[English] 日本語
Yorodumi
- EMDB-3914: Substrate processing state 26S proteasome (SPS1) -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 3914
TitleSubstrate processing state 26S proteasome (SPS1)
Map datain situ reconstruction of Rat proteasome in substrate processing states 1
SampleSubstrate processing state 26S proteasome (SPS1)
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
  • 26S proteasome subunit S5a
  • (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 / homologyRpn11/EIF3F, C-terminal / von Willebrand factor, type A / Proteasome subunit beta 4 / Proteasome beta-type subunit, conserved site / Armadillo-type fold / 26S proteasome regulatory subunit, C-terminal / Tetratricopeptide-like helical domain superfamily / Armadillo-like helical / DSS1/SEM1 / 26S proteasome non-ATPase regulatory subunit Rpn12 ...Rpn11/EIF3F, C-terminal / von Willebrand factor, type A / Proteasome subunit beta 4 / Proteasome beta-type subunit, conserved site / Armadillo-type fold / 26S proteasome regulatory subunit, C-terminal / Tetratricopeptide-like helical domain superfamily / Armadillo-like helical / DSS1/SEM1 / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome regulatory subunit P45-like / ATPase, AAA-type, conserved site / ATPase, AAA-type, core / Ubiquitin interacting motif / AAA+ ATPase domain / Proteasome/cyclosome repeat / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / Proteasome, subunit alpha/beta / Proteasome component (PCI) domain / JAB1/MPN/MOV34 metalloenzyme domain / Proteasome alpha-subunit, N-terminal domain / Peptidase T1A, proteasome beta-subunit / 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 / 26S Proteasome non-ATPase regulatory subunit 12 / Proteasome subunit beta 5 / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome regulatory subunit RPN2, C-terminal / Proteasome subunit alpha 1 / 26S Proteasome non-ATPase regulatory subunit 6 / 26S proteasome non-ATPase regulatory subunit 3 / 26S Proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit 10B / 26S proteasome regulatory subunit 8 / 26S Proteasome regulatory subunit 6B / 26S Proteasome regulatory subunit 6A / 26S Proteasome regulatory subunit 7 / 26S Proteasome regulatory subunit 4 / Proteasome subunit beta 7 / Proteasome subunit beta 2 / Proteasome subunit beta 1 / Proteasome subunit alpha 7 / Proteasome subunit beta 6 / Proteasome alpha-type subunit / Proteasome subunit alpha4 / Proteasome subunit alpha2 / Proteasome subunit alpha6 / 26S Proteasome non-ATPase regulatory subunit 7/8 / Proteasome subunit alpha5 / Proteasome beta 3 subunit / CSN8/PSMD8/EIF3K / Proteasomal ATPase OB C-terminal domain / Nucleophile aminohydrolases, N-terminal / P-loop containing nucleoside triphosphate hydrolase / Proteasome subunit Rpn10 / Proteasome beta subunit, C-terminal / Proteasome B-type subunit / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / Proteasome subunit alpha 3 / 26S proteasome regulatory subunit Rpn6, N-terminal / VWFA domain profile. / 26S proteasome subunit RPN7 / Proteasome beta subunits C terminal / Maintenance of mitochondrial structure and function / von Willebrand factor type A domain / Proteasomal ATPase OB C-terminal domain / 26S proteasome regulatory subunit RPN2 C-terminal domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome subunit RPN6 C-terminal helix domain / Proteasome alpha-type subunits signature. / AAA-protein family signature. / Proteasome beta-type subunits signature. / MPN domain profile. / CSN8/PSMD8/EIF3K family / PCI domain profile. / Ubiquitin-interacting motif (UIM) domain profile. / Proteasome alpha-type subunit profile. / Proteasome beta-type subunit profile. / Autodegradation of Cdh1 by Cdh1:APC/C / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / UCH proteinases / Ub-specific processing proteases / Metalloprotease DUBs / Neutrophil degranulation / CDT1 association with the CDC6:ORC:origin complex / Neddylation / Proteasome subunit A N-terminal signature / 26S Proteasome non-ATPase regulatory subunit 11 / Proteasome/cyclosome repeat / 6S proteasome subunit Rpn6, C-terminal helix domain / Proteasome regulatory subunit C-terminal / DSS1/SEM1 family / ATPase family associated with various cellular activities (AAA) / Proteasome subunit / Ubiquitin interaction motif
Function and homology information
SourceRattus norvegicus (Norway rat) / Rat (rat)
Methodsubtomogram averaging / cryo EM / 15.4 Å resolution
AuthorsGuo Q / Lehmer C / Martinez-Sanchez A / Rudack T / Beck F / Hartmann H / Hipp MS / Hartl FU / Edbauer D / Baumeister W / Fernandez-Busnadiego R
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 / 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 ...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: 6epd

SummaryFull reportAbout validation report
DateDeposition: Oct 11, 2017 / Header (metadata) release: Dec 20, 2017 / Map release: Feb 7, 2018 / Last update: Feb 21, 2018

-
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-6epd
  • Surface level: 0.4
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

Fileemd_3914.map.gz (map file in CCP4 format, 2917 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
90 pix
3.42 Å/pix.
= 307.8 Å
90 pix
3.42 Å/pix.
= 307.8 Å
90 pix
3.42 Å/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 Level:0.4 (by author), 0.4 (movie #1):
Minimum - Maximum-0.43242818 - 0.80991423
Average (Standard dev.)-0.033788875 (0.17499371)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions909090
Origin-44.0-44.0-44.0
Limit45.045.045.0
Spacing909090
CellA=B=C: 307.80002 Å
α=β=γ: 90.0 deg.

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-0.4320.810-0.034

-
Supplemental data

-
Sample components

+
Entire Substrate processing state 26S proteasome (SPS1)

EntireName: Substrate processing state 26S proteasome (SPS1)
Details: in situ proteasome structure generated by subtomogram averaging
Number of components: 33

+
Component #1: protein, Substrate processing state 26S proteasome (SPS1)

ProteinName: Substrate processing state 26S proteasome (SPS1)
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 S5a / 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: 2136 / Number of class averages: 4
3D reconstructionSoftware: RELION / Resolution: 15.4 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 EBI / 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