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- EMDB-9221: Cryo-EM structures and dynamics of substrate-engaged human 26S pr... -

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Entry
Database: EMDB / ID: 9221
TitleCryo-EM structures and dynamics of substrate-engaged human 26S proteasome
Map dataThe complete map of state ED1 of substrate-engaged human proteasome, low pass-filtered to 3 Angstrom without amplitude correction
SampleProteasome
  • (26S proteasome non-ATPase regulatory subunit ...) x 11
  • 26S proteasome complex subunit SEM1
  • (26S proteasome regulatory subunit ...) x 5
  • Rpt2, NP_002793.2 (26SHA chain B)
  • substrate
  • (Proteasome subunit alpha type- ...) x 8
  • (Proteasome subunit beta type- ...) x 7
  • (ligand) x 4
Function / homologyProteasome subunit alpha6 / 26S proteasome regulatory subunit 8 / 26S Proteasome non-ATPase regulatory subunit 12 / 26S Proteasome non-ATPase regulatory subunit 11 / 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 6B / 26S Proteasome non-ATPase regulatory subunit 14 ...Proteasome subunit alpha6 / 26S proteasome regulatory subunit 8 / 26S Proteasome non-ATPase regulatory subunit 12 / 26S Proteasome non-ATPase regulatory subunit 11 / 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 6B / 26S Proteasome non-ATPase regulatory subunit 14 / 26S Proteasome regulatory subunit 6A / Peptidase T1A, proteasome beta-subunit / Proteasome alpha-subunit, N-terminal domain / JAB1/MPN/MOV34 metalloenzyme domain / Proteasome component (PCI) domain / Proteasome, subunit alpha/beta / 26S Proteasome non-ATPase regulatory subunit 13 / Winged helix-like DNA-binding domain superfamily / von Willebrand factor, type A / Proteasome/cyclosome repeat / 26S proteasome subunit RPN7 / Proteasome subunit A N-terminal signature / CSN8/PSMD8/EIF3K family / Proteasome regulatory subunit C-terminal / DSS1/SEM1 family / Ubiquitin interaction motif / PCI domain / Winged helix DNA-binding domain superfamily / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Proteasome subunit / ATPase family associated with various cellular activities (AAA) / Proteasome subunit beta 5 / Proteasome subunit alpha 3 / MPN domain / von Willebrand factor A-like domain superfamily / Proteasome/cyclosome repeat / AAA+ ATPase domain / 26S Proteasome regulatory subunit 4 / 26S Proteasome non-ATPase regulatory subunit 7/8 / P-loop containing nucleoside triphosphate hydrolase / Nucleophile aminohydrolases, N-terminal / Proteasomal ATPase OB C-terminal domain / CSN8/PSMD8/EIF3K / Proteasome beta 3 subunit / Proteasome subunit alpha5 / 26S Proteasome regulatory subunit 7 / Rpn11/EIF3F, C-terminal / Proteasome subunit alpha2 / Proteasome subunit alpha4 / Proteasome subunit beta 6 / Proteasome subunit alpha 1 / Proteasome subunit alpha 7 / Proteasome subunit beta 1 / Proteasome subunit beta 2 / Proteasome subunit Rpn10 / Proteasome beta subunit, C-terminal / Ubiquitin interacting motif / Tetratricopeptide-like helical domain superfamily / ATPase, AAA-type, core / ATPase, AAA-type, conserved site / 26S proteasome regulatory subunit P45-like / 26S proteasome non-ATPase regulatory subunit Rpn12 / DSS1/SEM1 / Armadillo-like helical / 26S proteasome regulatory subunit, C-terminal / Proteasome B-type subunit / 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 / Proteasome beta subunits C terminal / Maintenance of mitochondrial structure and function / von Willebrand factor type A domain / Regulation of RAS by GAPs / Ub-specific processing proteases / UCH proteinases / MAPK6/MAPK4 signaling / Defective CFTR causes cystic fibrosis / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / Hedgehog 'on' state / Neutrophil degranulation / GLI3 is processed to GLI3R by the proteasome / Degradation of GLI2 by the proteasome / Degradation of GLI1 by the proteasome / CLEC7A (Dectin-1) signaling / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants that don't undergo autocatalytic processing are degraded by ERAD / Hedgehog ligand biogenesis / Metalloprotease DUBs / CDT1 association with the CDC6:ORC:origin complex / Proteasomal ATPase OB C-terminal domain / Regulation of RUNX3 expression and activity / Antigen processing: Ubiquitination & Proteasome degradation / Negative regulation of NOTCH4 signaling / Interleukin-1 signaling / Regulation of expression of SLITs and ROBOs
Function and homology information
SourceHomo sapiens (human) / Saccharomyces cerevisiae RM11-1a (yeast)
Methodsingle particle reconstruction / cryo EM / 3.3 Å resolution
AuthorsMao YD
CitationJournal: Nature / Year: 2018
Title: Cryo-EM structures and dynamics of substrate-engaged human 26S proteasome.
Authors: Yuanchen Dong / Shuwen Zhang / Zhaolong Wu / Xuemei Li / Wei Li Wang / Yanan Zhu / Svetla Stoilova-McPhie / Ying Lu / Daniel Finley / Youdong Mao
Validation ReportPDB-ID: 6msj

SummaryFull reportAbout validation report
DateDeposition: Oct 16, 2018 / Header (metadata) release: Nov 21, 2018 / Map release: Nov 21, 2018 / Last update: Nov 21, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-6msj
  • Surface level: 0.006
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_9221.map.gz (map file in CCP4 format, 864001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
600 pix
0.69 Å/pix.
= 411. Å
600 pix
0.69 Å/pix.
= 411. Å
600 pix
0.69 Å/pix.
= 411. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.685 Å
Density
Contour Level:0.006 (by author), 0.006 (movie #1):
Minimum - Maximum-0.005119373 - 0.017518379
Average (Standard dev.)0.00003029608 (0.0010034199)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions600600600
Origin0.00.00.0
Limit599.0599.0599.0
Spacing600600600
CellA=B=C: 411.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.6850.6850.685
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z411.000411.000411.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ240240240
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0050.0180.000

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Supplemental data

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Sample components

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Entire Proteasome

EntireName: Proteasome / Number of components: 39

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Component #1: protein, Proteasome

ProteinName: Proteasome / Recombinant expression: No
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #2: protein, 26S proteasome non-ATPase regulatory subunit 1

ProteinName: 26S proteasome non-ATPase regulatory subunit 1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 105.958234 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #3: protein, 26S proteasome non-ATPase regulatory subunit 3

ProteinName: 26S proteasome non-ATPase regulatory subunit 3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 60.935297 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #4: protein, 26S proteasome non-ATPase regulatory subunit 12

ProteinName: 26S proteasome non-ATPase regulatory subunit 12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.979359 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: 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: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #6: protein, 26S proteasome non-ATPase regulatory subunit 6

ProteinName: 26S proteasome non-ATPase regulatory subunit 6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.592285 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #7: protein, 26S proteasome non-ATPase regulatory subunit 7

ProteinName: 26S proteasome non-ATPase regulatory subunit 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 37.086441 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #8: protein, 26S proteasome non-ATPase regulatory subunit 13

ProteinName: 26S proteasome non-ATPase regulatory subunit 13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 42.995359 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #9: protein, 26S proteasome non-ATPase regulatory subunit 4

ProteinName: 26S proteasome non-ATPase regulatory subunit 4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 40.78159 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #10: protein, 26S proteasome non-ATPase regulatory subunit 14

ProteinName: 26S proteasome non-ATPase regulatory subunit 14 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.488824 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #11: protein, 26S proteasome non-ATPase regulatory subunit 8

ProteinName: 26S proteasome non-ATPase regulatory subunit 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 39.536676 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #12: protein, 26S proteasome complex subunit SEM1

ProteinName: 26S proteasome complex subunit SEM1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.284611 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #13: protein, 26S proteasome non-ATPase regulatory subunit 2

ProteinName: 26S proteasome non-ATPase regulatory subunit 2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 98.425414 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #14: protein, 26S proteasome regulatory subunit 7

ProteinName: 26S proteasome regulatory subunit 7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.700805 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #15: protein, Rpt2, NP_002793.2 (26SHA chain B)

ProteinName: Rpt2, NP_002793.2 (26SHA chain B) / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.260504 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #16: protein, 26S proteasome regulatory subunit 8

ProteinName: 26S proteasome regulatory subunit 8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 44.852121 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #17: protein, 26S proteasome regulatory subunit 6B

ProteinName: 26S proteasome regulatory subunit 6B / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.426141 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #18: protein, 26S proteasome regulatory subunit 10B

ProteinName: 26S proteasome regulatory subunit 10B / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.867027 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #19: protein, 26S proteasome regulatory subunit 6A

ProteinName: 26S proteasome regulatory subunit 6A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.266457 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #20: protein, substrate

ProteinName: substrate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 3.08179 kDa
SourceSpecies: Saccharomyces cerevisiae RM11-1a (yeast)
Source (engineered)Expression System: Escherichia coli K-12 (bacteria)

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Component #21: protein, Proteasome subunit alpha type-6

ProteinName: Proteasome subunit alpha type-6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.301262 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #22: protein, Proteasome subunit alpha type-2

ProteinName: Proteasome subunit alpha type-2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 25.796338 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #23: protein, Proteasome subunit alpha type-4

ProteinName: Proteasome subunit alpha type-4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 29.394648 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #24: protein, Proteasome subunit alpha type-7

ProteinName: Proteasome subunit alpha type-7 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 27.798695 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #25: protein, Proteasome subunit alpha type-5

ProteinName: Proteasome subunit alpha type-5 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 26.304779 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #26: protein, Proteasome subunit alpha type-1

ProteinName: Proteasome subunit alpha type-1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 30.150277 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #27: protein, Proteasome subunit alpha type-3

ProteinName: Proteasome subunit alpha type-3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 28.338057 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #28: protein, Proteasome subunit beta type-6

ProteinName: Proteasome subunit beta type-6 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 25.246455 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #29: protein, Proteasome subunit beta type-7

ProteinName: Proteasome subunit beta type-7 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 29.869223 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #30: protein, Proteasome subunit beta type-3

ProteinName: Proteasome subunit beta type-3PSMB3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 22.841701 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #31: protein, Proteasome subunit beta type-2

ProteinName: Proteasome subunit beta type-2PSMB2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 22.864277 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #32: protein, Proteasome subunit beta type-5

ProteinName: Proteasome subunit beta type-5PSMB5 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 28.379053 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #33: protein, Proteasome subunit beta type-1

ProteinName: Proteasome subunit beta type-1PSMB1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 26.391201 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #34: protein, Proteasome subunit beta type-4

ProteinName: Proteasome subunit beta type-4PSMB4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 29.099986 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #35: protein, Proteasome subunit alpha type-6

ProteinName: Proteasome subunit alpha type-6 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 26.727658 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #36: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #37: ligand, ADENOSINE-5'-TRIPHOSPHATE

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

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Component #38: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 4 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #39: ligand, ADENOSINE-5'-DIPHOSPHATE

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.427201 kDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
Support filmunspecified
VitrificationCryogen name: ETHANE

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

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 288915
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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