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- PDB-5mpd: 26S proteasome in presence of ATP (s1) -

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Entry
Database: PDB / ID: 5mpd
Title26S proteasome in presence of ATP (s1)
DescriptorUbiquitin carboxyl-terminal hydrolase RPN11
(26S PROTEASOME ...) x 12
KeywordsHYDROLASE / Macromolecular complex / 26S proteasome / Protease / hydrolase
Specimen sourceSaccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast / Baker's yeast /
MethodElectron microscopy (4.1 A resolution / 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

DateDeposition: Dec 16, 2016 / Release: Mar 8, 2017

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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
Buried area (A2)44960
ΔGint (kcal/M)-245
Surface area (A2)235420
MethodPISA

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Components

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26S PROTEASOME ... , 12 types, 12 molecules WTXYZNSPQRUO

#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
#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
#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
#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
#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
#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
#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
#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
#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
#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
#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
#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

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Polypeptide(L) , 1 types, 1 molecules V

#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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: 26S proteasome of Saccharomyces cerevisiae in presence of ATP (s1)
Type: COMPLEX
Specimen supportGrid material: COPPER / Grid mesh size: 400 /inch.
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE-PROPANE / Humidity: 95

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Electron microscopy imaging

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

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Processing

3D reconstructionResolution: 4.1 A / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 286500

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