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- PDB-5mpc: 26S proteasome in presence of BeFx (s4) -

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Basic information

Entry
Database: PDB / ID: 5mpc
Title26S proteasome in presence of BeFx (s4)
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
  • (Ubiquitin carboxyl-terminal hydrolase ...) x 2
  • 26S protease subunit RPT4Proteasome endopeptidase complex
  • 26S proteasome complex subunit SEM1Proteasome
  • Probable proteasome subunit alpha type-7
KeywordsHYDROLASE / Macromolecular complex / 26S proteasome / Protease
Function / homology
Function and homology information


mitochondria-associated ubiquitin-dependent protein catabolic process / negative regulation of proteasomal protein catabolic process / SAGA complex localization to transcription regulatory region / regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome storage granule assembly / peroxisome fission / transcription export complex 2 / maintenance of DNA trinucleotide repeats / proteasome regulatory particle assembly / protein deneddylation ...mitochondria-associated ubiquitin-dependent protein catabolic process / negative regulation of proteasomal protein catabolic process / SAGA complex localization to transcription regulatory region / regulation of proteasomal ubiquitin-dependent protein catabolic process / proteasome storage granule assembly / peroxisome fission / transcription export complex 2 / maintenance of DNA trinucleotide repeats / proteasome regulatory particle assembly / protein deneddylation / protein-containing complex localization => GO:0031503 / nonfunctional rRNA decay / filamentous growth / 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 / K48-linked polyubiquitin modification-dependent protein binding / 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 / endopeptidase activator activity / proteasome core complex / isopeptidase activity / proteasome complex / proteasome core complex, beta-subunit complex / proteasome endopeptidase complex / proteasome core complex, alpha-subunit complex / proteasome assembly / 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 / 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 / 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
Ubiquitin carboxyl-terminal hydrolase 14-like / Proteasome subunit Rpn10 / Rpn9 C-terminal helix / Rpn9, C-terminal helix / 26S proteasome regulatory subunit 8 / HEAT repeats / Pru (pleckstrin-like receptor for ubiquitin) domain profile. / Proteasome complex subunit Rpn13 ubiquitin receptor / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Proteasomal ubiquitin receptor Rpn13/ADRM1 ...Ubiquitin carboxyl-terminal hydrolase 14-like / Proteasome subunit Rpn10 / Rpn9 C-terminal helix / Rpn9, C-terminal helix / 26S proteasome regulatory subunit 8 / HEAT repeats / Pru (pleckstrin-like receptor for ubiquitin) domain profile. / Proteasome complex subunit Rpn13 ubiquitin receptor / Proteasomal ubiquitin receptor Rpn13/ADRM1, Pru domain superfamily / Proteasomal ubiquitin receptor Rpn13/ADRM1 / 26S Proteasome non-ATPase regulatory subunit 6 / 26S proteasome regulatory subunit, C-terminal / Proteasome regulatory subunit C-terminal / 26S proteasome non-ATPase regulatory subunit Rpn12 / 26S proteasome non-ATPase regulatory subunit 3 / DSS1/SEM1 family / 26S proteasome regulatory subunit RPN5, C-terminal domain / DSS1/SEM1 / 26S Proteasome non-ATPase regulatory subunit 12 / 26S proteasome regulatory subunit RPN5 C-terminal domain / 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 non-ATPase regulatory subunit 1 / 26S Proteasome non-ATPase regulatory subunit 13 / 26S proteasome regulatory subunit RPN2 C-terminal domain / 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 / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / RPN1 N-terminal domain / RPN1, N-terminal / 26S proteasome subunit RPN7 / 26S Proteasome regulatory subunit 6A / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / 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 / Proteasome/cyclosome repeat / von Willebrand factor type A domain / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / 26S proteasome regulatory subunit P45-like / Proteasomal ATPase OB C-terminal domain / Maintenance of mitochondrial structure and function / Proteasomal ATPase OB C-terminal domain / Rpn11/EIF3F, C-terminal / Ubiquitin specific protease (USP) domain signature 2. / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Ubiquitin carboxyl-terminal hydrolase / motif in proteasome subunits, Int-6, Nip-1 and TRIP-15 / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / PCI domain / PCI domain profile. / Proteasome component (PCI) domain / Ubiquitin specific protease (USP) domain profile. / Ubiquitin specific protease domain / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / 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 subunit beta 2 / Proteasome beta 3 subunit / Proteasome subunit alpha 1 / Proteasome subunit alpha2 / Proteasome subunit alpha6 / Proteasome subunit alpha4 / 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 / Proteasome alpha-type subunits signature. / Proteasome subunit A N-terminal signature / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / Proteasome subunit A N-terminal signature Add an annotation / Proteasome alpha-subunit, N-terminal domain / von Willebrand factor, type A / Proteasome alpha-type subunit profile. / Proteasome alpha-type subunit / MPN domain profile. / AAA ATPase, AAA+ lid domain / MPN domain / AAA+ lid domain / Proteasome B-type subunit
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 8 homolog / Ubiquitin carboxyl-terminal hydrolase RPN11 / Ubiquitin carboxyl-terminal hydrolase 6 ...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 8 homolog / Ubiquitin carboxyl-terminal hydrolase RPN11 / Ubiquitin carboxyl-terminal hydrolase 6 / 26S proteasome subunit RPT4 / 26S proteasome regulatory subunit RPN5 / 26S proteasome regulatory subunit RPN9 / 26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit RPN8 / 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: 7.7 Å
AuthorsWehmer, M. / Rudack, T. / Beck, F. / Aufderheide, A. / Pfeifer, G. / Plitzko, J.M. / Foerster, F. / Schulten, K. / Baumeister, W. / Sakata, E.
Funding support Germany, United States, 3items
OrganizationGrant numberCountry
German Research FoundationSFB-1035 Germany
National Science FoundationPHY1430124 United States
National Institutes of Health9P41GM104601 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Structural insights into the functional cycle of the ATPase module of the 26S proteasome.
Authors: Marc Wehmer / Till Rudack / Florian Beck / Antje Aufderheide / Günter Pfeifer / Jürgen M Plitzko / Friedrich Förster / Klaus Schulten / Wolfgang Baumeister / Eri Sakata /
Abstract: In eukaryotic cells, the ubiquitin-proteasome system (UPS) is responsible for the regulated degradation of intracellular proteins. The 26S holocomplex comprises the core particle (CP), where ...In eukaryotic cells, the ubiquitin-proteasome system (UPS) is responsible for the regulated degradation of intracellular proteins. The 26S holocomplex comprises the core particle (CP), where proteolysis takes place, and one or two regulatory particles (RPs). The base of the RP is formed by a heterohexameric AAA ATPase module, which unfolds and translocates substrates into the CP. Applying single-particle cryo-electron microscopy (cryo-EM) and image classification to samples in the presence of different nucleotides and nucleotide analogs, we were able to observe four distinct conformational states (s1 to s4). The resolution of the four conformers allowed for the construction of atomic models of the AAA ATPase module as it progresses through the functional cycle. In a hitherto unobserved state (s4), the gate controlling access to the CP is open. The structures described in this study allow us to put forward a model for the 26S functional cycle driven by ATP hydrolysis.
History
DepositionDec 16, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 2, 2017Group: Data collection / Category: em_software / Item: _em_software.name

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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
H: 26S protease regulatory subunit 7 homolog
I: 26S protease regulatory subunit 4 homolog
K: 26S protease regulatory subunit 6B homolog
L: 26S protease subunit RPT4
M: 26S protease regulatory subunit 6A
J: 26S protease regulatory subunit 8 homolog
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
8: Ubiquitin carboxyl-terminal hydrolase 6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,752,87760
Polymers1,749,84948
Non-polymers3,02912
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area244950 Å2
ΔGint-952 kcal/mol
Surface area525770 Å2
MethodPISA

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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: 28033.830 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: 27191.828 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: 28748.230 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: 28478.111 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: 28649.086 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: 25634.000 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 , 3 types, 4 molecules gGLY

#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: 31575.068 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
#18: 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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P53549
#25: 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

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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: 23573.604 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: 28299.889 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: 22627.842 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: 22545.676 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: 31670.539 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: 26905.076 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: 29471.289 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 protease regulatory subunit ... , 5 types, 5 molecules HIKMJ

#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 (strain ATCC 204508 / S288c) (yeast)
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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P40327
#17: 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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P33298
#19: 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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P33297
#20: 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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q01939

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

#21: 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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P38886
#23: 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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P32496
#24: 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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: O13563
#26: 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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P38764
#27: 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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P32565
#28: 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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P40016
#29: 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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q12250
#30: 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
#31: 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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q06103
#32: 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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q08723
#33: 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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: Q04062

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Ubiquitin carboxyl-terminal hydrolase ... , 2 types, 2 molecules V8

#22: 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 (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P43588, ubiquitinyl hydrolase 1
#34: Protein Ubiquitin carboxyl-terminal hydrolase 6 / Deubiquitinating enzyme 6 / Ubiquitin thioesterase 6 / Ubiquitin-specific-processing protease 6


Mass: 57188.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
References: UniProt: P43593, ubiquitinyl hydrolase 1

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Non-polymers , 3 types, 12 molecules

#35: 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
#36: Chemical
ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#37: 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

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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 proteasome of Saccharomyces cerevisiae in presence of BeFx (s4)
Type: COMPLEX / Entity ID: #1-#34 / Source: NATURAL
Molecular weightValue: 1.7 MDa / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288c (yeast)
Buffer solutionpH: 7.4
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 277 K

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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 / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansMovie frames/image: 7

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Processing

EM software
IDNameVersionCategory
1TOM Toolboxparticle selection
2EPUimage acquisition
4CTFFIND3CTF correction
7MDFFmodel fitting
9RELION1.4initial Euler assignment
10RELION1.4final Euler assignment
11RELION1.4classification
12RELION1.43D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27600 / Symmetry type: POINT

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