[English] 日本語
Yorodumi
- EMDB-3913: Ground state 26S proteasome (GS2) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3913
TitleGround state 26S proteasome (GS2)
Map data
SampleGround state 26S proteasome (GS2)
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
  • 26S proteasome subunit S5aProteasome
  • (Proteasome (Prosome, macropain) 26S subunit, non-ATPase, ...) x 5
  • (Proteasome 26S subunit, ...) x 2
  • RCG28037
  • (26S proteasome non-ATPase regulatory subunit ...) x 4
  • (26S proteasome regulatory subunit ...) x 5
Function / homology
Function and homology information


fluid transport / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / meiosis I / modulation by host of viral transcription / thyrotropin-releasing hormone receptor binding / positive regulation of inclusion body assembly / negative regulation of inflammatory response to antigenic stimulus / proteasome accessory complex / regulation of endopeptidase activity / proteasome-activating ATPase activity ...fluid transport / regulation of protein catabolic process at postsynapse, modulating synaptic transmission / meiosis I / modulation by host of viral transcription / thyrotropin-releasing hormone receptor binding / positive regulation of inclusion body assembly / negative regulation of inflammatory response to antigenic stimulus / proteasome accessory complex / regulation of endopeptidase activity / proteasome-activating ATPase activity / proteasome regulatory particle / nuclear proteasome complex / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / immune system process / protein K63-linked deubiquitination / blastocyst development / Lys63-specific deubiquitinase activity / cytosolic proteasome complex / myofibril / proteasome binding / enzyme regulator activity / polyubiquitin modification-dependent protein binding / regulation of protein catabolic process / NF-kappaB binding / endopeptidase activator activity / proteasomal ubiquitin-independent protein catabolic process / proteasome storage granule / proteasome complex / polysome / proteasome core complex / inclusion body / stem cell differentiation / proteasome core complex, beta-subunit complex / thiol-dependent ubiquitin-specific protease activity / proteasome endopeptidase complex / proteasome core complex, alpha-subunit complex / ubiquitin-dependent ERAD pathway / proteasome assembly / thiol-dependent ubiquitinyl hydrolase activity / threonine-type endopeptidase activity / mRNA export from nucleus / response to organonitrogen compound / sarcomere / TBP-class protein binding / regulation of proteasomal protein catabolic process / proteolysis involved in cellular protein catabolic process / proteasomal protein catabolic process / metallopeptidase activity / positive regulation of RNA polymerase II transcriptional preinitiation complex assembly / P-body / response to virus / protein catabolic process / negative regulation of neuron death / lipopolysaccharide binding / double-strand break repair via homologous recombination / response to organic cyclic compound / nuclear matrix / postsynapse / modulation of chemical synaptic transmission / proteasome-mediated ubiquitin-dependent protein catabolic process / double-strand break repair via nonhomologous end joining / cytoplasmic vesicle / peptidase activity / ubiquitin-dependent protein catabolic process / hydrolase activity / response to oxidative stress / endopeptidase activity / response to ethanol / dendritic spine / positive regulation of NF-kappaB transcription factor activity / ATPase activity / protein deubiquitination / centrosome / synapse / regulation of transcription by RNA polymerase II / signaling receptor binding / transcription factor binding / proteolysis / negative regulation of transcription, DNA-templated / ubiquitin protein ligase binding / structural molecule activity / perinuclear region of cytoplasm / positive regulation of transcription by RNA polymerase II / protein homodimerization activity / RNA binding / membrane / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol / cytoplasm
Proteasome component (PCI) domain / Proteasomal ATPase OB C-terminal domain / Proteasome alpha-type subunit / Proteasome B-type subunit / Proteasome beta subunit, C-terminal / Rpn11/EIF3F, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Nucleophile aminohydrolases, N-terminal / CSN8/PSMD8/EIF3K / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit ...Proteasome component (PCI) domain / Proteasomal ATPase OB C-terminal domain / Proteasome alpha-type subunit / Proteasome B-type subunit / Proteasome beta subunit, C-terminal / Rpn11/EIF3F, C-terminal / P-loop containing nucleoside triphosphate hydrolase / Nucleophile aminohydrolases, N-terminal / CSN8/PSMD8/EIF3K / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / Proteasome beta 3 subunit / ATPase, AAA-type, core / 26S Proteasome non-ATPase regulatory subunit 7/8 / Proteasome subunit alpha6 / Proteasome subunit alpha2 / Proteasome subunit beta 6 / Proteasome subunit alpha 1 / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / Proteasome subunit beta 1 / ATPase, AAA-type, conserved site / AAA+ ATPase domain / von Willebrand factor, type A / Proteasome/cyclosome repeat / Proteasome, subunit alpha/beta / JAB1/MPN/MOV34 metalloenzyme domain / Proteasome alpha-subunit, N-terminal domain / Peptidase T1A, proteasome beta-subunit / 26S proteasome regulatory subunit P45-like / Proteasome subunit beta 4 / 26S proteasome non-ATPase regulatory subunit Rpn12 / DSS1/SEM1 / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / 26S proteasome regulatory subunit, C-terminal / Armadillo-type fold / Proteasome beta-type subunit, conserved site / Proteasome subunit alpha 7 / Proteasome subunit alpha5 / Proteasome subunit beta 2 / Proteasome subunit alpha 3 / 26S Proteasome non-ATPase regulatory subunit 12 / 26S Proteasome non-ATPase regulatory subunit 13 / 26S Proteasome non-ATPase regulatory subunit 14 / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / von Willebrand factor A-like domain superfamily / MPN domain / Proteasome subunit beta 5 / 26S Proteasome non-ATPase regulatory subunit 6 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory subunit Rpn6, N-terminal / 6S proteasome subunit Rpn6, C-terminal helix domain / RPN1/RPN2, N-terminal / 26S proteasome regulatory subunit RPN5, C-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / AAA ATPase, AAA+ lid domain / 26S Proteasome non-ATPase regulatory subunit 11 / Ubiquitin interacting motif / Proteasome subunit beta 7 / 26S Proteasome regulatory subunit 7 / 26S Proteasome non-ATPase regulatory subunit 1 / 26S Proteasome regulatory subunit 4 / 26S proteasome non-ATPase regulatory subunit 3 / 26S Proteasome regulatory subunit 6B / 26S proteasome regulatory subunit 10B
26S proteasome non-ATPase regulatory subunit 13 / Proteasome subunit beta type-2 / 26S proteasome subunit S5a / Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 6 / 26S proteasome regulatory subunit 6A / 26S proteasome regulatory subunit 6B / 26S proteasome regulatory subunit 6A / 26S proteasome regulatory subunit 7 / Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 12 / Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 3 ...26S proteasome non-ATPase regulatory subunit 13 / Proteasome subunit beta type-2 / 26S proteasome subunit S5a / Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 6 / 26S proteasome regulatory subunit 6A / 26S proteasome regulatory subunit 6B / 26S proteasome regulatory subunit 6A / 26S proteasome regulatory subunit 7 / Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 12 / Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 3 / Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 14 / 26S proteasome non-ATPase regulatory subunit 2 / 26S proteasome regulatory subunit 8 / 26S proteasome regulatory subunit 4 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-7 / Proteasome subunit beta type-3 / RCG28037 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-5 / Proteasome subunit beta type-5 / Proteasome subunit beta type-6 / Proteasome subunit alpha type-4 / Proteasome subunit alpha type-3 / Proteasome subunit beta type-1 / Proteasome subunit alpha type-1 / Proteasome subunit alpha type-2 / 26S proteasome non-ATPase regulatory subunit 1 / Proteasome 26S subunit, ATPase 6 / 26S proteasome non-ATPase regulatory subunit 11 / Proteasome 26S subunit, non-ATPase 8 / Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 7 (Predicted) / Proteasome subunit beta type-7
Biological speciesRattus norvegicus (Norway rat) / Rat (rat)
Methodsubtomogram averaging / cryo EM / Resolution: 12.3 Å
AuthorsGuo Q / Lehmer C / Martinez-Sanchez A / Rudack T / Beck F / Hartmann H / Hipp MS / Hartl FU / Edbauer D / Baumeister W / Fernandez-Busnadiego R
Funding support Germany, United States, 4 items
OrganizationGrant numberCountry
European CommissionFP7 GA ERC-2012-SyG_318987-ToPAG Germany
German Research FoundationSFB-1035/Project A01 Germany
European CommissionFP7 GA ERC-2013-CoG_617198 DPR-MODELS Germany
National Institutes of Health9P41GM104601 United States
CitationJournal: Cell / Year: 2018
Title: In Situ Structure of Neuronal C9orf72 Poly-GA Aggregates Reveals Proteasome Recruitment.
Authors: Qiang Guo / Carina Lehmer / Antonio Martínez-Sánchez / Till Rudack / Florian Beck / Hannelore Hartmann / Manuela Pérez-Berlanga / Frédéric Frottin / Mark S Hipp / F Ulrich Hartl / ...Authors: Qiang Guo / Carina Lehmer / Antonio Martínez-Sánchez / Till Rudack / Florian Beck / Hannelore Hartmann / Manuela Pérez-Berlanga / Frédéric Frottin / Mark S Hipp / F Ulrich Hartl / Dieter Edbauer / Wolfgang Baumeister / Rubén Fernández-Busnadiego /
Abstract: Protein aggregation and dysfunction of the ubiquitin-proteasome system are hallmarks of many neurodegenerative diseases. Here, we address the elusive link between these phenomena by employing cryo- ...Protein aggregation and dysfunction of the ubiquitin-proteasome system are hallmarks of many neurodegenerative diseases. Here, we address the elusive link between these phenomena by employing cryo-electron tomography to dissect the molecular architecture of protein aggregates within intact neurons at high resolution. We focus on the poly-Gly-Ala (poly-GA) aggregates resulting from aberrant translation of an expanded GGGGCC repeat in C9orf72, the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. We find that poly-GA aggregates consist of densely packed twisted ribbons that recruit numerous 26S proteasome complexes, while other macromolecules are largely excluded. Proximity to poly-GA ribbons stabilizes a transient substrate-processing conformation of the 26S proteasome, suggesting stalled degradation. Thus, poly-GA aggregates may compromise neuronal proteostasis by driving the accumulation and functional impairment of a large fraction of cellular proteasomes.
Validation ReportPDB-ID: 6epc

SummaryFull reportAbout validation report
History
DepositionOct 11, 2017-
Header (metadata) releaseDec 20, 2017-
Map releaseFeb 7, 2018-
UpdateDec 11, 2019-
Current statusDec 11, 2019Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6epc
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_3913.map.gz / Format: CCP4 / Size: 2.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.42 Å/pix.
x 90 pix.
= 307.8 Å
3.42 Å/pix.
x 90 pix.
= 307.8 Å
3.42 Å/pix.
x 90 pix.
= 307.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.42 Å
Density
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.4
Minimum - Maximum-0.4004439 - 0.74689674
Average (Standard dev.)-0.037387155 (±0.16709301)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-44-44-44
Dimensions909090
Spacing909090
CellA=B=C: 307.80002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.423.423.42
M x/y/z909090
origin x/y/z0.0000.0000.000
length x/y/z307.800307.800307.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-128-128-128
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS-44-44-44
NC/NR/NS909090
D min/max/mean-0.4000.747-0.037

-
Supplemental data

-
Sample components

+
Entire Ground state 26S proteasome (GS2)

EntireName: Ground state 26S proteasome (GS2)
Details: in situ proteasome structure generated by subtomogram averaging
Number of components: 33

+
Component #1: protein, Ground state 26S proteasome (GS2)

ProteinName: Ground state 26S proteasome (GS2)
Details: in situ proteasome structure generated by subtomogram averaging
Recombinant expression: No
SourceSpecies: Rattus norvegicus (Norway rat)

+
Component #2: protein, Proteasome subunit alpha type-6

ProteinName: Proteasome subunit alpha type-6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.432459 kDa
SourceSpecies: Rat (rat)

+
Component #3: protein, Proteasome subunit alpha type-2

ProteinName: Proteasome subunit alpha type-2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.955549 kDa
SourceSpecies: Rat (rat)

+
Component #4: protein, Proteasome subunit alpha type-4

ProteinName: Proteasome subunit alpha type-4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.53983 kDa
SourceSpecies: Rat (rat)

+
Component #5: protein, Proteasome subunit alpha type-7

ProteinName: Proteasome subunit alpha type-7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.369439 kDa
SourceSpecies: Rat (rat)

+
Component #6: protein, Proteasome subunit alpha type-5

ProteinName: Proteasome subunit alpha type-5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.41685 kDa
SourceSpecies: Rat (rat)

+
Component #7: protein, Proteasome subunit alpha type-1

ProteinName: Proteasome subunit alpha type-1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.557541 kDa
SourceSpecies: Rat (rat)

+
Component #8: protein, Proteasome subunit alpha type-3

ProteinName: Proteasome subunit alpha type-3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.456275 kDa
SourceSpecies: Rat (rat)

+
Component #9: protein, Proteasome subunit beta type-6

ProteinName: Proteasome subunit beta type-6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 25.309576 kDa
SourceSpecies: Rat (rat)

+
Component #10: protein, Proteasome subunit beta type-7

ProteinName: Proteasome subunit beta type-7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.963461 kDa
SourceSpecies: Rat (rat)

+
Component #11: protein, Proteasome subunit beta type-3

ProteinName: Proteasome subunit beta type-3PSMB3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.988895 kDa
SourceSpecies: Rat (rat)

+
Component #12: protein, Proteasome subunit beta type-2

ProteinName: Proteasome subunit beta type-2PSMB2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.941381 kDa
SourceSpecies: Rat (rat)

+
Component #13: protein, Proteasome subunit beta type-5

ProteinName: Proteasome subunit beta type-5PSMB5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 28.615408 kDa
SourceSpecies: Rat (rat)

+
Component #14: protein, Proteasome subunit beta type-1

ProteinName: Proteasome subunit beta type-1PSMB1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.511301 kDa
SourceSpecies: Rat (rat)

+
Component #15: protein, Proteasome subunit beta type-4

ProteinName: Proteasome subunit beta type-4PSMB4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.226248 kDa
SourceSpecies: Rat (rat)

+
Component #16: protein, 26S proteasome subunit S5a

ProteinName: 26S proteasome subunit S5aProteasome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.775629 kDa
SourceSpecies: Rat (rat)

+
Component #17: protein, Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 14

ProteinName: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 14
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.620023 kDa
SourceSpecies: Rat (rat)

+
Component #18: protein, Proteasome 26S subunit, non-ATPase 8

ProteinName: Proteasome 26S subunit, non-ATPase 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.932082 kDa
SourceSpecies: Rat (rat)

+
Component #19: protein, RCG28037

ProteinName: RCG28037 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.284611 kDa
SourceSpecies: Rat (rat)

+
Component #20: protein, 26S proteasome non-ATPase regulatory subunit 2

ProteinName: 26S proteasome non-ATPase regulatory subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 100.300547 kDa
SourceSpecies: Rat (rat)

+
Component #21: protein, 26S proteasome non-ATPase regulatory subunit 1

ProteinName: 26S proteasome non-ATPase regulatory subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 105.870117 kDa
SourceSpecies: Rat (rat)

+
Component #22: protein, Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 3

ProteinName: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 3
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 60.77818 kDa
SourceSpecies: Rat (rat)

+
Component #23: protein, Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 12

ProteinName: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 12
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 53.011246 kDa
SourceSpecies: Rat (rat)

+
Component #24: protein, 26S proteasome non-ATPase regulatory subunit 11

ProteinName: 26S proteasome non-ATPase regulatory subunit 11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.526688 kDa
SourceSpecies: Rat (rat)

+
Component #25: protein, Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 6

ProteinName: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 6
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.658398 kDa
SourceSpecies: Rat (rat)

+
Component #26: protein, Proteasome (Prosome, macropain) 26S subunit, non-ATPase,...

ProteinName: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 7 (Predicted)
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 36.551824 kDa
SourceSpecies: Rat (rat)

+
Component #27: protein, 26S proteasome non-ATPase regulatory subunit 13

ProteinName: 26S proteasome non-ATPase regulatory subunit 13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 42.867223 kDa
SourceSpecies: Rat (rat)

+
Component #28: protein, 26S proteasome regulatory subunit 7

ProteinName: 26S proteasome regulatory subunit 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.640727 kDa
SourceSpecies: Rat (rat)

+
Component #29: protein, 26S proteasome regulatory subunit 4

ProteinName: 26S proteasome regulatory subunit 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.260504 kDa
SourceSpecies: Rat (rat)

+
Component #30: protein, 26S proteasome regulatory subunit 6B

ProteinName: 26S proteasome regulatory subunit 6B / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.468223 kDa
SourceSpecies: Rat (rat)

+
Component #31: protein, Proteasome 26S subunit, ATPase 6

ProteinName: Proteasome 26S subunit, ATPase 6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.867027 kDa
SourceSpecies: Rat (rat)

+
Component #32: protein, 26S proteasome regulatory subunit 6A

ProteinName: 26S proteasome regulatory subunit 6A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.611824 kDa
SourceSpecies: Rat (rat)

+
Component #33: protein, 26S proteasome regulatory subunit 8

ProteinName: 26S proteasome regulatory subunit 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.694047 kDa
SourceSpecies: Rat (rat)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: Cell / Method: cryo EM
Sample solutionpH: 7
Support filmThe grid was coated with C prior to use
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: OTHER / Temperature: 298 K / Humidity: 100 %

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.8 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 42000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 5000.0 - 7000.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric) / Number of subtomograms: 2070 / Number of class averages: 4
3D reconstructionSoftware: RELION / Resolution: 12.3 Å / Resolution method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Modeling #1Refinement protocol: flexible
Output model

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.:Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.:Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

Read more

-
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.

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