[English] 日本語
Yorodumi
- EMDB-49725: The structure of cerebellar GluA1/A4 ATD -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-49725
TitleThe structure of cerebellar GluA1/A4 ATD
Map data
Sample
  • Complex: CP-AMPA receptors
    • Protein or peptide: Glutamate receptor 1
    • Protein or peptide: Glutamate receptor 4
    • Protein or peptide: 11B8 scFv
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsiGluR / CP-AMPA receptors / MEMBRANE PROTEIN
Function / homology
Function and homology information


Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / COPII-mediated vesicle transport / positive regulation of membrane potential / positive regulation of locomotion involved in locomotory behavior / cellular response to ammonium ion / response to sucrose / proximal dendrite / myosin V binding ...Cargo concentration in the ER / cellular response to amine stimulus / axonal spine / COPII-mediated vesicle transport / positive regulation of membrane potential / positive regulation of locomotion involved in locomotory behavior / cellular response to ammonium ion / response to sucrose / proximal dendrite / myosin V binding / neuron spine / Trafficking of AMPA receptors / kainate selective glutamate receptor complex / cellular response to L-glutamate / regulation of monoatomic ion transmembrane transport / conditioned place preference / response to arsenic-containing substance / cellular response to dsRNA / regulation of synapse structure or activity / dendritic spine membrane / Synaptic adhesion-like molecules / long-term synaptic depression / beta-2 adrenergic receptor binding / cellular response to peptide hormone stimulus / response to morphine / neuronal cell body membrane / peptide hormone receptor binding / protein kinase A binding / response to psychosocial stress / spinal cord development / Activation of AMPA receptors / perisynaptic space / AMPA glutamate receptor activity / negative regulation of smooth muscle cell apoptotic process / : / Trafficking of GluR2-containing AMPA receptors / response to lithium ion / immunoglobulin binding / behavioral response to pain / AMPA glutamate receptor complex / ionotropic glutamate receptor complex / adenylate cyclase binding / asymmetric synapse / regulation of receptor recycling / excitatory synapse / positive regulation of excitatory postsynaptic potential / Unblocking of NMDA receptors, glutamate binding and activation / G-protein alpha-subunit binding / long-term memory / postsynaptic density, intracellular component / glutamate receptor binding / positive regulation of synaptic transmission / response to electrical stimulus / neuronal action potential / glutamate-gated receptor activity / response to fungicide / synapse assembly / presynaptic active zone membrane / somatodendritic compartment / cellular response to brain-derived neurotrophic factor stimulus / glutamate-gated calcium ion channel activity / ligand-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential / dendrite membrane / positive regulation of synaptic transmission, glutamatergic / dendritic shaft / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / synaptic transmission, glutamatergic / PDZ domain binding / cellular response to amino acid stimulus / response to cocaine / synaptic membrane / response to nutrient levels / modulation of chemical synaptic transmission / postsynaptic density membrane / : / terminal bouton / neuromuscular junction / cellular response to growth factor stimulus / recycling endosome / cerebral cortex development / regulation of synaptic plasticity / small GTPase binding / receptor internalization / response to peptide hormone / long-term synaptic potentiation / response to toxic substance / synaptic vesicle membrane / recycling endosome membrane / synaptic vesicle / cell-cell junction / G-protein beta-subunit binding / response to estradiol / presynapse / amyloid-beta binding / presynaptic membrane / cell body / early endosome membrane / scaffold protein binding / chemical synaptic transmission / dendritic spine
Similarity search - Function
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 1 / Glutamate receptor 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.53 Å
AuthorsFang CF / Gouaux E
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Nature / Year: 2025
Title: Gating and noelin clustering of native Ca2+-permeable AMPA receptors
Authors: Fang C / Spangler CJ / Park J / Sheldon N / Trussell LO / Gouaux E
History
DepositionMar 14, 2025-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_49725.png

Downloads & links

-
Map

FileDownload / File: emd_49725.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 448 pix.
= 421.12 Å		0.94 Å/pix.
x 448 pix.
= 421.12 Å		0.94 Å/pix.
x 448 pix.
= 421.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.186
Minimum - Maximum-0.89702445 - 1.5609442
Average (Standard dev.)0.00006594976 (±0.023622794)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 421.12 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #1

Fileemd_49725_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_49725_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_49725_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : CP-AMPA receptors

EntireName: CP-AMPA receptors
Components
  • Complex: CP-AMPA receptors
    • Protein or peptide: Glutamate receptor 1
    • Protein or peptide: Glutamate receptor 4
    • Protein or peptide: 11B8 scFv
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

-
Supramolecule #1: CP-AMPA receptors

SupramoleculeName: CP-AMPA receptors / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Rattus norvegicus (Norway rat)

-
Macromolecule #1: Glutamate receptor 1

MacromoleculeName: Glutamate receptor 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 42.956734 KDa
SequenceString: ANFPNNIQIG GLFPNQQSQE HAAFRFALSQ LTEPPKLLPQ IDIVNISDSF EMTYRFCSQF SKGVYAIFGF YERRTVNMLT SFCGALHVC FITPSFPVDT SNQFVLQLRP ELQEALISII DHYKWQTFVY IYDADRGLSV LQRVLDTAAE KNWQVTAVNI L TTTEEGYR ...String:
ANFPNNIQIG GLFPNQQSQE HAAFRFALSQ LTEPPKLLPQ IDIVNISDSF EMTYRFCSQF SKGVYAIFGF YERRTVNMLT SFCGALHVC FITPSFPVDT SNQFVLQLRP ELQEALISII DHYKWQTFVY IYDADRGLSV LQRVLDTAAE KNWQVTAVNI L TTTEEGYR MLFQDLEKKK ERLVVVDCES ERLNAILGQI VKLEKNGIGY HYILANLGFM DIDLNKFKES GANVTGFQLV NY TDTIPAR IMQQWRTSDS RDHTRVDWKR PKYTSALTYD GVKVMAEAFQ SLRRQRIDIS RRGNAGDCLA NPAVPWGQGI DIQ RALQQV RFEGLTGNVQ FNEKGRRTNY TLHVIEMKHD GIRKIGYWNE DDKFVPA

UniProtKB: Glutamate receptor 1

-
Macromolecule #2: Glutamate receptor 4

MacromoleculeName: Glutamate receptor 4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 43.087867 KDa
SequenceString: AFPSSVQIGG LFIRNTDQEY TAFRLAIFLH NTSPNASEAP FNLVPHVDNI ETANSFAVTN AFCSQYSRGV FAIFGLYDKR SVHTLTSFC SALHISLITP SFPTEGESQF VLQLRPSLRG ALLSLLDHYE WNCFVFLYDT DRGYSILQAI MEKAGQNGWH V SAICVENF ...String:
AFPSSVQIGG LFIRNTDQEY TAFRLAIFLH NTSPNASEAP FNLVPHVDNI ETANSFAVTN AFCSQYSRGV FAIFGLYDKR SVHTLTSFC SALHISLITP SFPTEGESQF VLQLRPSLRG ALLSLLDHYE WNCFVFLYDT DRGYSILQAI MEKAGQNGWH V SAICVENF NDVSYRQLLE ELDRRQEKKF VIDCEIERLQ NILEQIVSVG KHVKGYHYII ANLGFKDISL ERFIHGGANV TG FQLVDFN TPMVTKLMDR WKKLDQREYP GSETPPKYTS ALTYDGVLVM AETFRSLRRQ KIDISRRGNA GDCLANPAAP WGQ GIDMER TLKQVRIQGL TGNVQFDHYG RRVNYTMDVF ELKSTGPRKV GYWNDMDKLV LI

UniProtKB: Glutamate receptor 4

-
Macromolecule #3: 11B8 scFv

MacromoleculeName: 11B8 scFv / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.511527 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: EVKLLESGGG LVQPGGSLKL SCAASGFDFS EYWMSWVRQA PGKGLEWIGE INPDSSSIDY TPSLKDKIII SRDNAKKTLY LQLSKVRSE DTALYYCARP RGNYVVMDYW GQGTSVTVSS SGGGGSGGGG SGGGGNIVLT QSPASLAVSL GQRATISCRA S ESVDSYGS ...String:
EVKLLESGGG LVQPGGSLKL SCAASGFDFS EYWMSWVRQA PGKGLEWIGE INPDSSSIDY TPSLKDKIII SRDNAKKTLY LQLSKVRSE DTALYYCARP RGNYVVMDYW GQGTSVTVSS SGGGGSGGGG SGGGGNIVLT QSPASLAVSL GQRATISCRA S ESVDSYGS SFVHWYQQKP GQPPKLLIFL ASKLESGVPA RFSGSGSRTD FTLTIDPVEA DDAATYYCQQ TNEDPYTFGG GT KLEIKRA SNWSHPQFEK

-
Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 4 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.1 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: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 2.2 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.53 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 36405
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

+
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