[English] 日本語
Yorodumi
- EMDB-4324: 26S proteasome, s6 state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4324
Title26S proteasome, s6 stateProteasome
Map data
Sample26S proteasomeProteasome
  • (Proteasome subunit alpha type- ...) x 6
  • Probable proteasome subunit alpha type-7
  • (Proteasome subunit beta type- ...) x 7
  • (26S proteasome ...Proteasome) x 18
  • Ubiquitin carboxyl-terminal hydrolase RPN11
  • (ligand) x 3
Function / homology
Function and homology information


SAGA complex localization to transcription regulatory region / proteasome storage granule assembly / peroxisome fission / transcription export complex 2 / proteasome regulatory particle assembly / maintenance of DNA trinucleotide repeats / protein deneddylation / nonfunctional rRNA decay / filamentous growth / protein-containing complex localization => GO:0031503 ...SAGA complex localization to transcription regulatory region / proteasome storage granule assembly / peroxisome fission / transcription export complex 2 / proteasome regulatory particle assembly / maintenance of DNA trinucleotide repeats / protein deneddylation / nonfunctional rRNA decay / filamentous growth / protein-containing complex localization => GO:0031503 / nuclear proteasome complex / proteasome regulatory particle / COP9 signalosome / mitochondrial fission / histone deubiquitination / proteasome-activating activity / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / Lys63-specific deubiquitinase activity / cytosolic proteasome complex / K48-linked polyubiquitin modification-dependent protein binding / proteasome binding / proteasome core complex assembly / peptide catabolic process / nuclear outer membrane-endoplasmic reticulum membrane network / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ub-specific processing proteases / regulation of protein catabolic process / proteasome storage granule / polyubiquitin modification-dependent protein binding / endopeptidase activator activity / proteasomal ubiquitin-independent protein catabolic process / proteasome core complex / isopeptidase activity / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome complex / proteasome assembly / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / ubiquitin-dependent ERAD pathway / mRNA export from nucleus / Neutrophil degranulation / enzyme regulator activity / TBP-class protein binding / nucleotide-excision repair / ubiquitin binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription elongation from RNA polymerase II promoter / double-strand break repair via homologous recombination / positive regulation of protein catabolic process / protein-macromolecule adaptor activity / metallopeptidase activity / regulation of cell cycle / negative regulation of DNA-binding transcription factor activity / ubiquitinyl hydrolase 1 / proteasome-mediated ubiquitin-dependent protein catabolic process / thiol-dependent deubiquitinase / positive regulation of DNA-binding transcription factor activity / ubiquitin-dependent protein catabolic process / chromatin remodeling / endopeptidase activity / protein deubiquitination / ATP hydrolysis activity / mRNA binding / protein domain specific binding / ubiquitin protein ligase binding / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / mitochondrion / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Proteasome subunit Rpn10 / Rpn9 C-terminal helix / Rpn9, C-terminal helix / 26S proteasome regulatory subunit 8 / Pru (pleckstrin-like receptor for ubiquitin) domain profile. / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Proteasome complex subunit Rpn13 ubiquitin receptor / 26S Proteasome non-ATPase regulatory subunit 6 / 26S proteasome non-ATPase regulatory subunit Rpn12 ...Proteasome subunit Rpn10 / Rpn9 C-terminal helix / Rpn9, C-terminal helix / 26S proteasome regulatory subunit 8 / Pru (pleckstrin-like receptor for ubiquitin) domain profile. / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Proteasome complex subunit Rpn13 ubiquitin receptor / 26S Proteasome non-ATPase regulatory subunit 6 / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit, C-terminal / 26S proteasome non-ATPase regulatory subunit 3 / Proteasome regulatory subunit C-terminal / DSS1/SEM1 family / 26S proteasome regulatory subunit RPN5, C-terminal domain / DSS1_SEM1 / 26S Proteasome non-ATPase regulatory subunit 12 / DSS1/SEM1 / 26S proteasome regulatory subunit RPN5 C-terminal domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome regulatory subunit Rpn6, N-terminal / 6S proteasome subunit Rpn6, C-terminal helix domain / 26S proteasome subunit RPN6 C-terminal helix domain / 26S Proteasome non-ATPase regulatory subunit 13 / 26S proteasome regulatory subunit RPN2 C-terminal domain / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S Proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit RPN2, C-terminal / 26S Proteasome non-ATPase regulatory subunit 7/8 / 26S Proteasome non-ATPase regulatory subunit 14 / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / RPN1 N-terminal domain / RPN1, N-terminal / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / 26S proteasome subunit RPN7 / 26S Proteasome regulatory subunit 6A / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S Proteasome regulatory subunit 7 / Proteasome/cyclosome repeat / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / 26S Proteasome regulatory subunit 6B / Proteasome/cyclosome repeat / von Willebrand factor type A domain / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / 26S proteasome regulatory subunit P45-like / Proteasomal ATPase OB C-terminal domain / Maintenance of mitochondrial structure and function / Rpn11/EIF3F, C-terminal / Proteasomal ATPase OB C-terminal domain / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / Proteasome component (PCI) domain / PCI domain profile. / Ubiquitin-interacting motif (UIM) domain profile. / Ubiquitin interacting motif / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Proteasome subunit beta Pre3 / Proteasome subunit beta 5 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 7 / Proteasome subunit beta 4 / Proteasome subunit beta 1 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha 1 / Proteasome subunit alpha2 / Proteasome subunit alpha4 / Proteasome subunit alpha5 / Proteasome subunit alpha 3 / VWFA domain profile. / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / Proteasome beta-type subunit, conserved site / Proteasome alpha-type subunits signature. / Proteasome subunit A N-terminal signature / von Willebrand factor, type A / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / MPN domain / MPN domain profile. / Proteasome alpha-type subunit profile. / Proteasome alpha-type subunit / Proteasome beta-type subunit profile. / Proteasome B-type subunit / AAA+ lid domain / AAA ATPase, AAA+ lid domain / Proteasome subunit / Proteasome, subunit alpha/beta / TPR repeat profile. / AAA-protein family signature. / ATPase, AAA-type, conserved site / TPR repeat region circular profile. / von Willebrand factor A-like domain superfamily / Tetratricopeptide repeat
Similarity search - Domain/homology
26S proteasome regulatory subunit 7 homolog / 26S proteasome regulatory subunit 4 homolog / 26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit RPN3 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4 / 26S proteasome subunit RPT4 / Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome regulatory subunit 8 homolog ...26S proteasome regulatory subunit 7 homolog / 26S proteasome regulatory subunit 4 homolog / 26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit RPN3 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4 / 26S proteasome subunit RPT4 / Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome regulatory subunit 8 homolog / 26S proteasome regulatory subunit RPN9 / 26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit RPN5 / Proteasome subunit beta type-1 / Probable proteasome subunit alpha type-7 / 26S proteasome regulatory subunit 6B homolog / Proteasome subunit beta type-6 / 26S proteasome regulatory subunit RPN13 / 26S proteasome complex subunit SEM1 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-2 / 26S proteasome regulatory subunit 6A / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 / Proteasome subunit alpha type-5 / 26S proteasome regulatory subunit RPN12 / 26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit RPN6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsEisele MR / Reed RG / Rudack T / Schweitzer A / Beck F / Nagy I / Pfeifer G / Plitzko JM / Baumeister W / Tomko RJ / Sakata E
CitationJournal: Cell Rep / Year: 2018
Title: Expanded Coverage of the 26S Proteasome Conformational Landscape Reveals Mechanisms of Peptidase Gating.
Authors: Markus R Eisele / Randi G Reed / Till Rudack / Andreas Schweitzer / Florian Beck / Istvan Nagy / Günter Pfeifer / Jürgen M Plitzko / Wolfgang Baumeister / Robert J Tomko / Eri Sakata /
Abstract: The proteasome is the central protease for intracellular protein breakdown. Coordinated binding and hydrolysis of ATP by the six proteasomal ATPase subunits induces conformational changes that drive ...The proteasome is the central protease for intracellular protein breakdown. Coordinated binding and hydrolysis of ATP by the six proteasomal ATPase subunits induces conformational changes that drive the unfolding and translocation of substrates into the proteolytic 20S core particle for degradation. Here, we combine genetic and biochemical approaches with cryo-electron microscopy and integrative modeling to dissect the relationship between individual nucleotide binding events and proteasome conformational dynamics. We demonstrate unique impacts of ATP binding by individual ATPases on the proteasome conformational distribution and report two conformational states of the proteasome suggestive of a rotary ATP hydrolysis mechanism. These structures, coupled with functional analyses, reveal key roles for the ATPases Rpt1 and Rpt6 in gating substrate entry into the core particle. This deepened knowledge of proteasome conformational dynamics reveals key elements of intersubunit communication within the proteasome and clarifies the regulation of substrate entry into the proteolytic chamber.
History
DepositionMar 5, 2018-
Header (metadata) releaseMay 30, 2018-
Map releaseAug 22, 2018-
UpdateAug 22, 2018-
Current statusAug 22, 2018Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6fvy
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_4324.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.38 Å/pix.
x 384 pix.
= 529.92 Å
1.38 Å/pix.
x 384 pix.
= 529.92 Å
1.38 Å/pix.
x 384 pix.
= 529.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.38 Å
Density
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.078178994 - 0.12130537
Average (Standard dev.)0.000004878251 (±0.0037215422)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 529.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.381.381.38
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z529.920529.920529.920
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0780.1210.000

-
Supplemental data

-
Sample components

+
Entire 26S proteasome

EntireName: 26S proteasomeProteasome / Number of Components: 37

+
Component #1: protein, 26S proteasome

ProteinName: 26S proteasomeProteasome / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)

+
Component #2: protein, Proteasome subunit alpha type-1

ProteinName: Proteasome subunit alpha type-1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 27.359104 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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

ProteinName: Proteasome subunit alpha type-2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 26.959527 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #4: protein, Proteasome subunit alpha type-3

ProteinName: Proteasome subunit alpha type-3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 26.74909 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #5: protein, Proteasome subunit alpha type-4

ProteinName: Proteasome subunit alpha type-4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 28.259838 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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

ProteinName: Proteasome subunit alpha type-5 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 26.924156 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #7: protein, Proteasome subunit alpha type-6

ProteinName: Proteasome subunit alpha type-6 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 25.355631 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #8: protein, Probable proteasome subunit alpha type-7

ProteinName: Probable proteasome subunit alpha type-7 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 27.005641 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #9: protein, Proteasome subunit beta type-1

ProteinName: Proteasome subunit beta type-1PSMB1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 21.517186 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #10: protein, Proteasome subunit beta type-2

ProteinName: Proteasome subunit beta type-2PSMB2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 24.48677 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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

ProteinName: Proteasome subunit beta type-3PSMB3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 22.496645 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #12: protein, Proteasome subunit beta type-4

ProteinName: Proteasome subunit beta type-4PSMB4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 22.218338 kDa
SourceSpecies: Baker's yeast (baker's yeast)

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

ProteinName: Proteasome subunit beta type-5PSMB5 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 23.325248 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #14: protein, Proteasome subunit beta type-6

ProteinName: Proteasome subunit beta type-6 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 24.883928 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #15: protein, Proteasome subunit beta type-7

ProteinName: Proteasome subunit beta type-7 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 25.832336 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #16: protein, 26S proteasome regulatory subunit RPN10

ProteinName: 26S proteasome regulatory subunit RPN10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 21.818613 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #17: protein, Ubiquitin carboxyl-terminal hydrolase RPN11

ProteinName: Ubiquitin carboxyl-terminal hydrolase RPN11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 32.490963 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #18: protein, 26S proteasome regulatory subunit RPN12

ProteinName: 26S proteasome regulatory subunit RPN12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.111098 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #19: protein, 26S proteasome regulatory subunit RPN13

ProteinName: 26S proteasome regulatory subunit RPN13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 14.654642 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #20: protein, 26S proteasome complex subunit SEM1

ProteinName: 26S proteasome complex subunit SEM1Proteasome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.397102 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #21: protein, 26S proteasome regulatory subunit RPN1

ProteinName: 26S proteasome regulatory subunit RPN1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 106.895875 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #22: protein, 26S proteasome regulatory subunit RPN2

ProteinName: 26S proteasome regulatory subunit RPN2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 101.894094 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #23: protein, 26S proteasome regulatory subunit RPN3

ProteinName: 26S proteasome regulatory subunit RPN3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 55.378328 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #24: protein, 26S proteasome regulatory subunit RPN5

ProteinName: 26S proteasome regulatory subunit RPN5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 51.341758 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #25: protein, 26S proteasome regulatory subunit RPN6

ProteinName: 26S proteasome regulatory subunit RPN6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.839812 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #26: protein, 26S proteasome regulatory subunit RPN7

ProteinName: 26S proteasome regulatory subunit RPN7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.307477 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #27: protein, 26S proteasome regulatory subunit RPN8

ProteinName: 26S proteasome regulatory subunit RPN8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.557316 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #28: protein, 26S proteasome regulatory subunit RPN9

ProteinName: 26S proteasome regulatory subunit RPN9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.194625 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #29: protein, 26S proteasome regulatory subunit 7 homolog

ProteinName: 26S proteasome regulatory subunit 7 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.318613 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #30: protein, 26S proteasome regulatory subunit 4 homolog

ProteinName: 26S proteasome regulatory subunit 4 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.229602 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #31: protein, 26S proteasome regulatory subunit 6B homolog

ProteinName: 26S proteasome regulatory subunit 6B homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 44.353523 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #32: protein, 26S proteasome subunit RPT4

ProteinName: 26S proteasome subunit RPT4Proteasome / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 43.931473 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #33: protein, 26S proteasome regulatory subunit 6A

ProteinName: 26S proteasome regulatory subunit 6A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.902141 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #34: protein, 26S proteasome regulatory subunit 8 homolog

ProteinName: 26S proteasome regulatory subunit 8 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.342742 kDa
SourceSpecies: Baker's yeast (baker's yeast)

+
Component #35: ligand, ADENOSINE-5'-TRIPHOSPHATE

LigandName: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

+
Component #36: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #37: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.4
VitrificationCryogen Name: OTHER

-
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: 35 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 184988
3D reconstructionResolution: 6.1 Å / Resolution Method: FSC 0.143 CUT-OFF

-
Atomic model buiding

Output model

+
About Yorodumi

-
News

-
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

+
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

-
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