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- EMDB-9218: Cryo-EM structures and dynamics of substrate-engaged human 26S pr... -

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Entry
Database: EMDB / ID: 9218
TitleCryo-EM structures and dynamics of substrate-engaged human 26S proteasome
Map dataThe complete map of state EB 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 6
  • Ubiquitin
  • substrate
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
  • (ligand) x 4
Function / homology26S Proteasome non-ATPase regulatory subunit 12 / Proteasome/cyclosome repeat / Translesion Synthesis by POLH / Recognition of DNA damage by PCNA-containing replication complex / Translesion synthesis by REV1 / Proteasome beta-type subunit profile. / Proteasome alpha-type subunit profile. / Ubiquitin-interacting motif (UIM) domain profile. / PCI domain profile. / Peptidase T1A, proteasome beta-subunit ...26S Proteasome non-ATPase regulatory subunit 12 / Proteasome/cyclosome repeat / Translesion Synthesis by POLH / Recognition of DNA damage by PCNA-containing replication complex / Translesion synthesis by REV1 / Proteasome beta-type subunit profile. / Proteasome alpha-type subunit profile. / Ubiquitin-interacting motif (UIM) domain profile. / PCI domain profile. / Peptidase T1A, proteasome beta-subunit / Proteasome alpha-subunit, N-terminal domain / JAB1/MPN/MOV34 metalloenzyme domain / Ubiquitin domain / Proteasome component (PCI) domain / Proteasome, subunit alpha/beta / von Willebrand factor, type A / ISG15 antiviral mechanism / 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 / 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 beta 4 / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / Activation of NF-kappaB in B cells / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / Membrane binding and targetting of GAG proteins / Regulation of activated PAK-2p34 by proteasome mediated degradation / NF-kB is activated and signals survival / p75NTR recruits signalling complexes / NRIF signals cell death from the nucleus / Downstream TCR signaling / TCF dependent signaling in response to WNT / Degradation of beta-catenin by the destruction complex / SCF(Skp2)-mediated degradation of p27/p21 / EGFR downregulation / Vif-mediated degradation of APOBEC3G / Vpu mediated degradation of CD4 / APC-Cdc20 mediated degradation of Nek2A / Assembly Of The HIV Virion / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / APC/C:Cdc20 mediated degradation of Securin / SCF-beta-TrCP mediated degradation of Emi1 / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Cyclin B / DDX58/IFIH1-mediated induction of interferon-alpha/beta / TICAM1, RIP1-mediated IKK complex recruitment / NOD1/2 Signaling Pathway / Budding and maturation of HIV virion / Downregulation of ERBB2:ERBB3 signaling / Spry regulation of FGF signaling / Downregulation of ERBB4 signaling / Cross-presentation of soluble exogenous antigens (endosomes) / ER-Phagosome pathway / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / Ubiquitin conserved site / VWFA domain profile. / PCI domain / 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 alpha 3 / Proteasome subunit beta 5 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / ATPase family associated with various cellular activities (AAA) / Proteasome subunit / Ubiquitin family / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Proteasome/cyclosome repeat / 26S Proteasome non-ATPase regulatory subunit 11 / Ubiquitin interaction motif / DSS1/SEM1 family / Proteasome regulatory subunit C-terminal / 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 / Proteasomal ATPase OB C-terminal domain / Ubiquitin domain signature. / Proteasome alpha-type subunits signature. / AAA-protein family signature. / Proteasome beta-type subunits signature. / MPN domain profile. / 26S Proteasome non-ATPase regulatory subunit 6 / Ubiquitin
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: 2019
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: 6mse

SummaryFull reportAbout validation report
DateDeposition: Oct 16, 2018 / Header (metadata) release: Nov 21, 2018 / Map release: Nov 21, 2018 / Last update: Feb 6, 2019

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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-6mse
  • 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_9218.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-0.0041106823 - 0.016195307
Average (Standard dev.)0.000048416252 (0.0009165844)
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/NZ-16-63-38
NX/NY/NZ727975
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS600600600
D min/max/mean-0.0040.0160.000

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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, 26S proteasome regulatory subunit 4

ProteinName: 26S proteasome regulatory subunit 4 / 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, Ubiquitin

ProteinName: Ubiquitin / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 8.604845 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #21: protein, substrate

ProteinName: substrate / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.445026 kDa
SourceSpecies: Saccharomyces cerevisiae RM11-1a (yeast)
Source (engineered)Expression System: Escherichia coli O103:H2 str. 12009 (bacteria)

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Component #22: protein, Proteasome subunit alpha type-6

ProteinName: Proteasome subunit alpha type-6 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 27.301262 kDa
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Homo sapiens (human)

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Component #23: 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 #24: 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 #25: 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 #26: 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 #27: 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 #28: 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 #29: 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 #30: 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 #31: 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 #32: 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 #33: 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 #34: 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 #35: 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 #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: 3 / Recombinant expression: No
MassTheoretical: 0.507181 kDa

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Component #38: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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

LigandName: ADENOSINE-5'-DIPHOSPHATE / Number of Copies: 2 / 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: 242965
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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