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- PDB-3jcp: Structure of yeast 26S proteasome in M2 state derived from Titan ... -

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Entry
Database: PDB / ID: 3jcp
TitleStructure of yeast 26S proteasome in M2 state derived from Titan dataset
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
  • 26S protease subunit RPT4Proteasome endopeptidase complex
  • 26S proteasome complex subunit SEM1
  • Probable proteasome subunit alpha type-7
  • Ubiquitin carboxyl-terminal hydrolase RPN11
KeywordsHYDROLASE / protein complex
Function / homology26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / Proteasome subunit beta Pre3 / 26S Proteasome non-ATPase regulatory subunit 6 / 26S Proteasome non-ATPase regulatory subunit 12 / 26S Proteasome non-ATPase regulatory subunit 13 / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / von Willebrand factor A-like domain superfamily / MPN domain / Proteasome subunit alpha 3 ...26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / Proteasome subunit beta Pre3 / 26S Proteasome non-ATPase regulatory subunit 6 / 26S Proteasome non-ATPase regulatory subunit 12 / 26S Proteasome non-ATPase regulatory subunit 13 / Winged helix-like DNA-binding domain superfamily / Winged helix DNA-binding domain superfamily / von Willebrand factor A-like domain superfamily / MPN domain / Proteasome subunit alpha 3 / Proteasome subunit alpha 7-like / 26S Proteasome non-ATPase regulatory subunit 1 / Proteasomal ubiquitin receptor Rpn13/ADRM1 superfamily / ATPase family associated with various cellular activities (AAA) / Proteasome subunit / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / PCI domain / Proteasome/cyclosome repeat / Proteasome complex subunit Rpn13 ubiquitin receptor / DSS1/SEM1 family / 26S proteasome non-ATPase regulatory subunit 3 / 26S proteasome regulatory subunit 8 / CSN8/PSMD8/EIF3K family / Proteasome subunit alpha5 / Proteasome B-type subunit / Proteasome beta subunit, C-terminal / Rpn11/EIF3F, C-terminal / Proteasome subunit Rpn10 / P-loop containing nucleoside triphosphate hydrolase / Nucleophile aminohydrolases, N-terminal / CSN8/PSMD8/EIF3K / Proteasome beta 3 subunit / 26S Proteasome non-ATPase regulatory subunit 7/8 / 26S Proteasome regulatory subunit 6B / Proteasome subunit alpha6 / Proteasome subunit alpha2 / Proteasome subunit alpha4 / Proteasome subunit alpha 1 / Proteasome subunit beta 2 / Proteasome subunit beta 7 / 26S Proteasome regulatory subunit 4 / 26S Proteasome regulatory subunit 7 / 26S Proteasome regulatory subunit 6A / Proteasome regulatory subunit C-terminal / Proteasome subunit A N-terminal signature / Tetratricopeptide repeat / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Metalloprotease DUBs / Neutrophil degranulation / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / rt:r-sce-69229: / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Antigen processing: Ubiquitination & Proteasome degradation / MAPK6/MAPK4 signaling / AAA+ lid domain / Proteasomal ATPase OB C-terminal domain / HEAT repeats / 26S proteasome regulatory subunit RPN2 C-terminal domain / Rpn9 C-terminal helix / 26S proteasome regulatory subunit RPN5 C-terminal domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome subunit RPN6 C-terminal helix domain / RPN1/RPN2 N-terminal domain / Ub-specific processing proteases / TNFR2 non-canonical NF-kB pathway / 26S proteasome subunit RPN7 / MPN domain profile. / Proteasome beta subunits C terminal / Maintenance of mitochondrial structure and function / von Willebrand factor type A domain / Proteasome alpha-type subunits signature. / AAA-protein family signature. / Proteasome beta-type subunits signature. / TPR repeat profile. / VWFA domain profile. / PCI domain profile. / AUF1 (hnRNP D0) binds and destabilizes mRNA / TPR repeat region circular profile. / Ubiquitin-interacting motif (UIM) domain profile. / Proteasome alpha-type subunit profile. / Proteasome beta-type subunit profile. / Cross-presentation of soluble exogenous antigens (endosomes) / L13a-mediated translational silencing of Ceruloplasmin expression / SCF-beta-TrCP mediated degradation of Emi1 / SCF(Skp2)-mediated degradation of p27/p21 / ABC-family proteins mediated transport / Proteasome alpha-type subunit / Proteasome subunit beta 1 / 26S proteasome regulatory subunit Rpn7/COP9 signalosome complex subunit 1 / ATPase, AAA-type, conserved site / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / Peptidase T1A, proteasome beta-subunit / Proteasome alpha-subunit, N-terminal domain / JAB1/MPN/MOV34 metalloenzyme domain / Proteasome component (PCI) domain / Proteasome/cyclosome repeat / von Willebrand factor, type A
Function and homology information
Specimen sourceSaccharomyces cerevisiae S288c (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4.6 Å resolution
AuthorsLuan, B. / Huang, X.L. / Wu, J.P. / Shi, Y.G. / Wang, F.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Structure of an endogenous yeast 26S proteasome reveals two major conformational states.
Authors: Bai Luan / Xiuliang Huang / Jianping Wu / Ziqing Mei / Yiwei Wang / Xiaobin Xue / Chuangye Yan / Jiawei Wang / Daniel J Finley / Yigong Shi / Feng Wang
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jan 6, 2016 / Release: Jun 15, 2016
RevisionDateData content typeGroupProviderType
1.0Jun 15, 2016Structure modelrepositoryInitial release
1.1Jul 6, 2016Structure modelOther

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Structure viewerMolecule:
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Assembly

Deposited unit
1: Proteasome subunit beta type-6
2: Proteasome subunit beta type-7
3: Proteasome subunit beta type-1
4: Proteasome subunit beta type-2
5: Proteasome subunit beta type-3
6: Proteasome subunit beta type-4
7: Proteasome subunit beta type-5
8: Proteasome subunit beta type-6
9: 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
H: 26S protease regulatory subunit 7 homolog
I: 26S protease regulatory subunit 4 homolog
J: 26S protease regulatory subunit 8 homolog
K: 26S protease regulatory subunit 6B homolog
L: 26S protease subunit RPT4
M: 26S protease regulatory subunit 6A
N: 26S proteasome regulatory subunit RPN2
O: 26S proteasome regulatory subunit RPN9
P: 26S proteasome regulatory subunit RPN5
Q: 26S proteasome regulatory subunit RPN6
R: 26S proteasome regulatory subunit RPN7
S: 26S proteasome regulatory subunit RPN3
T: 26S proteasome regulatory subunit RPN12
U: 26S proteasome regulatory subunit RPN8
V: Ubiquitin carboxyl-terminal hydrolase RPN11
W: 26S proteasome regulatory subunit RPN10
X: 26S proteasome regulatory subunit RPN13
Y: 26S proteasome complex subunit SEM1
Z: 26S proteasome regulatory subunit RPN1
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


Theoretical massNumber of molelcules
Total (without water)1,692,66047
Polyers1,692,66047
Non-polymers00
Water0
1


  • idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Proteasome subunit beta type- ... , 7 types, 14 molecules 18293h4i5j6k7l

#1: Protein/peptide Proteasome subunit beta type-6 / / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5


Mass: 26905.076 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P23724, proteasome endopeptidase complex
#2: Protein/peptide Proteasome subunit beta type-7 / / Macropain subunit PRE4 / Multicatalytic endopeptidase complex subunit PRE4 / Proteasome component PRE4 / Proteinase YSCE subunit PRE4


Mass: 29471.289 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P30657, proteasome endopeptidase complex
#3: Protein/peptide Proteasome subunit beta type-1 / PSMB1 / Macropain subunit PRE3 / Multicatalytic endopeptidase complex subunit PRE3 / Proteasome component PRE3 / Proteinase YSCE subunit PRE3


Mass: 23573.604 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P38624, proteasome endopeptidase complex
#4: Protein/peptide Proteasome subunit beta type-2 / PSMB2 / Macropain subunit PUP1 / Multicatalytic endopeptidase complex subunit PUP1 / Proteasome component PUP1 / Proteinase YSCE subunit PUP1


Mass: 28299.889 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P25043, proteasome endopeptidase complex
#5: Protein/peptide 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: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P25451, proteasome endopeptidase complex
#6: Protein/peptide Proteasome subunit beta type-4 / PSMB4 / Macropain subunit C11 / Multicatalytic endopeptidase complex subunit C11 / Proteasome component C11 / Proteinase YSCE subunit 11


Mass: 22545.676 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P22141, proteasome endopeptidase complex
#7: Protein/peptide Proteasome subunit beta type-5 / PSMB5 / Macropain subunit PRE2 / Multicatalytic endopeptidase complex subunit PRE2 / Proteasome component PRE2 / Proteinase YSCE subunit PRE2


Mass: 31670.539 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P30656, proteasome endopeptidase complex

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

#8: Protein/peptide Proteasome subunit alpha type-1 / / 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: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P21243, proteasome endopeptidase complex
#9: Protein/peptide Proteasome subunit alpha type-2 / / Macropain subunit Y7 / Multicatalytic endopeptidase complex subunit Y7 / Proteasome component Y7 / Proteinase YSCE subunit 7


Mass: 27191.828 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P23639, proteasome endopeptidase complex
#10: Protein/peptide Proteasome subunit alpha type-3 / / Macropain subunit Y13 / Multicatalytic endopeptidase complex subunit Y13 / Proteasome component Y13 / Proteinase YSCE subunit 13


Mass: 28748.230 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P23638, proteasome endopeptidase complex
#11: Protein/peptide Proteasome subunit alpha type-4 / / Macropain subunit PRE6 / Multicatalytic endopeptidase complex subunit PRE6 / Proteasome component PRE6 / Proteinase YSCE subunit PRE6


Mass: 28478.111 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P40303, proteasome endopeptidase complex
#12: Protein/peptide Proteasome subunit alpha type-5 / / Macropain subunit PUP2 / Multicatalytic endopeptidase complex subunit PUP2 / Proteasome component PUP2 / Proteinase YSCE subunit PUP2


Mass: 28649.086 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P32379, proteasome endopeptidase complex
#13: Protein/peptide Proteasome subunit alpha type-6 / / Macropain subunit PRE5 / Multicatalytic endopeptidase complex subunit PRE5 / Proteasome component PRE5 / Proteinase YSCE subunit PRE5


Mass: 25634.000 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P40302, proteasome endopeptidase complex

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Protein/peptide , 4 types, 5 molecules GgLVY

#14: Protein/peptide Probable proteasome subunit alpha type-7 / Macropain subunit C1 / Multicatalytic endopeptidase complex subunit C1 / Proteasome component C1 / Proteinase YSCE subunit 1


Mass: 31575.068 Da / Num. of mol.: 2 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c
References: UniProt: P21242, proteasome endopeptidase complex
#19: Protein/peptide 26S protease subunit RPT4 / Proteasome endopeptidase complex / 26S protease subunit SUG2 / Proteasomal cap subunit


Mass: 49480.137 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P53549
#29: Protein/peptide Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome regulatory subunit RPN11 / Protein MPR1


Mass: 34442.281 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P43588, ubiquitinyl hydrolase 1
#32: Protein/peptide 26S proteasome complex subunit SEM1


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

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26S protease regulatory subunit ... , 5 types, 5 molecules HIJKM

#15: Protein/peptide 26S protease regulatory subunit 7 homolog / Protein CIM5 / Tat-binding homolog 3


Mass: 52054.891 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P33299
#16: Protein/peptide 26S protease regulatory subunit 4 homolog / Tat-binding homolog 5


Mass: 48898.160 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P40327
#17: Protein/peptide 26S protease regulatory subunit 8 homolog / Protein CIM3 / Protein SUG1 / Tat-binding protein TBY1


Mass: 45342.742 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q01939
#18: Protein/peptide 26S protease regulatory subunit 6B homolog / Protein YNT1 / Tat-binding homolog 2


Mass: 47953.676 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P33298
#20: Protein/peptide 26S protease regulatory subunit 6A / Tat-binding protein homolog 1 / TBP-1


Mass: 48315.727 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P33297

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

#21: Protein/peptide 26S proteasome regulatory subunit RPN2


Mass: 104351.883 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P32565
#22: Protein/peptide 26S proteasome regulatory subunit RPN9 / Proteasome non-ATPase subunit 7


Mass: 45839.348 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q04062
#23: Protein/peptide 26S proteasome regulatory subunit RPN5 / Proteasome non-ATPase subunit 5


Mass: 51840.352 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q12250
#24: Protein/peptide 26S proteasome regulatory subunit RPN6 / Proteasome non-ATPase subunit 4


Mass: 49839.812 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q12377
#25: Protein/peptide 26S proteasome regulatory subunit RPN7


Mass: 49016.367 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q06103
#26: Protein/peptide 26S proteasome regulatory subunit RPN3


Mass: 60464.605 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P40016
#27: Protein/peptide 26S proteasome regulatory subunit RPN12 / Nuclear integrity protein 1


Mass: 31952.119 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P32496
#28: Protein/peptide 26S proteasome regulatory subunit RPN8


Mass: 38365.508 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: Q08723
#30: Protein/peptide 26S proteasome regulatory subunit RPN10


Mass: 29776.098 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38886
#31: Protein/peptide 26S proteasome regulatory subunit RPN13 / Proteasome non-ATPase subunit 13


Mass: 17919.002 Da / Num. of mol.: 1 / Source: (natural) Saccharomyces cerevisiae S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: O13563
#33: Protein/peptide 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 S288c (yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38764

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeParent ID
1yeast 26S proteasome in M2 stateCOMPLEX0
226S proteasome1
Molecular weightValue: 2.5 MDa / Experimental value: NO
Buffer solutionName: 50mM Tris pH 7.5, 100mM NaCl, 5mM MgCl2, 2mM ATP / Details: 50mM Tris pH 7.5, 100mM NaCl, 5mM MgCl2, 2mM ATP / pH: 7.5
SpecimenConc.: 15 mg/ml / Embedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Quantifoil Cu R2.0/2.0 200 mesh
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Nov 2, 2015
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 / Nominal defocus max: 2.5 nm / Nominal defocus min: 1.5 nm / Cs: 2.7 mm / Camera length: 0 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 100 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingFilm or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2Relion3D reconstruction
CTF correctionDetails: Each micrographs
SymmetryPoint symmetry: C1
3D reconstructionResolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 25151
Details: The particles were selected in RELION and manually checked. 3D classification and refinement were performed in RELION. Single particle--Applied symmetry: C1
Symmetry type: POINT
Atomic model buildingDetails: REFINEMENT PROTOCOL--rigid body DETAILS--The domains were separately fitted in chimera and then manual checked in Coot. The final model is refined with Phenix.
Ref protocol: RIGID BODY FIT / Ref space: REAL
Atomic model buildingPDB-ID: 4CR2
Number of atoms included #LASTProtein: 104170 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 104170

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