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- PDB-5mpe: 26S proteasome in presence of ATP (s2) -

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Basic information

Entry
Database: PDB / ID: 5mpe
Title26S proteasome in presence of ATP (s2)
DescriptorUbiquitin carboxyl-terminal hydrolase RPN11
26S proteasome complex subunit SEM1
(26S proteasome regulatory subunit ...) x 11
KeywordsHYDROLASE / Macromolecular complex / 26S proteasome / Protease / hydrolase
Specimen sourceSaccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
MethodElectron microscopy (4.5 Å resolution / Particle / Single particle)
AuthorsWehmer, M. / Rudack, T. / Beck, F. / Aufderheide, A. / Pfeifer, G. / Plitzko, J.M. / Foerster, F. / Schulten, K. / Baumeister, W. / Sakata, E.
CitationProc. Natl. Acad. Sci. U.S.A., 2017, 114, 1305-1310

Proc. Natl. Acad. Sci. U.S.A., 2017, 114, 1305-1310 StrPapers
Structural insights into the functional cycle of the ATPase module of the 26S proteasome.
Marc Wehmer / Till Rudack / Florian Beck / Antje Aufderheide / Günter Pfeifer / Jürgen M Plitzko / Friedrich Förster / Klaus Schulten / Wolfgang Baumeister / Eri Sakata

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 16, 2016 / Release: Mar 8, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 8, 2017Structure modelrepositoryInitial release
1.1Aug 2, 2017Structure modelData collectionem_software_em_software.name

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Assembly

Deposited unit
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


Theoretical massNumber of molelcules
Total (without water)633,80613
Polyers633,80613
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_5551
MethodPISA
#2
W: 26S proteasome regulatory subunit RPN10
V: Ubiquitin carboxyl-terminal hydrolase RPN11
T: 26S proteasome regulatory subunit RPN12
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


Theoretical massNumber of molelcules
Total (without water)615,88712
Polyers615,88712
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)46590
ΔGint (kcal/M)-252
Surface area (Å2)223570
MethodPISA

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Components

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

#1: Polypeptide(L)26S proteasome regulatory subunit RPN10


Mass: 29776.098 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P38886

Cellular component

Molecular function

Biological process

  • proteasome assembly (GO: 0043248)
  • proteasome-mediated ubiquitin-dependent protein catabolic process (GO: 0043161)
  • ubiquitin-dependent protein catabolic process (GO: 0006511)
#3: Polypeptide(L)26S proteasome regulatory subunit RPN12 / Nuclear integrity protein 1


Mass: 31952.119 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P32496

Cellular component

Biological process

  • proteasome assembly (GO: 0043248)
  • proteasome-mediated ubiquitin-dependent protein catabolic process (GO: 0043161)
  • ubiquitin-dependent protein catabolic process (GO: 0006511)
#4: Polypeptide(L)26S proteasome regulatory subunit RPN13 / Proteasome non-ATPase subunit 13


Mass: 17919.002 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: O13563

Cellular component

Molecular function

Biological process

  • ubiquitin-dependent protein catabolic process (GO: 0006511)
#6: Polypeptide(L)26S proteasome regulatory subunit RPN1 / HMG-CoA reductase degradation protein 2 / Proteasome non-ATPase subunit 1


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

Cellular component

Molecular function

Biological process

  • proteasome-mediated ubiquitin-dependent protein catabolic process (GO: 0043161)
  • regulation of protein catabolic process (GO: 0042176)
  • ubiquitin-dependent protein catabolic process (GO: 0006511)
#7: Polypeptide(L)26S proteasome regulatory subunit RPN2


Mass: 104351.883 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P32565

Cellular component

Molecular function

Biological process

  • proteasome assembly (GO: 0043248)
  • proteasome-mediated ubiquitin-dependent protein catabolic process (GO: 0043161)
  • regulation of protein catabolic process (GO: 0042176)
  • ubiquitin-dependent protein catabolic process (GO: 0006511)
#8: Polypeptide(L)26S proteasome regulatory subunit RPN3


Mass: 60464.605 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P40016

Cellular component

  • proteasome regulatory particle, lid subcomplex (GO: 0008541)

Molecular function

Biological process

  • regulation of protein catabolic process (GO: 0042176)
  • ubiquitin-dependent protein catabolic process (GO: 0006511)
#9: Polypeptide(L)26S proteasome regulatory subunit RPN5 / Proteasome non-ATPase subunit 5


Mass: 51840.352 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q12250

Cellular component

Biological process

  • proteasome-mediated ubiquitin-dependent protein catabolic process (GO: 0043161)
  • protein deneddylation (GO: 0000338)
#10: Polypeptide(L)26S proteasome regulatory subunit RPN6 / Proteasome non-ATPase subunit 4


Mass: 49839.812 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q12377

Cellular component

Molecular function

Biological process

#11: Polypeptide(L)26S proteasome regulatory subunit RPN7


Mass: 49016.367 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q06103

Cellular component

Molecular function

Biological process

  • proteasome-mediated ubiquitin-dependent protein catabolic process (GO: 0043161)
  • ubiquitin-dependent protein catabolic process (GO: 0006511)
#12: Polypeptide(L)26S proteasome regulatory subunit RPN8


Mass: 38365.508 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q08723

Cellular component

Biological process

  • proteasome-mediated ubiquitin-dependent protein catabolic process (GO: 0043161)
  • ubiquitin-dependent protein catabolic process (GO: 0006511)
#13: Polypeptide(L)26S proteasome regulatory subunit RPN9 / Proteasome non-ATPase subunit 7


Mass: 45839.348 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: Q04062

Cellular component

Molecular function

Biological process

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Polypeptide(L) , 2 types, 2 molecules VY

#2: Polypeptide(L)Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome regulatory subunit RPN11 / Protein MPR1


Mass: 34442.281 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: P43588, EC: 3.4.19.12

Cellular component

Molecular function

Biological process

#5: Polypeptide(L)26S proteasome complex subunit SEM1


Mass: 10397.102 Da / Num. of mol.: 1
Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
References: UniProt: O94742

Cellular component

Biological process

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: 26S proteasome of Saccharomyces cerevisiae in presence of ATP (s2)
Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13 / Source: NATURAL
Molecular weightValue: 1.7 deg. / Units: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Saccharomyces cerevisiae S288c
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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95 % / Chamber temperature: 277 kelvins

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3500 nm / Nominal defocus min: 1500 nm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 10 sec. / Electron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
Image scansMovie frames/image: 20

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Processing

EM software
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1TOM ToolboxPARTICLE SELECTION1
2TOM2IMAGE ACQUISITION1
4CTFFIND3CTF CORRECTION1
7MDFFMODEL FITTING1
9RELION1.4INITIAL EULER ASSIGNMENT1
10RELION1.4FINAL EULER ASSIGNMENT1
11RELION1.4CLASSIFICATION1
12RELION1.4RECONSTRUCTION1
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 193337 / Symmetry type: POINT

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