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- EMDB-3914: Substrate processing state 26S proteasome (SPS1) -

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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 / homology26S Proteasome regulatory subunit 6A / Proteasome subunit alpha2 / P-loop containing nucleoside triphosphate hydrolase / Nucleophile aminohydrolases, N-terminal / CSN8/PSMD8/EIF3K / Proteasome beta 3 subunit / Proteasome subunit alpha5 / 26S Proteasome non-ATPase regulatory subunit 7/8 / Proteasome subunit alpha6 / Proteasome subunit alpha4 ...26S Proteasome regulatory subunit 6A / Proteasome subunit alpha2 / P-loop containing nucleoside triphosphate hydrolase / Nucleophile aminohydrolases, N-terminal / CSN8/PSMD8/EIF3K / Proteasome beta 3 subunit / Proteasome subunit alpha5 / 26S Proteasome non-ATPase regulatory subunit 7/8 / Proteasome subunit alpha6 / Proteasome subunit alpha4 / Rpn11/EIF3F, C-terminal / Proteasome subunit beta 6 / Proteasome subunit alpha 1 / Proteasome subunit alpha 7 / Proteasome subunit beta 1 / Proteasome subunit beta 2 / Proteasome subunit beta 7 / 26S Proteasome regulatory subunit 4 / Proteasome subunit Rpn10 / Proteasome beta subunit, C-terminal / 26S Proteasome regulatory subunit 6B / Armadillo-like helical / AAA+ ATPase domain / Ubiquitin interacting motif / ATPase, AAA-type, core / ATPase, AAA-type, conserved site / 26S proteasome regulatory subunit P45-like / 26S proteasome non-ATPase regulatory subunit Rpn12 / DSS1/SEM1 / Tetratricopeptide-like helical domain superfamily / Proteasome B-type subunit / 26S proteasome regulatory subunit, C-terminal / Armadillo-type fold / Proteasome beta-type subunit, conserved site / Proteasome subunit beta 4 / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / Proteasome alpha-type subunit / 26S Proteasome regulatory subunit 7 / 26S proteasome regulatory subunit 8 / Proteasome/cyclosome repeat / AAA-protein family signature. / CSN8/PSMD8/EIF3K family / Proteasome subunit A N-terminal signature / 26S proteasome subunit RPN7 / Proteasome beta subunits C terminal / Maintenance of mitochondrial structure and function / von Willebrand factor type A domain / Proteasome alpha-type subunits signature. / Proteasome beta-type subunits signature. / DSS1/SEM1 family / VWFA domain profile. / MPN domain profile. / PCI domain profile. / Ubiquitin-interacting motif (UIM) domain profile. / Proteasome alpha-type subunit profile. / Proteasome beta-type subunit profile. / Activation of NF-kappaB in B cells / Proteasome regulatory subunit C-terminal / Ubiquitin interaction motif / 26S proteasome regulatory subunit 10B / Winged helix-like DNA-binding domain superfamily / 26S Proteasome non-ATPase regulatory subunit 1 / 26S proteasome non-ATPase regulatory subunit 3 / 26S Proteasome non-ATPase regulatory subunit 6 / 26S Proteasome non-ATPase regulatory subunit 11 / 26S Proteasome non-ATPase regulatory subunit 12 / 26S Proteasome non-ATPase regulatory subunit 13 / 26S Proteasome non-ATPase regulatory subunit 14 / Winged helix DNA-binding domain superfamily / Proteasome/cyclosome repeat / von Willebrand factor A-like domain superfamily / MPN domain / Proteasome subunit alpha 3 / Proteasome subunit beta 5 / ATPase family associated with various cellular activities (AAA) / Proteasome subunit / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / PCI domain / von Willebrand factor, type A / Proteasome, subunit alpha/beta / Cross-presentation of soluble exogenous antigens (endosomes) / CDT1 association with the CDC6:ORC:origin complex / CLEC7A (Dectin-1) signaling / Proteasome component (PCI) domain / Degradation of GLI1 by the proteasome / GLI3 is processed to GLI3R by the proteasome / Hedgehog 'on' state / Regulation of RAS by GAPs / TNFR2 non-canonical NF-kB pathway / NIK-->noncanonical NF-kB signaling / MAPK6/MAPK4 signaling / UCH proteinases / Ub-specific processing proteases / Metalloprotease DUBs / Neutrophil degranulation / Orc1 removal from chromatin / Hedgehog ligand biogenesis / CDK-mediated phosphorylation and removal of Cdc6
Function and homology information
SourceRattus norvegicus (Norway rat)
Methodsubtomogram averaging / cryo EM / 15.4 Å resolution
AuthorsGuo Q / Lehmer C
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

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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
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  • Surface view with fitted model
  • Atomic models: : PDB-6epd
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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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-44-44-44
Limit454545
Spacing909090
CellA=B=C: 307.80002 Å
α=β=γ: 90 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

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Supplemental data

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Sample components

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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

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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)

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

ProteinName: Proteasome subunit alpha type-6 / Recombinant expression: No
MassTheoretical: 27.432459 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: Proteasome subunit alpha type-2 / Recombinant expression: No
MassTheoretical: 25.955549 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: Proteasome subunit alpha type-4 / Recombinant expression: No
MassTheoretical: 29.53983 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: Proteasome subunit alpha type-7 / Recombinant expression: No
MassTheoretical: 28.369439 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: Proteasome subunit alpha type-5 / Recombinant expression: No
MassTheoretical: 26.41685 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: Proteasome subunit alpha type-1 / Recombinant expression: No
MassTheoretical: 29.557541 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: Proteasome subunit alpha type-3 / Recombinant expression: No
MassTheoretical: 28.456275 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: Proteasome subunit beta type-6 / Recombinant expression: No
MassTheoretical: 25.309576 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: Proteasome subunit beta type-7 / Recombinant expression: No
MassTheoretical: 29.963461 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: Proteasome subunit beta type-3PSMB3 / Recombinant expression: No
MassTheoretical: 22.988895 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: Proteasome subunit beta type-2PSMB2 / Recombinant expression: No
MassTheoretical: 22.941381 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: Proteasome subunit beta type-5PSMB5 / Recombinant expression: No
MassTheoretical: 28.615408 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: Proteasome subunit beta type-1PSMB1 / Recombinant expression: No
MassTheoretical: 26.511301 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: Proteasome subunit beta type-4PSMB4 / Recombinant expression: No
MassTheoretical: 29.226248 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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Component #16: protein, 26S proteasome subunit S5a

ProteinName: 26S proteasome subunit S5a / Recombinant expression: No
MassTheoretical: 40.775629 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 14
Recombinant expression: No
MassTheoretical: 34.620023 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: Proteasome 26S subunit, non-ATPase 8 / Recombinant expression: No
MassTheoretical: 39.932082 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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Component #19: protein, RCG28037

ProteinName: RCG28037 / Recombinant expression: No
MassTheoretical: 8.284611 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: 26S proteasome non-ATPase regulatory subunit 2 / Recombinant expression: No
MassTheoretical: 100.300547 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: 26S proteasome non-ATPase regulatory subunit 1 / Recombinant expression: No
MassTheoretical: 105.870117 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 3
Recombinant expression: No
MassTheoretical: 60.77818 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 12
Recombinant expression: No
MassTheoretical: 53.011246 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: 26S proteasome non-ATPase regulatory subunit 11 / Recombinant expression: No
MassTheoretical: 47.526688 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 6
Recombinant expression: No
MassTheoretical: 45.658398 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: Proteasome (Prosome, macropain) 26S subunit, non-ATPase, 7 (Predicted)
Recombinant expression: No
MassTheoretical: 36.551824 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: 26S proteasome non-ATPase regulatory subunit 13 / Recombinant expression: No
MassTheoretical: 42.867223 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: 26S proteasome regulatory subunit 7 / Recombinant expression: No
MassTheoretical: 48.640727 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: 26S proteasome regulatory subunit 4 / Recombinant expression: No
MassTheoretical: 49.260504 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: 26S proteasome regulatory subunit 6B / Recombinant expression: No
MassTheoretical: 47.468223 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: Proteasome 26S subunit, ATPase 6 / Recombinant expression: No
MassTheoretical: 45.867027 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: 26S proteasome regulatory subunit 6A / Recombinant expression: No
MassTheoretical: 49.611824 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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

ProteinName: 26S proteasome regulatory subunit 8 / Recombinant expression: No
MassTheoretical: 45.694047 kDa
SourceSpecies: Rattus norvegicus (Norway rat)

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Experimental details

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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: ETHANE-PROPANE MIXTURE / Temperature: 298 K / Humidity: 100 %

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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 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 5000 - 7000 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Tilt Angle: -50 - 70 deg.
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: subtomogram averaging / Applied symmetry: C1 (asymmetric)
3D reconstructionSoftware: RELION / Resolution: 15.4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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