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- EMDB-6694: Yeast proteasome-ADP-AlFx -

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Basic information

Entry
Database: EMDB / ID: 6694
TitleYeast proteasome-ADP-AlFx
Map data
Sampleyeast proteasome in complex with ADP-AlFx
  • (Proteasome subunit beta type- ...) x 7
  • (Proteasome subunit alpha type- ...) x 6
  • Probable proteasome subunit alpha type-7
  • (26S protease regulatory subunit ...) x 5
  • 26S protease subunit RPT4Proteasome endopeptidase complex
  • (26S proteasome regulatory subunit ...) x 11
  • Ubiquitin carboxyl-terminal hydrolase RPN11
  • 26S proteasome complex subunit SEM1
Function / homologyProteasome beta 3 subunit / Rpn11/EIF3F, C-terminal / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / Tetratricopeptide repeat / Proteasome alpha-type subunit / Proteasome B-type subunit / Proteasome beta subunit, C-terminal / Proteasome subunit Rpn10 / Proteasome subunit beta 4 ...Proteasome beta 3 subunit / Rpn11/EIF3F, C-terminal / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / Tetratricopeptide repeat / Proteasome alpha-type subunit / Proteasome B-type subunit / Proteasome beta subunit, C-terminal / Proteasome subunit Rpn10 / Proteasome subunit beta 4 / P-loop containing nucleoside triphosphate hydrolase / Nucleophile aminohydrolases, N-terminal / Proteasomal ATPase OB C-terminal domain / CSN8/PSMD8/EIF3K / Proteasome subunit alpha5 / 26S Proteasome non-ATPase regulatory subunit 7/8 / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / Proteasome beta-type subunit, conserved site / Proteasome subunit alpha2 / 26S proteasome regulatory subunit P45-like / Proteasome/cyclosome repeat / von Willebrand factor, type A / AAA+ ATPase domain / Ubiquitin interacting motif / ATPase, AAA-type, core / ATPase, AAA-type, conserved site / 26S proteasome non-ATPase regulatory subunit Rpn12 / Armadillo-type fold / Proteasomal ubiquitin receptor Rpn13/ADRM1 / DSS1/SEM1 / Armadillo-like helical / Tetratricopeptide-like helical domain superfamily / Tetratricopeptide repeat-containing domain / 26S proteasome regulatory subunit, C-terminal / Proteasome subunit alpha6 / Proteasome subunit alpha4 / Proteasome component (PCI) domain / PCI domain / Proteasome subunit alpha 7-like / Proteasomal ubiquitin receptor Rpn13/ADRM1 superfamily / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / ATPase family associated with various cellular activities (AAA) / Proteasome subunit / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Proteasome/cyclosome repeat / Proteasome subunit alpha 3 / Proteasome complex subunit Rpn13 ubiquitin receptor / DSS1/SEM1 family / Proteasome regulatory subunit C-terminal / CSN8/PSMD8/EIF3K family / Proteasome subunit A N-terminal signature / 26S proteasome subunit RPN7 / Proteasome subunit beta Pre3 / MPN domain / Proteasome subunit alpha 1 / 26S Proteasome regulatory subunit 6B / Proteasome subunit beta 1 / Proteasome subunit beta 2 / Proteasome subunit beta 7 / 26S Proteasome regulatory subunit 4 / 26S Proteasome regulatory subunit 7 / 26S Proteasome regulatory subunit 6A / 26S proteasome regulatory subunit 8 / von Willebrand factor A-like 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 12 / 26S Proteasome non-ATPase regulatory subunit 13 / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / Proteasome, subunit alpha/beta / JAB1/MPN/MOV34 metalloenzyme domain / Maintenance of mitochondrial structure and function / TNFR2 non-canonical NF-kB pathway / Proteasome alpha-type subunit profile. / Proteasome alpha-subunit, N-terminal domain / Proteasome beta-type subunit profile. / Cross-presentation of soluble exogenous antigens (endosomes) / L13a-mediated translational silencing of Ceruloplasmin expression / SCF-beta-TrCP mediated degradation of Emi1 / SCF(Skp2)-mediated degradation of p27/p21 / ABC-family proteins mediated transport / AUF1 (hnRNP D0) binds and destabilizes mRNA / MAPK6/MAPK4 signaling / TPR repeat region circular profile. / Ub-specific processing proteases / Metalloprotease DUBs / Neutrophil degranulation / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Antigen processing: Ubiquitination & Proteasome degradation / Ubiquitin-interacting motif (UIM) domain profile. / Proteasome beta subunits C terminal / Proteasome beta-type subunits signature. / PCI domain profile.
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast) / Baker's yeast (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 4.2 Å resolution
AuthorsDing Z / Cong Y
CitationJournal: Cell Res. / Year: 2017
Title: High-resolution cryo-EM structure of the proteasome in complex with ADP-AlFx.
Authors: Zhanyu Ding / Zhenglin Fu / Cong Xu / Yifan Wang / Yanxing Wang / Junrui Li / Liangliang Kong / Jinhuan Chen / Na Li / Rongguang Zhang / Yao Cong
Validation ReportPDB-ID: 5wvk

SummaryFull reportAbout validation report
DateDeposition: Dec 25, 2016 / Header (metadata) release: Feb 1, 2017 / Map release: Mar 22, 2017 / Last update: Mar 22, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.543
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.543
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5wvk
  • Surface level: 0.543
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6694.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.32 Å/pix.
= 474.48 Å
360 pix
1.32 Å/pix.
= 474.48 Å
360 pix
1.32 Å/pix.
= 474.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.318 Å
Density
Contour Level:0.543 (by author), 0.543 (movie #1):
Minimum - Maximum-0.738311 - 1.6660655
Average (Standard dev.)0.008360936 (0.08163116)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin0.00.00.0
Limit359.0359.0359.0
Spacing360360360
CellA=B=C: 474.47998 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3181.3181.318
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z474.480474.480474.480
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.7381.6660.008

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Supplemental data

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Sample components

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Entire yeast proteasome in complex with ADP-AlFx

EntireName: yeast proteasome in complex with ADP-AlFx / Number of components: 34

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Component #1: protein, yeast proteasome in complex with ADP-AlFx

ProteinName: yeast proteasome in complex with ADP-AlFx / Recombinant expression: No
MassExperimental: 1.6 MDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #2: protein, Proteasome subunit beta type-1

ProteinName: Proteasome subunit beta type-1PSMB1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 23.573604 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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

ProteinName: Proteasome subunit beta type-2PSMB2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 28.299889 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #4: protein, Proteasome subunit beta type-3

ProteinName: Proteasome subunit beta type-3PSMB3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 22.627842 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #5: protein, Proteasome subunit beta type-4

ProteinName: Proteasome subunit beta type-4PSMB4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 22.545676 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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

ProteinName: Proteasome subunit beta type-5PSMB5 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 31.670539 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #7: protein, Proteasome subunit beta type-6

ProteinName: Proteasome subunit beta type-6 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 26.905076 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #8: protein, Proteasome subunit beta type-7

ProteinName: Proteasome subunit beta type-7 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 29.471289 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #9: protein, Proteasome subunit alpha type-1

ProteinName: Proteasome subunit alpha type-1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 28.03383 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #10: protein, Proteasome subunit alpha type-2

ProteinName: Proteasome subunit alpha type-2 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 27.191828 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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

ProteinName: Proteasome subunit alpha type-3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 28.74823 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #12: protein, Proteasome subunit alpha type-4

ProteinName: Proteasome subunit alpha type-4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 28.478111 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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

ProteinName: Proteasome subunit alpha type-5 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 28.649086 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #14: protein, Proteasome subunit alpha type-6

ProteinName: Proteasome subunit alpha type-6 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 25.634 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #15: protein, Probable proteasome subunit alpha type-7

ProteinName: Probable proteasome subunit alpha type-7 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 31.575068 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #16: protein, 26S protease regulatory subunit 7 homolog

ProteinName: 26S protease regulatory subunit 7 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 52.054891 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #17: protein, 26S protease regulatory subunit 4 homolog

ProteinName: 26S protease regulatory subunit 4 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.89816 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #18: protein, 26S protease regulatory subunit 8 homolog

ProteinName: 26S protease regulatory subunit 8 homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.342742 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #19: protein, 26S protease regulatory subunit 6B homolog

ProteinName: 26S protease regulatory subunit 6B homolog / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 47.953676 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #20: protein, 26S protease subunit RPT4

ProteinName: 26S protease subunit RPT4Proteasome endopeptidase complex
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.480137 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #21: protein, 26S protease regulatory subunit 6A

ProteinName: 26S protease regulatory subunit 6A / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 48.315727 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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

ProteinName: 26S proteasome regulatory subunit RPN2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 104.351883 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #23: protein, 26S proteasome regulatory subunit RPN9

ProteinName: 26S proteasome regulatory subunit RPN9 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 45.839348 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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

ProteinName: 26S proteasome regulatory subunit RPN5 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 51.840352 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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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) / Strain: ATCC 204508 / S288c

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

ProteinName: 26S proteasome regulatory subunit RPN7 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 49.016367 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #27: protein, 26S proteasome regulatory subunit RPN3

ProteinName: 26S proteasome regulatory subunit RPN3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 60.464605 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #28: protein, 26S proteasome regulatory subunit RPN12

ProteinName: 26S proteasome regulatory subunit RPN12 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 31.952119 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #29: protein, 26S proteasome regulatory subunit RPN8

ProteinName: 26S proteasome regulatory subunit RPN8 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 38.365508 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #30: protein, Ubiquitin carboxyl-terminal hydrolase RPN11

ProteinName: Ubiquitin carboxyl-terminal hydrolase RPN11 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 34.442281 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #31: protein, 26S proteasome regulatory subunit RPN10

ProteinName: 26S proteasome regulatory subunit RPN10 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 29.776098 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #32: protein, 26S proteasome regulatory subunit RPN13

ProteinName: 26S proteasome regulatory subunit RPN13 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 17.919002 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #33: protein, 26S proteasome complex subunit SEM1

ProteinName: 26S proteasome complex subunit SEM1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.397102 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Component #34: protein, 26S proteasome regulatory subunit RPN1

ProteinName: 26S proteasome regulatory subunit RPN1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 109.601906 kDa
SourceSpecies: Baker's yeast (baker's yeast) / Strain: ATCC 204508 / S288c

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Experimental details

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Sample preparation

SpecimenSpecimen state: cell / Method: cryo EM
Sample solutionpH: 7.5
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: 38 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: 178576
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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