[English] 日本語
Yorodumi
- EMDB-23288: native AMPA receptor -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-23288
Titlenative AMPA receptor
Map data
Sample
  • Complex: GluA2/A3-asymmetric-conformation1 bound to Fabs
    • Complex: GluA2/A3-asymmetric-conformation
      • Protein or peptide: Glutamate receptor 3
      • Protein or peptide: Glutamate receptor
      • Protein or peptide: Protein cornichon homolog 2
      • Protein or peptide: Voltage-dependent calcium channel gamma-8 subunit
    • Complex: 5B2 Fab
      • Protein or peptide: 5B2 Fab Light Chain
      • Protein or peptide: 5B2 Fab Heavy Chain
    • Complex: 15F1 Fab
      • Protein or peptide: 15F1 Fab light chain
      • Protein or peptide: 15F1 Fab heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Biological speciesMus musculus (house mouse) / Mouse (mice)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.5 Å
AuthorsYu J / Rao P / Gouaux E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS038631 United States
CitationJournal: Science / Year: 2019
Title: Architecture and subunit arrangement of native AMPA receptors elucidated by cryo-EM.
Authors: Yan Zhao / Shanshuang Chen / Adam C Swensen / Wei-Jun Qian / Eric Gouaux /
Abstract: Glutamate-gated AMPA receptors mediate the fast component of excitatory signal transduction at chemical synapses throughout all regions of the mammalian brain. AMPA receptors are tetrameric ...Glutamate-gated AMPA receptors mediate the fast component of excitatory signal transduction at chemical synapses throughout all regions of the mammalian brain. AMPA receptors are tetrameric assemblies composed of four subunits, GluA1-GluA4. Despite decades of study, the subunit composition, subunit arrangement, and molecular structure of native AMPA receptors remain unknown. Here we elucidate the structures of 10 distinct native AMPA receptor complexes by single-particle cryo-electron microscopy (cryo-EM). We find that receptor subunits are arranged nonstochastically, with the GluA2 subunit preferentially occupying the B and D positions of the tetramer and with triheteromeric assemblies comprising a major population of native AMPA receptors. Cryo-EM maps define the structure for S2-M4 linkers between the ligand-binding and transmembrane domains, suggesting how neurotransmitter binding is coupled to ion channel gating.
History
DepositionJan 14, 2021-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateAug 10, 2022-
Current statusAug 10, 2022Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_23288.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.00687 Å
Density
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.0719863 - 0.3039929
Average (Standard dev.)3.193597e-05 (±0.012615396)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 515.51746 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Additional map: #2

Fileemd_23288_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Additional map: #1

Fileemd_23288_additional_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
Entire : GluA2/A3-asymmetric-conformation1 bound to Fabs

EntireName: GluA2/A3-asymmetric-conformation1 bound to Fabs
Components
  • Complex: GluA2/A3-asymmetric-conformation1 bound to Fabs
    • Complex: GluA2/A3-asymmetric-conformation
      • Protein or peptide: Glutamate receptor 3
      • Protein or peptide: Glutamate receptor
      • Protein or peptide: Protein cornichon homolog 2
      • Protein or peptide: Voltage-dependent calcium channel gamma-8 subunit
    • Complex: 5B2 Fab
      • Protein or peptide: 5B2 Fab Light Chain
      • Protein or peptide: 5B2 Fab Heavy Chain
    • Complex: 15F1 Fab
      • Protein or peptide: 15F1 Fab light chain
      • Protein or peptide: 15F1 Fab heavy chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

+
Supramolecule #1: GluA2/A3-asymmetric-conformation1 bound to Fabs

SupramoleculeName: GluA2/A3-asymmetric-conformation1 bound to Fabs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8

+
Supramolecule #2: GluA2/A3-asymmetric-conformation

SupramoleculeName: GluA2/A3-asymmetric-conformation / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Mus musculus (house mouse)

+
Supramolecule #3: 5B2 Fab

SupramoleculeName: 5B2 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5-#6
Source (natural)Organism: Mus musculus (house mouse)

+
Supramolecule #4: 15F1 Fab

SupramoleculeName: 15F1 Fab / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #7-#8
Source (natural)Organism: Mus musculus (house mouse)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

+
Macromolecule #1: Glutamate receptor 3

MacromoleculeName: Glutamate receptor 3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice)
Molecular weightTheoretical: 100.64082 KDa
SequenceString: MGQSVLRAVF FLVLGLLGHS HGGFPNTISI GGLFMRNTVQ EHSAFRFAVQ LYNTNQNTTE KPFHLNYHVD HLDSSNSFSV TNAFCSQFS RGVYAIFGFY DQMSMNTLTS FCGALHTSFV TPSFPTDADV QFVIQMRPAL KGAILSLLGY YKWEKFVYLY D TERGFSIL ...String:
MGQSVLRAVF FLVLGLLGHS HGGFPNTISI GGLFMRNTVQ EHSAFRFAVQ LYNTNQNTTE KPFHLNYHVD HLDSSNSFSV TNAFCSQFS RGVYAIFGFY DQMSMNTLTS FCGALHTSFV TPSFPTDADV QFVIQMRPAL KGAILSLLGY YKWEKFVYLY D TERGFSIL QAIMEAAVQN NWQVTARSVG NIKDIQEFRR IIEEMDRRQE KRYLIDCEVE RINTILEQVV ILGKHSRGYH YM LANLGFT DIVLERVMHG GANITGFQIV NNENPMVQQF IQRWVRLDER EFPEAKNAPL KYTSALTHDA ILVIAEAFRY LRR QRVDVS RRGSAGDCLA NPAVPWSQGI DIERALKMVQ VQGMTGNIQF DTYGRRTNYT IDVYEMKVSG SRKAGYWNEY ERFV PFSDQ QISNDSSSSE NRTIVVTTIL ESPYVMYKKN HEQLEGNERY EGYCVDLAYE IAKHVRIKYK LSIVGDGKYG ARDPE TKIW NGMVGELVYG RADIAVAPLT ITLVREEVID FSKPFMSLGI SIMIKKPQKS KPGVFSFLDP LAYEIWMCIV FAYIGV SVV LFLVSRFSPY EWHLEDNNEE PRDPQSPPDP PNEFGIFNSL WFSLGAFMQQ GCDISPRSLS GRIVGGVWWF FTLIIIS SY TANLAAFLTV ERMVSPIESA EDLAKQTEIA YGTLDSGSTK EFFRRSKIAV YEKMWSYMKS AEPSVFTKTT ADGVARVR K SKGKFAFLLE STMNEYIEQR KPCDTMKVGG NLDSKGYGVA TPKGSALRTP VNLAVLKLSE QGILDKLKNK WWYDKGECG AKDSGSKDKT SALSLSNVAG VFYILVGGLG LAMMVALIEF CYKSRAESKR MKLTKNTQNF KPAPATNTQN YATYREGYNV YGTESVKI

+
Macromolecule #2: Glutamate receptor

MacromoleculeName: Glutamate receptor / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice)
Molecular weightTheoretical: 98.899883 KDa
SequenceString: MQKIMHISVL LSPVLWGLIF GVSSNSIQIG GLFPRGADQE YSAFRVGMVQ FSTSEFRLTP HIDNLEVANS FAVTNAFCSQ FSRGVYAIF GFYDKKSVNT ITSFCGTLHV SFITPSFPTD GTHPFVIQMR PDLKGALLSL IEYYQWDKFA YLYDSDRGLS T LQAVLDSA ...String:
MQKIMHISVL LSPVLWGLIF GVSSNSIQIG GLFPRGADQE YSAFRVGMVQ FSTSEFRLTP HIDNLEVANS FAVTNAFCSQ FSRGVYAIF GFYDKKSVNT ITSFCGTLHV SFITPSFPTD GTHPFVIQMR PDLKGALLSL IEYYQWDKFA YLYDSDRGLS T LQAVLDSA AEKKWQVTAI NVGNINNDKK DETYRSLFQD LELKKERRVI LDCERDKVND IVDQVITIGK HVKGYHYIIA NL GFTDGDL LKIQFGGANV SGFQIVDYDD SLVSKFIERW STLEEKEYPG AHTATIKYTS ALTYDAVQVM TEAFRNLRKQ RIE ISRRGN AGDCLANPAV PWGQGVEIER ALKQVQVEGL SGNIKFDQNG KRINYTINIM ELKTNGPRKI GYWSEVDKMV VTLT ELPSG NDTSGLENKT VVVTTILESP YVMMKKNHEM LEGNERYEGY CVDLAAEIAK HCGFKYKLTI VGDGKYGARD ADTKI WNGM VGELVYGKAD IAIAPLTITL VREEVIDFSK PFMSLGISIM IKKPQKSKPG VFSFLDPLAY EIWMCIVFAY IGVSVV LFL VSRFSPYEWH TEEFEDGRET QSSESTNEFG IFNSLWFSLG AFMRQGCDIS PRSLSGRIVG GVWWFFTLII ISSYTAN LA AFLTVERMVS PIESAEDLSK QTEIAYGTLD SGSTKEFFRR SKIAVFDKMW TYMRSAEPSV FVRTTAEGVA RVRKSKGK Y AYLLESTMNE YIEQRKPCDT MKVGGNLDSK GYGIATPKGS SLRNAVNLAV LKLNEQGLLD KLKNKWWYDK GECGSGGGD SKEKTSALSL SNVAGVFYIL VGGLGLAMLV ALIEFCYKSR AEAKRMKVAK NAQNINPSSS QNSQNFATYK EGYNVYGIES VKI

+
Macromolecule #3: Protein cornichon homolog 2

MacromoleculeName: Protein cornichon homolog 2 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice)
Molecular weightTheoretical: 18.94842 KDa
SequenceString:
MAFTFAAFCY MLTLVLCASL IFFVIWHIIA FDELRTDFKN PIDQGNPARA RERLKNIERI CCLLRKLVVP EYSIHGLFCL MFLCAAEWV TLGLNIPLLF YHLWRYFHRP ADGSEVMYDA VSIMNADILN YCQKESWCKL AFYLLSFFYY LYSMVYTLVS F

+
Macromolecule #4: Voltage-dependent calcium channel gamma-8 subunit

MacromoleculeName: Voltage-dependent calcium channel gamma-8 subunit / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mouse (mice)
Molecular weightTheoretical: 43.502938 KDa
SequenceString: MESLKRWNEE RGLWCEKGVQ VLLTTIGAFS AFGLMTIAIS TDYWLYTRAL ICNTTNLTAG DDGPPHRGGS GSSEKKDPGG LTHSGLWRI CCLEGLKRGV CVKINHFPED TDYDHDSAEY LLRVVRASSI FPILSAILLL LGGVCVAASR VYKSKRNIIL G AGILFVAA ...String:
MESLKRWNEE RGLWCEKGVQ VLLTTIGAFS AFGLMTIAIS TDYWLYTRAL ICNTTNLTAG DDGPPHRGGS GSSEKKDPGG LTHSGLWRI CCLEGLKRGV CVKINHFPED TDYDHDSAEY LLRVVRASSI FPILSAILLL LGGVCVAASR VYKSKRNIIL G AGILFVAA GLSNIIGVIV YISANAGEPG PKRDEEKKNH YSYGWSFYFG GLSFILAEVI GVLAVNIYIE RSREAHCQSR SD LLKAGGG AGGSGGSGPS AILRLPSYRF RYRRRSRSSS RGSSEASPSR DASPGGPGGP GFASTDISMY TLSRDPSKGS VAA GLASAG GGGSGAGVGA YGGAAGAAGG GGAGSERDRG SSAGFLTLHN AFPKEAASGV TVTVTGPPAA PAPAPAPPAP AAPA PGTLS KEAAASNTNT LNRKTTPV

+
Macromolecule #5: 5B2 Fab Light Chain

MacromoleculeName: 5B2 Fab Light Chain / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 18.570826 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)

+
Macromolecule #6: 5B2 Fab Heavy Chain

MacromoleculeName: 5B2 Fab Heavy Chain / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 21.038842 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)

+
Macromolecule #7: 15F1 Fab light chain

MacromoleculeName: 15F1 Fab light chain / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 25.11166 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MEIQMTQTTS SLSASLGDRV TISCRASQDI SNYLSWYQQK PDGTVKLLIY YTSRLHSGVP SRFSGSGSGI DYSLTINNLE QEDFATYFC QQGNTLPLTF GAGTKLELKR ADAAPTVSIF PPSSEQLTSG GASVVCFLNN FYPKDINVKW KIDGSERQNG V LNSWTDQD ...String:
MEIQMTQTTS SLSASLGDRV TISCRASQDI SNYLSWYQQK PDGTVKLLIY YTSRLHSGVP SRFSGSGSGI DYSLTINNLE QEDFATYFC QQGNTLPLTF GAGTKLELKR ADAAPTVSIF PPSSEQLTSG GASVVCFLNN FYPKDINVKW KIDGSERQNG V LNSWTDQD SKDSTYSMSS TLTLTKDEYE RHNSYTCEAT HKTSTSPIVK SFNRNECSNW SHPQFEK

+
Macromolecule #8: 15F1 Fab heavy chain

MacromoleculeName: 15F1 Fab heavy chain / type: protein_or_peptide / ID: 8 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 27.975439 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MVSAIVLYVL LAAAAHSAFA MQAQLKESGP GLVAPSQSLS ITCTVSGFSL TNYGVHWVRQ PPGKGLEWLG VIWAGGSTNY NSALMSRVS ISKDNSKSQV FLKMNSLQTD DTVMYYCARE DYDYDWHFDV WGAGTTVTVS SAKTTPPSVY PLAPGSAAQT N SMVTLGCL ...String:
MVSAIVLYVL LAAAAHSAFA MQAQLKESGP GLVAPSQSLS ITCTVSGFSL TNYGVHWVRQ PPGKGLEWLG VIWAGGSTNY NSALMSRVS ISKDNSKSQV FLKMNSLQTD DTVMYYCARE DYDYDWHFDV WGAGTTVTVS SAKTTPPSVY PLAPGSAAQT N SMVTLGCL VKGYFPEPVT VTWNSGSLSS GVHTFPAVLQ SDLYTLSSSV TVPSSTWPSE TVTCNVAHPA SSTKVDKKLE VL FQGPGSG SADTITIRGY VRDNR

+
Macromolecule #11: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 11 / Number of copies: 2 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11397
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

+
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://pdbjlvh1.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