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- PDB-6j30: yeast proteasome in Ub-engaged state (C2) -

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Entry
Database: PDB / ID: 6j30
Titleyeast proteasome in Ub-engaged state (C2)
Components
  • (26S proteasome ...) x 18
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • Probable proteasome subunit alpha type-7
  • Ubiquitin carboxyl-terminal hydrolase RPN11
KeywordsHYDROLASE / Proteasome / K48-Ub4 / Ub-bound / cryo-EM
Function / homology26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / 26S Proteasome non-ATPase regulatory subunit 12 / 26S Proteasome regulatory subunit 4 / 26S Proteasome regulatory subunit 7 / 26S Proteasome regulatory subunit 6A / 26S Proteasome regulatory subunit 6B / in:ipr035261: / 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 RPN1 C-terminal / 26S Proteasome non-ATPase regulatory subunit 12 / 26S Proteasome regulatory subunit 4 / 26S Proteasome regulatory subunit 7 / 26S Proteasome regulatory subunit 6A / 26S Proteasome regulatory subunit 6B / in:ipr035261: / 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 13 / Proteasome subunit beta 2 / 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 Pre3 / in:ipr037560: / Proteasomal ubiquitin receptor Rpn13/ADRM1 superfamily / Proteasome subunit beta 7 / Proteasome subunit beta 1 / 26S proteasome regulatory subunit RPN2, C-terminal / Rpn11/EIF3F, C-terminal / 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 / Tetratricopeptide repeat / Proteasome alpha-type subunit / Proteasome B-type subunit / Proteasome beta subunit, C-terminal / Proteasome subunit Rpn10 / Proteasome subunit alpha 1 / 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 / Proteasome subunit alpha6 / Proteasome subunit alpha2 / in:ipr034647: / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / 26S proteasome regulatory subunit Rpn6, N-terminal / Armadillo-type fold / Ub-specific processing proteases / MPN domain profile. / PCI domain profile. / TPR repeat region circular profile. / Ubiquitin-interacting motif (UIM) domain profile. / Proteasome alpha-type subunit profile. / Proteasome beta-type subunit profile. / L13a-mediated translational silencing of Ceruloplasmin expression / rt:r-sce-187577: / Metalloprotease DUBs / TPR repeat profile. / Neutrophil degranulation / Orc1 removal from chromatin / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / AAA+ lid domain / HEAT repeats / Rpn9 C-terminal helix / 26S proteasome regulatory subunit RPN5 C-terminal domain / RPN1/RPN2 N-terminal domain / VWFA domain profile. / Proteasome beta-type subunits signature. / 6S proteasome subunit Rpn6, C-terminal helix domain / CSN8/PSMD8/EIF3K family / ATPase family associated with various cellular activities (AAA) / Proteasome subunit / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / PCI domain / Proteasome/cyclosome repeat / Proteasome complex subunit Rpn13 ubiquitin receptor / DSS1/SEM1 family / Proteasome regulatory subunit C-terminal / Proteasome subunit A N-terminal signature / AAA-protein family 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 / 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. / Proteasome beta-type subunit, conserved site / Proteasome beta 3 subunit / 26S proteasome regulatory subunit, C-terminal / AAA+ ATPase domain / Proteasome alpha-subunit, N-terminal domain / JAB1/MPN/MOV34 metalloenzyme domain / Tetratricopeptide repeat-containing domain / Proteasome component (PCI) domain / Proteasome, subunit alpha/beta / Proteasome/cyclosome repeat / von Willebrand factor, type A
Function and homology information
Specimen sourceSaccharomyces cerevisiae S288c (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsCong, Y.
CitationJournal: Mol. Cell / Year: 2019
Title: Structural Snapshots of 26S Proteasome Reveal Tetraubiquitin-Induced Conformations.
Authors: Zhanyu Ding / Cong Xu / Indrajit Sahu / Yifan Wang / Zhenglin Fu / Min Huang / Catherine C L Wong / Michael H Glickman / Yao Cong /
Abstract: The 26S proteasome is the ATP-dependent protease responsible for regulating the proteome of eukaryotic cells through degradation of mainly ubiquitin-tagged substrates. In order to understand how ...The 26S proteasome is the ATP-dependent protease responsible for regulating the proteome of eukaryotic cells through degradation of mainly ubiquitin-tagged substrates. In order to understand how proteasome responds to ubiquitin signal, we resolved an ensemble of cryo-EM structures of proteasome in the presence of K48-Ub, with three of them resolved at near-atomic resolution. We identified a conformation with stabilized ubiquitin receptors and a previously unreported orientation of the lid, assigned as a Ub-accepted state C1-b. We determined another structure C3-b with localized K48-Ub to the toroid region of Rpn1, assigned as a substrate-processing state. Our structures indicate that tetraUb induced conformational changes in proteasome could initiate substrate degradation. We also propose a CP gate-opening mechanism involving the propagation of the motion of the lid to the gate through the Rpn6-α2 interaction. Our results enabled us to put forward a model of a functional cycle for proteasomes induced by tetraUb and nucleotide.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 3, 2019 / Release: Mar 20, 2019
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 20, 2019Structure modelrepositoryInitial release
1.1Apr 10, 2019Structure modelData collection / Database referencescitation_citation.journal_volume / _citation.page_first

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Assembly

Deposited unit
1: Proteasome subunit beta type-1
2: Proteasome subunit beta type-2
3: Proteasome subunit beta type-3
4: Proteasome subunit beta type-4
5: Proteasome subunit beta type-5
6: Proteasome subunit beta type-6
7: Proteasome subunit beta type-7
b: Proteasome subunit beta type-1
i: Proteasome subunit beta type-2
h: Proteasome subunit beta type-3
g: Proteasome subunit beta type-4
f: Proteasome subunit beta type-5
e: Proteasome subunit beta type-6
a: Proteasome subunit beta type-7
A: Proteasome subunit alpha type-1
B: Proteasome subunit alpha type-2
C: Proteasome subunit alpha type-3
D: Proteasome subunit alpha type-4
E: Proteasome subunit alpha type-5
F: Proteasome subunit alpha type-6
G: Probable proteasome subunit alpha type-7
c: Proteasome subunit alpha type-1
j: Proteasome subunit alpha type-2
d: Proteasome subunit alpha type-3
n: Proteasome subunit alpha type-4
m: Proteasome subunit alpha type-5
l: Proteasome subunit alpha type-6
k: Probable proteasome subunit alpha type-7
H: 26S proteasome regulatory subunit 7 homolog
I: 26S proteasome regulatory subunit 4 homolog
J: 26S proteasome regulatory subunit 8 homolog
K: 26S proteasome regulatory subunit 6B homolog
L: 26S proteasome subunit RPT4
M: 26S proteasome regulatory subunit 6A
N: 26S proteasome regulatory subunit RPN2
O: 26S proteasome regulatory subunit RPN9
P: 26S proteasome regulatory subunit RPN5
Q: 26S proteasome regulatory subunit RPN6
R: 26S proteasome regulatory subunit RPN7
S: 26S proteasome regulatory subunit RPN3
T: 26S proteasome regulatory subunit RPN12
U: 26S proteasome regulatory subunit RPN8
V: Ubiquitin carboxyl-terminal hydrolase RPN11
W: 26S proteasome regulatory subunit RPN10
X: 26S proteasome regulatory subunit RPN13
Y: 26S proteasome complex subunit SEM1
Z: 26S proteasome regulatory subunit RPN1


Theoretical massNumber of molelcules
Total (without water)1,692,66047
Polyers1,692,66047
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Proteasome subunit beta type- ... , 7 types, 14 molecules 1b2i3h4g5f6e7a

#1: Protein/peptide Proteasome subunit beta type-1 / PSMB1 / Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component PRE3 / Proteinase YSCE subunit PRE3


Mass: 23573.604 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P38624, proteasome endopeptidase complex
#2: Protein/peptide Proteasome subunit beta type-2 / PSMB2 / Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component PUP1 / Proteinase YSCE subunit PUP1


Mass: 28299.889 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P25043, proteasome endopeptidase complex
#3: Protein/peptide Proteasome subunit beta type-3 / PSMB3 / Macropain subunit PUP3 / Multicatalytic endopeptidase complex subunit PUP3 / Proteasome component PUP3


Mass: 22627.842 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P25451, proteasome endopeptidase complex
#4: Protein/peptide Proteasome subunit beta type-4 / PSMB4 / Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 / Proteinase YSCE subunit 11


Mass: 22545.676 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P22141, proteasome endopeptidase complex
#5: Protein/peptide Proteasome subunit beta type-5 / PSMB5 / Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteasome component PRE2 / Proteinase YSCE subunit PRE2


Mass: 31670.539 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P30656, proteasome endopeptidase complex
#6: Protein/peptide Proteasome subunit beta type-6 / / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5


Mass: 26905.076 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P23724, proteasome endopeptidase complex
#7: Protein/peptide Proteasome subunit beta type-7 / / Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component PRE4 / Proteinase YSCE subunit PRE4


Mass: 29471.289 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P30657, proteasome endopeptidase complex

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Proteasome subunit alpha type- ... , 6 types, 12 molecules AcBjCdDnEmFl

#8: Protein/peptide Proteasome subunit alpha type-1 / / Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7-alpha / Proteasome component Y8 / Proteinase YSCE subunit 7 / SCL1 suppressor protein


Mass: 28033.830 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P21243, proteasome endopeptidase complex
#9: Protein/peptide Proteasome subunit alpha type-2 / / Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / Proteinase YSCE subunit 7


Mass: 27191.828 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P23639, proteasome endopeptidase complex
#10: Protein/peptide Proteasome subunit alpha type-3 / / Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 / Proteinase YSCE subunit 13


Mass: 28748.230 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P23638, proteasome endopeptidase complex
#11: Protein/peptide Proteasome subunit alpha type-4 / / Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component PRE6 / Proteinase YSCE subunit PRE6


Mass: 28478.111 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P40303, proteasome endopeptidase complex
#12: Protein/peptide Proteasome subunit alpha type-5 / / Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component PUP2 / Proteinase YSCE subunit PUP2


Mass: 28649.086 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P32379, proteasome endopeptidase complex
#13: Protein/peptide Proteasome subunit alpha type-6 / / Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component PRE5 / Proteinase YSCE subunit PRE5


Mass: 25634.000 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P40302, proteasome endopeptidase complex

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Protein/peptide , 2 types, 3 molecules GkV

#14: Protein/peptide Probable proteasome subunit alpha type-7 / Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / Proteinase YSCE subunit 1


Mass: 31575.068 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P21242, proteasome endopeptidase complex
#29: Protein/peptide Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome regulatory subunit RPN11 / Protein MPR1


Mass: 34442.281 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P43588, ubiquitinyl hydrolase 1

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26S proteasome ... , 18 types, 18 molecules HIJKLMNOPQRSTUWXYZ

#15: Protein/peptide 26S proteasome regulatory subunit 7 homolog / Protein CIM5 / Tat-binding homolog 3


Mass: 52054.891 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P33299
#16: Protein/peptide 26S proteasome regulatory subunit 4 homolog / Tat-binding homolog 5


Mass: 48898.160 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P40327
#17: Protein/peptide 26S proteasome regulatory subunit 8 homolog / Protein CIM3 / Protein SUG1 / Tat-binding protein TBY1


Mass: 45342.742 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q01939
#18: Protein/peptide 26S proteasome regulatory subunit 6B homolog / Protein YNT1 / Tat-binding homolog 2


Mass: 47953.676 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P33298
#19: Protein/peptide 26S proteasome subunit RPT4 / 26S protease subunit SUG2 / Proteasomal cap subunit


Mass: 49480.137 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P53549
#20: Protein/peptide 26S proteasome regulatory subunit 6A / Tat-binding protein homolog 1 / TBP-1


Mass: 48315.727 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P33297
#21: Protein/peptide 26S proteasome regulatory subunit RPN2


Mass: 104351.883 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P32565
#22: Protein/peptide 26S proteasome regulatory subunit RPN9 / Proteasome non-ATPase subunit 7


Mass: 45839.348 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q04062
#23: Protein/peptide 26S proteasome regulatory subunit RPN5 / Proteasome non-ATPase subunit 5


Mass: 51840.352 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q12250
#24: Protein/peptide 26S proteasome regulatory subunit RPN6 / Proteasome non-ATPase subunit 4


Mass: 49839.812 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q12377
#25: Protein/peptide 26S proteasome regulatory subunit RPN7


Mass: 49016.367 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q06103
#26: Protein/peptide 26S proteasome regulatory subunit RPN3


Mass: 60464.605 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P40016
#27: Protein/peptide 26S proteasome regulatory subunit RPN12 / Nuclear integrity protein 1


Mass: 31952.119 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P32496
#28: Protein/peptide 26S proteasome regulatory subunit RPN8


Mass: 38365.508 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q08723
#30: Protein/peptide 26S proteasome regulatory subunit RPN10


Mass: 29776.098 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38886
#31: Protein/peptide 26S proteasome regulatory subunit RPN13 / Proteasome non-ATPase subunit 13


Mass: 17919.002 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: O13563
#32: Protein/peptide 26S proteasome complex subunit SEM1


Mass: 10397.102 Da / Num. of mol.: 1 / Fragment: SEM1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: O94742
#33: Protein/peptide 26S proteasome regulatory subunit RPN1 / HMG-CoA reductase degradation protein 2 / Proteasome non-ATPase subunit 1


Mass: 109601.906 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38764

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Yeast proteasome / Type: COMPLEX
Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33
Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 38 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 40585 / Symmetry type: POINT
Refine LS restraints

Refinement-ID: ELECTRON MICROSCOPY

TypeDev idealNumber
f_bond_d0.001108088
f_angle_d0.407146060
f_dihedral_angle_d5.25590738
f_chiral_restr0.03916593
f_plane_restr0.00318829

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