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- PDB-6fvu: 26S proteasome, s2 state -

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Entry
Database: PDB / ID: 6fvu
Title26S proteasome, s2 state
Components
  • (26S proteasome ...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 / 26S proteasome / AAA+ ATPase
Function / homology
Function and homology information


SAGA complex localization to transcription regulatory region / proteasome storage granule assembly / peroxisome fission / transcription export complex 2 / proteasome regulatory particle assembly / maintenance of DNA trinucleotide repeats / protein deneddylation / nonfunctional rRNA decay / filamentous growth / protein-containing complex localization => GO:0031503 ...SAGA complex localization to transcription regulatory region / proteasome storage granule assembly / peroxisome fission / transcription export complex 2 / proteasome regulatory particle assembly / maintenance of DNA trinucleotide repeats / protein deneddylation / nonfunctional rRNA decay / filamentous growth / protein-containing complex localization => GO:0031503 / nuclear proteasome complex / proteasome regulatory particle / COP9 signalosome / mitochondrial fission / histone deubiquitination / proteasome-activating activity / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / Lys63-specific deubiquitinase activity / cytosolic proteasome complex / K48-linked polyubiquitin modification-dependent protein binding / proteasome binding / peptide catabolic process / proteasome core complex assembly / nuclear outer membrane-endoplasmic reticulum membrane network / TNFR2 non-canonical NF-kB pathway / Cross-presentation of soluble exogenous antigens (endosomes) / Ub-specific processing proteases / regulation of protein catabolic process / proteasome storage granule / polyubiquitin modification-dependent protein binding / endopeptidase activator activity / proteasomal ubiquitin-independent protein catabolic process / proteasome core complex / isopeptidase activity / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome complex / proteasome assembly / proteasome core complex, alpha-subunit complex / threonine-type endopeptidase activity / ubiquitin-dependent ERAD pathway / mRNA export from nucleus / Neutrophil degranulation / enzyme regulator activity / TBP-class protein binding / nucleotide-excision repair / ubiquitin binding / positive regulation of RNA polymerase II transcription preinitiation complex assembly / positive regulation of transcription elongation from RNA polymerase II promoter / double-strand break repair via homologous recombination / positive regulation of protein catabolic process / protein-macromolecule adaptor activity / metallopeptidase activity / regulation of cell cycle / negative regulation of DNA-binding transcription factor activity / ubiquitinyl hydrolase 1 / proteasome-mediated ubiquitin-dependent protein catabolic process / thiol-dependent deubiquitinase / positive regulation of DNA-binding transcription factor activity / ubiquitin-dependent protein catabolic process / chromatin remodeling / endopeptidase activity / protein deubiquitination / ATP hydrolysis activity / mRNA binding / protein domain specific binding / ubiquitin protein ligase binding / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / mitochondrion / ATP binding / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Proteasome subunit Rpn10 / Rpn9, C-terminal helix / Rpn9 C-terminal helix / 26S proteasome regulatory subunit 8 / HEAT repeats / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Proteasome complex subunit Rpn13 ubiquitin receptor / Pru (pleckstrin-like receptor for ubiquitin) domain profile. / Proteasomal ubiquitin receptor Rpn13/ADRM1 / 26S proteasome non-ATPase regulatory subunit 3 ...Proteasome subunit Rpn10 / Rpn9, C-terminal helix / Rpn9 C-terminal helix / 26S proteasome regulatory subunit 8 / HEAT repeats / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Proteasome complex subunit Rpn13 ubiquitin receptor / Pru (pleckstrin-like receptor for ubiquitin) domain profile. / Proteasomal ubiquitin receptor Rpn13/ADRM1 / 26S proteasome non-ATPase regulatory subunit 3 / 26S proteasome non-ATPase regulatory subunit Rpn12 / Proteasome regulatory subunit C-terminal / 26S Proteasome non-ATPase regulatory subunit 6 / 26S proteasome regulatory subunit, C-terminal / 26S proteasome regulatory subunit RPN5 C-terminal domain / DSS1/SEM1 family / 26S proteasome regulatory subunit RPN5, C-terminal domain / DSS1/SEM1 / 26S Proteasome non-ATPase regulatory subunit 12 / DSS1_SEM1 / 26S proteasome subunit RPN6 C-terminal helix domain / 6S proteasome subunit Rpn6, C-terminal helix domain / 26S proteasome regulatory subunit Rpn6, N-terminal / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S Proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit RPN2 C-terminal domain / 26S Proteasome non-ATPase regulatory subunit 13 / 26S Proteasome non-ATPase regulatory subunit 14 / 26S Proteasome non-ATPase regulatory subunit 7/8 / RPN1, N-terminal / RPN1 N-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / 26S Proteasome regulatory subunit 6A / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S proteasome subunit RPN7 / 26S Proteasome regulatory subunit 7 / Proteasome/cyclosome repeat / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / 26S Proteasome regulatory subunit 6B / von Willebrand factor type A domain / Proteasome/cyclosome repeat / CSN8/PSMD8/EIF3K family / CSN8/PSMD8/EIF3K / 26S proteasome regulatory subunit P45-like / Rpn11/EIF3F, C-terminal / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Maintenance of mitochondrial structure and function / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / PCI domain / PCI domain profile. / Proteasome component (PCI) domain / Ubiquitin-interacting motif (UIM) domain profile. / Ubiquitin interacting motif / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / Proteasome subunit beta Pre3 / Proteasome subunit beta 5 / Proteasome beta subunits C terminal / Proteasome beta subunit, C-terminal / Proteasome subunit beta 7 / Proteasome subunit beta 4 / Proteasome subunit beta 1 / Proteasome subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha6 / Proteasome subunit alpha2 / Proteasome subunit alpha4 / Proteasome subunit alpha 1 / Proteasome subunit alpha5 / Proteasome subunit alpha 3 / VWFA domain profile. / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / Proteasome beta-type subunit, conserved site / Proteasome alpha-type subunits signature. / Proteasome subunit A N-terminal signature / von Willebrand factor, type A / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / MPN domain / MPN domain profile. / Proteasome alpha-type subunit / Proteasome alpha-type subunit profile. / Proteasome beta-type subunit profile. / Proteasome B-type subunit / AAA+ lid domain / AAA ATPase, AAA+ lid domain / Proteasome subunit / Proteasome, subunit alpha/beta / TPR repeat profile. / AAA-protein family signature. / ATPase, AAA-type, conserved site / TPR repeat region circular profile. / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
26S proteasome regulatory subunit 6B 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 / Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome regulatory subunit 4 homolog / 26S proteasome subunit RPT4 ...26S proteasome regulatory subunit 6B 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 / Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome regulatory subunit 4 homolog / 26S proteasome subunit RPT4 / 26S proteasome regulatory subunit 8 homolog / 26S proteasome regulatory subunit RPN9 / 26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit RPN5 / 26S proteasome regulatory subunit 7 homolog / ADENOSINE-5'-DIPHOSPHATE / 26S proteasome regulatory subunit 6A / Proteasome subunit alpha type-3 / ADENOSINE-5'-TRIPHOSPHATE / 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-2 / 26S proteasome regulatory subunit RPN2 / Proteasome subunit beta type-6 / Proteasome subunit beta type-2 / Proteasome subunit beta type-3 / Proteasome subunit beta type-5 / Proteasome subunit beta type-7 / Proteasome subunit alpha type-5 / 26S proteasome regulatory subunit RPN12 / 26S proteasome regulatory subunit RPN6
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsEisele, M.R. / Reed, R.G. / Rudack, T. / Schweitzer, A. / Beck, F. / Nagy, I. / Pfeifer, G. / Plitzko, J.M. / Baumeister, W. / Tomko, R.J. / Sakata, E.
CitationJournal: Cell Rep / Year: 2018
Title: Expanded Coverage of the 26S Proteasome Conformational Landscape Reveals Mechanisms of Peptidase Gating.
Authors: Markus R Eisele / Randi G Reed / Till Rudack / Andreas Schweitzer / Florian Beck / Istvan Nagy / Günter Pfeifer / Jürgen M Plitzko / Wolfgang Baumeister / Robert J Tomko / Eri Sakata /
Abstract: The proteasome is the central protease for intracellular protein breakdown. Coordinated binding and hydrolysis of ATP by the six proteasomal ATPase subunits induces conformational changes that drive ...The proteasome is the central protease for intracellular protein breakdown. Coordinated binding and hydrolysis of ATP by the six proteasomal ATPase subunits induces conformational changes that drive the unfolding and translocation of substrates into the proteolytic 20S core particle for degradation. Here, we combine genetic and biochemical approaches with cryo-electron microscopy and integrative modeling to dissect the relationship between individual nucleotide binding events and proteasome conformational dynamics. We demonstrate unique impacts of ATP binding by individual ATPases on the proteasome conformational distribution and report two conformational states of the proteasome suggestive of a rotary ATP hydrolysis mechanism. These structures, coupled with functional analyses, reveal key roles for the ATPases Rpt1 and Rpt6 in gating substrate entry into the core particle. This deepened knowledge of proteasome conformational dynamics reveals key elements of intersubunit communication within the proteasome and clarifies the regulation of substrate entry into the proteolytic chamber.
History
DepositionMar 5, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 22, 2018Provider: repository / Type: Initial release

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)1,583,26959
Polymers1,580,16047
Non-polymers3,10912
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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

#1: 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: 27200.947 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P21243, proteasome endopeptidase complex
#2: 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: 27060.631 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P23639, proteasome endopeptidase complex
#3: 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: 27050.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P23638, proteasome endopeptidase complex
#4: 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: 28202.787 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P40303, proteasome endopeptidase complex
#5: 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: 27442.787 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P32379, proteasome endopeptidase complex
#6: 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: 25198.438 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P40302, proteasome endopeptidase complex

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Protein , 2 types, 3 molecules gGV

#7: 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: 26734.328 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P21242, proteasome endopeptidase complex
#16: Protein Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome regulatory subunit RPN11 / Protein MPR1


Mass: 32490.963 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P43588, ubiquitinyl hydrolase 1

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Proteasome subunit beta type- ... , 7 types, 14 molecules h1i2j3k4l5m6n7

#8: 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: 21517.186 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P38624, proteasome endopeptidase complex
#9: 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: 24486.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P25043, proteasome endopeptidase complex
#10: Protein Proteasome subunit beta type-3 / PSMB3 / Macropain subunit PUP3 / Multicatalytic endopeptidase complex subunit PUP3 / Proteasome component PUP3


Mass: 22496.645 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P25451, proteasome endopeptidase complex
#11: 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: 22218.338 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P22141, proteasome endopeptidase complex
#12: 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: 23325.248 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P30656, proteasome endopeptidase complex
#13: Protein Proteasome subunit beta type-6 / / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5


Mass: 24883.928 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P23724, proteasome endopeptidase complex
#14: 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: 25832.336 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P30657, proteasome endopeptidase complex

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

#15: Protein 26S proteasome regulatory subunit RPN10


Mass: 21818.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P38886
#17: Protein 26S proteasome regulatory subunit RPN12 / Nuclear integrity protein 1


Mass: 31111.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P32496
#18: Protein 26S proteasome regulatory subunit RPN13 / Proteasome non-ATPase subunit 13


Mass: 14654.642 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: O13563
#19: 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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: O94742
#20: Protein 26S proteasome regulatory subunit RPN1 / HMG-CoA reductase degradation protein 2 / Proteasome non-ATPase subunit 1


Mass: 106895.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P38764
#21: Protein 26S proteasome regulatory subunit RPN2


Mass: 101894.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P32565
#22: Protein 26S proteasome regulatory subunit RPN3


Mass: 55378.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P40016
#23: Protein 26S proteasome regulatory subunit RPN5 / Proteasome non-ATPase subunit 5


Mass: 51341.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q12377
#25: Protein 26S proteasome regulatory subunit RPN7


Mass: 46307.477 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q06103
#26: Protein 26S proteasome regulatory subunit RPN8


Mass: 34557.316 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q08723
#27: Protein 26S proteasome regulatory subunit RPN9 / Proteasome non-ATPase subunit 7


Mass: 45194.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q04062
#28: Protein 26S proteasome regulatory subunit 7 homolog / Protein CIM5 / Tat-binding homolog 3


Mass: 47318.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P33299
#29: Protein 26S proteasome regulatory subunit 4 homolog / Tat-binding homolog 5


Mass: 43128.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P40327
#30: Protein 26S proteasome regulatory subunit 6B homolog / Protein YNT1 / Tat-binding homolog 2


Mass: 44353.523 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P33298
#31: Protein 26S proteasome subunit RPT4 / Proteasome / 26S protease subunit SUG2 / Proteasomal cap subunit


Mass: 43931.473 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P53549
#32: Protein 26S proteasome regulatory subunit 6A / Tat-binding protein homolog 1 / TBP-1


Mass: 46902.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P33297
#33: Protein 26S proteasome 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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q01939

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Non-polymers , 3 types, 12 molecules

#34: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#35: Chemical
ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#36: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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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: 26S proteasomeProteasome / Type: COMPLEX / Entity ID: #1-#33 / Source: NATURAL
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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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: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 193337 / Symmetry type: POINT

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External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

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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Yorodumi

Thousand views of thousand structures

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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