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- PDB-6fvw: 26S proteasome, s4 state -

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Basic information

Entry
Database: PDB / ID: 6fvw
Title26S proteasome, s4 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 / maintenance of DNA trinucleotide repeats / proteasome regulatory particle assembly / protein deneddylation / cellular protein-containing complex localization / nonfunctional rRNA decay / filamentous growth ...SAGA complex localization to transcription regulatory region / proteasome storage granule assembly / peroxisome fission / transcription export complex 2 / maintenance of DNA trinucleotide repeats / proteasome regulatory particle assembly / protein deneddylation / cellular protein-containing complex localization / nonfunctional rRNA decay / filamentous growth / K48-linked polyubiquitin modification-dependent protein binding / nuclear proteasome complex / proteasome regulatory particle / COP9 signalosome / mitochondrial fission / histone deubiquitination / proteasome regulatory particle, lid subcomplex / proteasome-activating activity / proteasome regulatory particle, base subcomplex / Lys63-specific deubiquitinase activity / cytosolic proteasome complex / 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 / polyubiquitin modification-dependent protein binding / proteasome storage granule / proteasomal ubiquitin-independent protein catabolic process / proteasome complex / endopeptidase activator activity / proteasome core complex / isopeptidase activity / proteasome endopeptidase complex / proteasome core complex, beta-subunit complex / proteasome core complex, alpha-subunit complex / proteasome assembly / threonine-type endopeptidase activity / ubiquitin-dependent ERAD pathway / mRNA export from nucleus / Neutrophil degranulation / TBP-class protein binding / enzyme regulator activity / 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 / positive regulation of protein catabolic process / double-strand break repair via homologous recombination / protein-macromolecule adaptor activity / metallopeptidase activity / regulation of cell cycle / negative regulation of DNA-binding transcription factor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / 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 / Proteasome complex subunit Rpn13 ubiquitin receptor / Pru (pleckstrin-like receptor for ubiquitin) domain profile. / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasome regulatory subunit C-terminal ...Proteasome subunit Rpn10 / Rpn9 C-terminal helix / Rpn9, C-terminal helix / 26S proteasome regulatory subunit 8 / HEAT repeats / Proteasome complex subunit Rpn13 ubiquitin receptor / Pru (pleckstrin-like receptor for ubiquitin) domain profile. / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Proteasomal ubiquitin receptor Rpn13/ADRM1 / Proteasome regulatory subunit C-terminal / 26S Proteasome non-ATPase regulatory subunit 6 / 26S proteasome regulatory subunit, C-terminal / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome non-ATPase regulatory subunit 3 / 26S Proteasome non-ATPase regulatory subunit 12 / DSS1_SEM1 / 26S proteasome regulatory subunit RPN5 C-terminal domain / 26S proteasome regulatory subunit RPN5, C-terminal domain / DSS1/SEM1 family / 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 non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit RPN2 C-terminal domain / 26S Proteasome non-ATPase regulatory subunit 13 / 26S proteasome regulatory subunit RPN2, C-terminal / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn2/Psmd1 subunit / 26S Proteasome non-ATPase regulatory subunit 7/8 / 26S Proteasome non-ATPase regulatory subunit 14 / RPN1, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / RPN1 N-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 26S Proteasome regulatory subunit 6A / 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 / CSN8/PSMD8/EIF3K family / 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 subunit beta 7 / Proteasome beta subunit, C-terminal / Proteasome beta subunits C terminal / Proteasome subunit beta 4 / Proteasome subunit beta 1 / Proteasome beta 3 subunit / Proteasome subunit beta 2 / Proteasome subunit alpha 1 / Proteasome subunit alpha4 / Proteasome subunit alpha2 / Proteasome subunit alpha6 / Proteasome subunit alpha5 / Proteasome subunit alpha 3 / VWFA domain profile. / Proteasome beta-type subunits signature. / Peptidase T1A, proteasome beta-subunit / Proteasome beta-type subunit, conserved site / AAA ATPase, AAA+ lid domain / AAA+ lid domain / Proteasome subunit A N-terminal signature / JAB/MPN domain / Proteasome alpha-type subunits signature. / JAB1/MPN/MOV34 metalloenzyme domain / Proteasome alpha-subunit, N-terminal domain / Proteasome subunit A N-terminal signature Add an annotation / von Willebrand factor, type A / MPN domain profile. / Proteasome alpha-type subunit / MPN domain / Proteasome alpha-type subunit profile. / Proteasome beta-type subunit profile. / Proteasome B-type subunit / Proteasome subunit / AAA-protein family signature. / ATPase, AAA-type, conserved site / Proteasome, subunit alpha/beta / TPR repeat profile. / TPR repeat region circular profile. / von Willebrand factor A-like domain superfamily
Similarity search - Domain/homology
26S proteasome regulatory subunit 4 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 RPN9 / Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome subunit RPT4 ...26S proteasome regulatory subunit 4 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 RPN9 / Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome subunit RPT4 / 26S proteasome regulatory subunit 8 homolog / 26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit RPN5 / 26S proteasome regulatory subunit 6B homolog / 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 29, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 21, 2018Group: Advisory / Data collection / Derived calculations
Category: pdbx_validate_close_contact / struct_conn / struct_conn_type

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Structure visualization

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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)1,581,24559
Polymers1,578,21647
Non-polymers3,02912
Water36020
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: 27359.104 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: 26844.439 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: 26749.090 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: 28259.838 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: 26924.156 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: 25355.631 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: 27005.641 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c
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)
Strain: ATCC 204508 / S288c / 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)
Strain: ATCC 204508 / S288c
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)
Strain: ATCC 204508 / S288c
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)
Strain: ATCC 204508 / S288c
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)
Strain: ATCC 204508 / S288c
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)
Strain: ATCC 204508 / S288c
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)
Strain: ATCC 204508 / S288c
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)
Strain: ATCC 204508 / S288c
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)
Strain: ATCC 204508 / S288c / 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)
Strain: ATCC 204508 / S288c / 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)
Strain: ATCC 204508 / S288c / 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)
Strain: ATCC 204508 / S288c / 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)
Strain: ATCC 204508 / S288c / 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)
Strain: ATCC 204508 / S288c / 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)
Strain: ATCC 204508 / S288c / 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)
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 (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / 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)
Strain: ATCC 204508 / S288c / 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)
Strain: ATCC 204508 / S288c / 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)
Strain: ATCC 204508 / S288c / 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)
Strain: ATCC 204508 / S288c / References: UniProt: P33299
#29: Protein 26S proteasome regulatory subunit 4 homolog / Tat-binding homolog 5


Mass: 43229.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: P40327
#30: Protein 26S proteasome regulatory subunit 6B homolog / Protein YNT1 / Tat-binding homolog 2


Mass: 43325.488 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / 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)
Strain: ATCC 204508 / S288c / 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)
Strain: ATCC 204508 / S288c / References: UniProt: P33297
#33: Protein 26S proteasome regulatory subunit 8 homolog / Protein CIM3 / Protein SUG1 / Tat-binding protein TBY1


Mass: 45110.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / References: UniProt: Q01939

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Non-polymers , 4 types, 32 molecules

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


Mass: 507.181 Da / Num. of mol.: 4 / 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.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#37: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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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: 35 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: 351984 / Symmetry type: POINT

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