/z288.640288.640288.640
α/β/γ90.00090.00090.000
start NX/NY/NZ-190-190-190
NX/NY/NZ380380380
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS164164164
D min/max/mean-0.2740.2780.002

-
Supplemental data

-
Mask #1

Fileemd_8090_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Mask #2

Fileemd_8090_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: None

Fileemd_8090_half_map_1.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: None

Fileemd_8090_half_map_2.map
AnnotationNone
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : AMPA GluA2/3 heterotetramer

EntireName: AMPA GluA2/3 heterotetramer
Components
  • Complex: AMPA GluA2/3 heterotetramer
    • Protein or peptide: Glutamate receptor 2GRIA2
    • Protein or peptide: Glutamate receptor 3

-
Supramolecule #1: AMPA GluA2/3 heterotetramer

SupramoleculeName: AMPA GluA2/3 heterotetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Full-length GluA2/3 heterotetramer containing the A2_N292C and A3_265C mutations
Source (natural)Organism: Rattus norvegicus (Norway rat)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293 GntI- / Recombinant plasmid: prk5 and pIRES2-EGFP
Molecular weightTheoretical: 400 KDa

-
Macromolecule #1: Glutamate receptor 2

MacromoleculeName: Glutamate receptor 2 / type: protein_or_peptide / ID: 1
Details: The sequence corresponds to mature rat GluA2 (residues 22-883, isoform Flip, edited at R/G and Q/R sites) with a Myc tag after the first residue and the N292C mutation
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 97.663188 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VEQKLISEED LSSNSIQIGG LFPRGADQEY SAFRVGMVQF STSEFRLTPH IDNLEVANSF AVTNAFCSQF SRGVYAIFGF YDKKSVNTI TSFCGTLHVS FITPSFPTDG THPFVIQMRP DLKGALLSLI EYYQWDKFAY LYDSDRGLST LQAVLDSAAE K KWQVTAIN ...String:
VEQKLISEED LSSNSIQIGG LFPRGADQEY SAFRVGMVQF STSEFRLTPH IDNLEVANSF AVTNAFCSQF SRGVYAIFGF YDKKSVNTI TSFCGTLHVS FITPSFPTDG THPFVIQMRP DLKGALLSLI EYYQWDKFAY LYDSDRGLST LQAVLDSAAE K KWQVTAIN VGNINNDKKD ETYRSLFQDL ELKKERRVIL DCERDKVNDI VDQVITIGKH VKGYHYIIAN LGFTDGDLLK IQ FGGANVS GFQIVDYDDS LVSKFIERWS TLEEKEYPGA HTATIKYTSA LTYDAVQVMT EAFRCLRKQR IEISRRGNAG DCL ANPAVP WGQGVEIERA LKQVQVEGLS GNIKFDQNGK RINYTINIME LKTNGPRKIG YWSEVDKMVV TLTELPSGND TSGL ENKTV VVTTILESPY VMMKKNHEML EGNERYEGYC VDLAAEIAKH CGFKYKLTIV GDGKYGARDA DTKIWNGMVG ELVYG KADI AIAPLTITLV REEVIDFSKP FMSLGISIMI KKPQKSKPGV FSFLDPLAYE IWMCIVFAYI GVSVVLFLVS RFSPYE WHT EEFEDGRETQ SSESTNEFGI FNSLWFSLGA FMQQGCDISP RSLSGRIVGG VWWFFTLIII SSYTANLAAF LTVERMV SP IESAEDLSKQ TEIAYGTLDS GSTKEFFRRS KIAVFDKMWT YMRSAEPSVF VRTTAEGVAR VRKSKGKYAY LLESTMNE Y IEQRKPCDTM KVGGNLDSKG YGIATPKGSS LGTPVNLAVL KLSEQGVLDK LKNKWWYDKG ECGAKDSGSK EKTSALSLS NVAGVFYILV GGLGLAMLVA LIEFCYKSRA EAKRMKVAKN PQNINPSSSQ NSQNFATYKE GYNVYGIESV KI

-
Macromolecule #2: Glutamate receptor 3

MacromoleculeName: Glutamate receptor 3 / type: protein_or_peptide / ID: 2
Details: The sequence corresponds to the mature rat GluA3 subunit (residues 23-888, Flip isoform) with a Flag tag after the first residue and mutated at R439G and R265C
Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 99.075664 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GDYKDDDDKF PNTISIGGLF MRNTVQEHSA FRFAVQLYNT NQNTTEKPFH LNYHVDHLDS SNSFSVTNAF CSQFSRGVYA IFGFYDQMS MNTLTSFCGA LHTSFVTPSF PTDADVQFVI QMRPALKGAI LSLLSYYKWE KFVYLYDTER GFSVLQAIME A AVQNNWQV ...String:
GDYKDDDDKF PNTISIGGLF MRNTVQEHSA FRFAVQLYNT NQNTTEKPFH LNYHVDHLDS SNSFSVTNAF CSQFSRGVYA IFGFYDQMS MNTLTSFCGA LHTSFVTPSF PTDADVQFVI QMRPALKGAI LSLLSYYKWE KFVYLYDTER GFSVLQAIME A AVQNNWQV TARSVGNIKD VQEFRRIIEE MDRRQEKRYL IDCEVERINT ILEQVVILGK HSRGYHYMLA NLGFTDILLE RV MHGGANI TGFQIVNNEN PMVQQFIQRW VRLDECEFPE AKNAPLKYTS ALTHDAILVI AEAFRYLRRQ RVDVSRRGSA GDC LANPAV PWSQGIDIER ALKMVQVQGM TGNIQFDTYG RRTNYTIDVY EMKVSGSRKA GYWNEYERFV PFSDQQISND SSSS ENRTI VVTTILESPY VMYKKNHEQL EGNERYEGYC VDLAYEIAKH VGIKYKLSIV GDGKYGARDP ETKIWNGMVG ELVYG RADI AVAPLTITLV REEVIDFSKP FMSLGISIMI KKPQKSKPGV FSFLDPLAYE IWMCIVFAYI GVSVVLFLVS RFSPYE WHL EDNNEEPRDP QSPPDPPNEF GIFNSLWFSL GAFMQQGCDI SPRSLSGRIV GGVWWFFTLI IISSYTANLA AFLTVER MV SPIESAEDLA KQTEIAYGTL DSGSTKEFFR RSKIAVYEKM WSYMKSAEPS VFTKTTADGV ARVRKSKGKF AFLLESTM N EYIEQRKPCD TMKVGGNLDS KGYGVATPKG SALGTPVNLA VLKLSEQGIL DKLKNKWWYD KGECGAKDSG SKDKTSALS LSNVAGVFYI LVGGLGLAMM VALIEFCYKS RAESKRMKLT KNTQNFKPAP ATNTQNYATY REGYNVYGTE SVKI

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.03 mg/mL
BufferpH: 7.4 / Details: 25 mM Tris pH 7.4, 0.25 % DDM, 150 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Incubated for 1 minute, blotted for 3 seconds.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 28409 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm
Specialist opticsEnergy filter - Name: GIF Quantum / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-20 / Number grids imaged: 2 / Number real images: 980 / Average exposure time: 25.0 sec. / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 107939
CTF correctionSoftware - Name: Gctf
Startup modelType of model: OTHER
Details: Initial model was created with EMAN2 using ten 2D classes generated with 10,631 particles and was low-pass filter at 60A.
Initial angle assignmentType: NOT APPLICABLE / Software - Name: RELION
Final 3D classificationNumber classes: 3 / Software - Name: RELION
Details: After 2D classification, motion correction and B-factor weighting, 107,939 particles were used for 3D-classification in three steps.
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 8.25 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 25238
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial model
PDB IDChain

3hsy

chain_id: B

1fto

chain_id: B

3ua8


3o21

chain_id: D

3kg2

DetailsFor GluA2 chains (A,C), 2 copies of GluA2NTD (3HSY) and two copies of GluA2 LBD (1FTO) were fitted. For GluA3 chains (B,D), 2 copies of GluA3NTD (3O21) and two copies of GluA2 LBD (3UA8) were fitted.For the TMD region, the 4 chains of 3KG2 TMD(residues 509-544 594-629 784-817) were fitted as a rigid body. After fitting the sequence was corrected including mutations and side chains were removed.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5ide:
Cryo-EM structure of GluA2/3 AMPA receptor heterotetramer (model I)

+
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