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- PDB-6j2q: Yeast proteasome in Ub-accepted state (C1-b) -

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Basic information

Entry
Database: PDB / ID: 6j2q
TitleYeast proteasome in Ub-accepted state (C1-b)
Components
  • (26S protease regulatory subunit ...) x 5
  • (26S proteasome regulatory subunit ...) x 11
  • (Proteasome subunit alpha type- ...) x 6
  • (Proteasome subunit beta type- ...) x 7
  • 26S protease subunit RPT4Proteasome endopeptidase complex
  • 26S proteasome complex subunit SEM1Proteasome
  • Probable proteasome subunit alpha type-7
  • Ubiquitin carboxyl-terminal hydrolase RPN11
KeywordsHYDROLASE / Proteasome / K48-Ub4 / Ub-bound / cryo-EM
Function / homology
Function and homology information


SAGA complex localization to transcription regulatory region / proteasome storage granule assembly / peroxisome fission / filamentous growth / transcription export complex 2 / maintenance of DNA trinucleotide repeats / proteasome regulatory particle assembly / protein deneddylation / nonfunctional rRNA decay / cellular protein-containing complex localization ...SAGA complex localization to transcription regulatory region / proteasome storage granule assembly / peroxisome fission / filamentous growth / transcription export complex 2 / maintenance of DNA trinucleotide repeats / proteasome regulatory particle assembly / protein deneddylation / nonfunctional rRNA decay / cellular protein-containing complex localization / histone deubiquitination / K48-linked polyubiquitin modification-dependent protein binding / proteasome-activating ATPase activity / nuclear proteasome complex / proteasome regulatory particle / mitochondrial fission / COP9 signalosome / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / Lys63-specific deubiquitinase activity / cytosolic proteasome complex / proteasome binding / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / polyubiquitin modification-dependent protein binding / regulation of protein catabolic process / peptide catabolic process / endopeptidase activator activity / proteasome complex / proteasome storage granule / proteasomal ubiquitin-independent protein catabolic process / proteasome core complex / proteasome core complex, beta-subunit complex / thiol-dependent ubiquitin-specific protease activity / proteasome endopeptidase complex / ubiquitin-dependent ERAD pathway / proteasome core complex, alpha-subunit complex / proteasome assembly / threonine-type endopeptidase activity / mRNA export from nucleus / ubiquitinyl hydrolase 1 / TBP-class protein binding / enzyme regulator activity / proteasomal protein catabolic process / positive regulation of transcription elongation from RNA polymerase II promoter / nucleotide-excision repair / ubiquitin binding / positive regulation of RNA polymerase II transcriptional preinitiation complex assembly / metallopeptidase activity / positive regulation of protein catabolic process / protein-macromolecule adaptor activity / double-strand break repair via homologous recombination / regulation of cell cycle / negative regulation of DNA-binding transcription factor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitin-dependent protein catabolic process / positive regulation of DNA-binding transcription factor activity / chromatin remodeling / endopeptidase activity / ATPase activity / protein deubiquitination / mRNA binding / endoplasmic reticulum membrane / protein domain specific binding / ubiquitin protein ligase binding / structural molecule activity / endoplasmic reticulum / mitochondrion / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / Proteasome subunit beta 1 / CSN8/PSMD8/EIF3K / Proteasome beta 3 subunit / Proteasome subunit alpha5 / 26S Proteasome non-ATPase regulatory subunit 7/8 / Proteasome subunit alpha6 / Proteasome subunit alpha2 / Proteasome subunit alpha 1 / Proteasome subunit beta 2 ...26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / Proteasome subunit beta 1 / CSN8/PSMD8/EIF3K / Proteasome beta 3 subunit / Proteasome subunit alpha5 / 26S Proteasome non-ATPase regulatory subunit 7/8 / Proteasome subunit alpha6 / Proteasome subunit alpha2 / Proteasome subunit alpha 1 / Proteasome subunit beta 2 / Nucleophile aminohydrolases, N-terminal / Proteasome subunit beta 7 / 26S Proteasome regulatory subunit 4 / 26S Proteasome regulatory subunit 7 / 26S Proteasome regulatory subunit 6B / 26S proteasome regulatory subunit 10B / 26S Proteasome non-ATPase regulatory subunit 1 / 26S proteasome non-ATPase regulatory subunit 3 / 26S Proteasome non-ATPase regulatory subunit 6 / Proteasomal ATPase OB C-terminal domain / P-loop containing nucleoside triphosphate hydrolase / 26S Proteasome non-ATPase regulatory subunit 13 / Armadillo-type fold / 26S proteasome non-ATPase regulatory subunit Rpn12 / 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 beta-type subunit, conserved site / Proteasome subunit Rpn10 / 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 B-type subunit / Proteasome beta subunit, C-terminal / Rpn11/EIF3F, C-terminal / 26S Proteasome non-ATPase regulatory subunit 12 / 26S Proteasome non-ATPase regulatory subunit 14 / ATPase, AAA-type, conserved site / 26S proteasome subunit RPN6 C-terminal helix domain / Proteasome/cyclosome repeat / HEAT repeats / 26S proteasome regulatory subunit RPN2 C-terminal domain / PCI domain / Rpn9 C-terminal helix / 26S proteasome regulatory subunit RPN5 C-terminal domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome subunit RPN7 / AAA+ lid domain / Proteasome regulatory subunit C-terminal / CSN8/PSMD8/EIF3K family / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Maintenance of mitochondrial structure and function / von Willebrand factor type A domain / Proteasome complex subunit Rpn13 ubiquitin receptor / DSS1/SEM1 family / RPN1/RPN2 N-terminal domain / Proteasomal ATPase OB C-terminal domain / ATPase family associated with various cellular activities (AAA) / Winged helix-like DNA-binding domain superfamily / 26S proteasome regulatory subunit RPN2, C-terminal / Winged helix DNA-binding domain superfamily / von Willebrand factor A-like domain superfamily / MPN domain / Proteasome subunit alpha 3 / Proteasome subunit beta Pre3 / Proteasomal ubiquitin receptor Rpn13/ADRM1 superfamily / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / 26S proteasome regulatory subunit Rpn6, N-terminal / Proteasome subunit A N-terminal signature / 6S proteasome subunit Rpn6, C-terminal helix domain / Rpn9, C-terminal helix / RPN1/RPN2, N-terminal / 26S proteasome regulatory subunit RPN5, C-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / AAA ATPase, AAA+ lid domain / Proteasome subunit / Proteasome beta subunits C terminal / 26S proteasome regulatory subunit P45-like / Proteasome alpha-type subunit / ATPase, AAA-type, core / Proteasome component (PCI) domain / Ubiquitin interacting motif / Proteasome alpha-subunit, N-terminal domain / JAB1/MPN/MOV34 metalloenzyme domain / Peptidase T1A, proteasome beta-subunit / Proteasome, subunit alpha/beta / Proteasome/cyclosome repeat / von Willebrand factor, type A / AAA+ ATPase domain
26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit RPN6 / 26S proteasome regulatory subunit RPN5 / 26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit 8 homolog / 26S proteasome regulatory subunit RPN9 / Proteasome subunit beta type-7 / 26S proteasome regulatory subunit RPN13 / 26S proteasome complex subunit SEM1 / Probable proteasome subunit alpha type-7 ...26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit RPN6 / 26S proteasome regulatory subunit RPN5 / 26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit 8 homolog / 26S proteasome regulatory subunit RPN9 / Proteasome subunit beta type-7 / 26S proteasome regulatory subunit RPN13 / 26S proteasome complex subunit SEM1 / Probable proteasome subunit alpha type-7 / Proteasome subunit alpha type-1 / Proteasome subunit beta type-4 / Proteasome subunit alpha type-3 / Proteasome subunit alpha type-2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit alpha type-5 / 26S proteasome subunit RPT4 / 26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit 6A / 26S proteasome regulatory subunit 6B homolog / 26S proteasome regulatory subunit 7 homolog / Proteasome subunit beta type-1 / 26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit RPN3 / Proteasome subunit alpha type-6 / Proteasome subunit alpha type-4 / 26S proteasome regulatory subunit 4 homolog / Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome regulatory subunit RPN12
Biological speciesSaccharomyces cerevisiae S288c (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 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
History
DepositionJan 2, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

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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 protease regulatory subunit 7 homolog
I: 26S protease regulatory subunit 4 homolog
J: 26S protease regulatory subunit 8 homolog
K: 26S protease regulatory subunit 6B homolog
L: 26S protease subunit RPT4
M: 26S protease 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
Polymers1,692,66047
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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

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


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


Mass: 28299.889 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P25043, proteasome endopeptidase complex
#3: Protein 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 method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P25451, proteasome endopeptidase complex
#4: Protein Proteasome subunit beta type-4 / PSMB4 / Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 ...Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 / Proteinase YSCE subunit 11


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


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


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


Mass: 29471.289 Da / Num. of mol.: 2 / Source method: isolated from a natural source / 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 Proteasome subunit alpha type-1 / / Macropain subunit C7-alpha / Multicatalytic endopeptidase complex C7 / Proteasome component C7- ...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 method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P21243, proteasome endopeptidase complex
#9: Protein Proteasome subunit alpha type-2 / / Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / ...Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / Proteinase YSCE subunit 7


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


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


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


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


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

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Protein , 4 types, 5 molecules GkLVY

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


Mass: 31575.068 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P21242, proteasome endopeptidase complex
#19: Protein 26S protease subunit RPT4 / Proteasome endopeptidase complex / 26S protease subunit SUG2 / Proteasomal cap subunit


Mass: 49480.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P53549
#29: Protein Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome regulatory subunit RPN11 / Protein MPR1


Mass: 34442.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P43588, ubiquitinyl hydrolase 1
#32: Protein 26S proteasome complex subunit SEM1 / Proteasome


Mass: 10397.102 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: O94742

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26S protease regulatory subunit ... , 5 types, 5 molecules HIJKM

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


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


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


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


Mass: 47953.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P33298
#20: Protein 26S protease regulatory subunit 6A / Tat-binding protein homolog 1 / TBP-1


Mass: 48315.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P33297

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26S proteasome regulatory subunit ... , 11 types, 11 molecules NOPQRSTUWXZ

#21: Protein 26S proteasome regulatory subunit RPN2


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


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


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


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


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


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


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


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


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


Mass: 17919.002 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: O13563
#33: Protein 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 method: isolated from a natural source / 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 26S proteasomeProteasome / 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 / 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: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77729 / Symmetry type: POINT
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001108151
ELECTRON MICROSCOPYf_angle_d0.369146131
ELECTRON MICROSCOPYf_dihedral_angle_d5.08690792
ELECTRON MICROSCOPYf_chiral_restr0.03916606
ELECTRON MICROSCOPYf_plane_restr0.00318834

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

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Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.:Changes in new EM Navigator and Yorodumi

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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