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- PDB-5t0j: Structural basis for dynamic regulation of the human 26S proteasome -

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Entry
Database: PDB / ID: 5t0j
TitleStructural basis for dynamic regulation of the human 26S proteasome
Components
  • (26S protease regulatory subunit ...) x 6
  • (26S proteasome non-ATPase regulatory subunit ...) x 11
  • (Proteasome subunit alpha type- ...) x 7
  • (Proteasome subunit beta type- ...) x 7
  • 26S proteasome complex subunit DSS1
KeywordsHYDROLASE / ubiquitin-proteasome system / AAA-ATPase
Function / homology26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / CSN8/PSMD8/EIF3K family / von Willebrand factor A-like domain superfamily / MPN domain / Proteasome subunit alpha 3 / Proteasome subunit beta 5 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / ATPase family associated with various cellular activities (AAA) / Proteasome subunit / JAB1/Mov34/MPN/PAD-1 ubiquitin protease ...26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / CSN8/PSMD8/EIF3K family / von Willebrand factor A-like domain superfamily / MPN domain / Proteasome subunit alpha 3 / Proteasome subunit beta 5 / 26S Proteasome non-ATPase regulatory subunit 12/COP9 signalosome complex subunit 4 / ATPase family associated with various cellular activities (AAA) / Proteasome subunit / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / PCI domain / Proteasome/cyclosome repeat / Ubiquitin interaction motif / DSS1/SEM1 family / Proteasome regulatory subunit C-terminal / Proteasome subunit A N-terminal signature / Winged helix-like DNA-binding domain superfamily / 26S proteasome subunit RPN7 / Proteasome beta subunits C terminal / Maintenance of mitochondrial structure and function / von Willebrand factor type A domain / Proteasomal ATPase OB C-terminal domain / Proteasome alpha-type subunits signature. / AAA-protein family signature. / Proteasome beta-type subunits signature. / VWFA domain profile. / MPN domain profile. / PCI domain profile. / Ubiquitin-interacting motif (UIM) domain profile. / Proteasome alpha-type subunit profile. / Proteasome beta-type subunit profile. / Winged helix DNA-binding domain superfamily / 26S Proteasome non-ATPase regulatory subunit 14 / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Proteasome subunit beta 6 / Proteasome beta subunit, C-terminal / Rpn11/EIF3F, C-terminal / Proteasome subunit Rpn10 / P-loop containing nucleoside triphosphate hydrolase / Nucleophile aminohydrolases, N-terminal / Proteasomal ATPase OB C-terminal domain / CSN8/PSMD8/EIF3K / Proteasome beta 3 subunit / Proteasome subunit alpha5 / 26S Proteasome non-ATPase regulatory subunit 7/8 / Proteasome subunit alpha6 / Proteasome subunit alpha2 / Proteasome subunit alpha4 / Proteasome subunit alpha 7 / 26S Proteasome non-ATPase regulatory subunit 13 / Proteasome subunit beta 1 / Proteasome subunit beta 2 / Proteasome subunit beta 7 / 26S Proteasome regulatory subunit 4 / 26S Proteasome regulatory subunit 7 / 26S Proteasome regulatory subunit 6A / 26S Proteasome regulatory subunit 6B / 26S proteasome regulatory subunit 8 / 26S proteasome regulatory subunit 10B / 26S Proteasome non-ATPase regulatory subunit 1 / 26S proteasome non-ATPase regulatory subunit 3 / 26S Proteasome non-ATPase regulatory subunit 6 / 26S Proteasome non-ATPase regulatory subunit 11 / 26S Proteasome non-ATPase regulatory subunit 12 / Activation of NF-kappaB in B cells / ER-Phagosome pathway / Proteasome alpha-type subunit / RUNX1 regulates transcription of genes involved in differentiation of HSCs / MAPK6/MAPK4 signaling / UCH proteinases / Ub-specific processing proteases / Metalloprotease DUBs / Neutrophil degranulation / CDT1 association with the CDC6:ORC:origin complex / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin-dependent degradation of Cyclin D1 / G2/M Checkpoints / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / The role of GTSE1 in G2/M progression after G2 checkpoint / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / Regulation of RUNX2 expression and activity / NIK-->noncanonical NF-kB signaling / Regulation of RUNX3 expression and activity / Regulation of PTEN stability and activity / Neddylation / Regulation of expression of SLITs and ROBOs / Interleukin-1 signaling / Negative regulation of NOTCH4 signaling / Antigen processing: Ubiquitination & Proteasome degradation / AAA+ lid domain / HEAT repeats / RPN1/RPN2 N-terminal domain / 26S proteasome regulatory subunit RPN2 C-terminal domain / 26S proteasome regulatory subunit RPN5 C-terminal domain / 26S proteasome regulatory subunit RPN6 N-terminal domain / 26S proteasome subunit RPN6 C-terminal helix domain / Defective CFTR causes cystic fibrosis / TNFR2 non-canonical NF-kB pathway / Cross-presentation of soluble exogenous antigens (endosomes)
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 8 Å resolution
AuthorsChen, S. / Wu, J. / Lu, Y. / Ma, Y.B. / Lee, B.H. / Yu, Z. / Ouyang, Q. / Finley, D. / Kirschner, M.W. / Mao, Y.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Structural basis for dynamic regulation of the human 26S proteasome.
Authors: Shuobing Chen / Jiayi Wu / Ying Lu / Yong-Bei Ma / Byung-Hoon Lee / Zhou Yu / Qi Ouyang / Daniel J Finley / Marc W Kirschner / Youdong Mao
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 16, 2016 / Release: Oct 19, 2016
RevisionDateData content typeGroupProviderType
1.0Oct 19, 2016Structure modelrepositoryInitial release
1.1Nov 16, 2016Structure modelDatabase references
1.2Nov 30, 2016Structure modelDatabase references

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Structure visualization

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Assembly

Deposited unit
f: 26S proteasome non-ATPase regulatory subunit 2
G: Proteasome subunit alpha type-6
H: Proteasome subunit alpha type-2
I: Proteasome subunit alpha type-4
J: Proteasome subunit alpha type-7
K: Proteasome subunit alpha type-5
L: Proteasome subunit alpha type-1
M: Proteasome subunit alpha type-3
N: Proteasome subunit beta type-6
O: Proteasome subunit beta type-7
P: Proteasome subunit beta type-3
Q: Proteasome subunit beta type-2
R: Proteasome subunit beta type-5
S: Proteasome subunit beta type-1
T: Proteasome subunit beta type-4
A: 26S protease regulatory subunit 7
B: 26S protease regulatory subunit 4
D: 26S protease regulatory subunit 6B
E: 26S protease regulatory subunit 10B
F: 26S protease regulatory subunit 6A
C: 26S protease regulatory subunit 8
U: 26S proteasome non-ATPase regulatory subunit 1
V: 26S proteasome non-ATPase regulatory subunit 3
W: 26S proteasome non-ATPase regulatory subunit 12
X: 26S proteasome non-ATPase regulatory subunit 11
Y: 26S proteasome non-ATPase regulatory subunit 6
Z: 26S proteasome non-ATPase regulatory subunit 7
a: 26S proteasome non-ATPase regulatory subunit 13
b: 26S proteasome non-ATPase regulatory subunit 4
c: 26S proteasome non-ATPase regulatory subunit 14
d: 26S proteasome non-ATPase regulatory subunit 8
e: 26S proteasome complex subunit DSS1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,265,68737
Polyers1,263,59332
Non-polymers2,0945
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area (Å2)141030
ΔGint (kcal/M)-643
Surface area (Å2)435050

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Components

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26S proteasome non-ATPase regulatory subunit ... , 11 types, 11 molecules fUVWXYZabcd

#1: Protein/peptide 26S proteasome non-ATPase regulatory subunit 2 / 26S proteasome regulatory subunit RPN1 / 26S proteasome regulatory subunit S2 / 26S proteasome subunit p97 / Protein 55.11 / Tumor necrosis factor type 1 receptor-associated protein 2


Mass: 82278.297 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q13200
#22: Protein/peptide 26S proteasome non-ATPase regulatory subunit 1 / 26S proteasome regulatory subunit RPN2 / 26S proteasome regulatory subunit S1 / 26S proteasome subunit p112


Mass: 105958.234 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q99460
#23: Protein/peptide 26S proteasome non-ATPase regulatory subunit 3 / 26S proteasome regulatory subunit RPN3 / 26S proteasome regulatory subunit S3 / Proteasome subunit p58


Mass: 60935.297 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O43242
#24: Protein/peptide 26S proteasome non-ATPase regulatory subunit 12 / 26S proteasome regulatory subunit RPN5 / 26S proteasome regulatory subunit p55


Mass: 52979.359 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O00232
#25: Protein/peptide 26S proteasome non-ATPase regulatory subunit 11 / 26S proteasome regulatory subunit RPN6 / 26S proteasome regulatory subunit S9 / 26S proteasome regulatory subunit p44.5


Mass: 47526.688 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: O00231
#26: Protein/peptide 26S proteasome non-ATPase regulatory subunit 6 / 26S proteasome regulatory subunit RPN7 / 26S proteasome regulatory subunit S10 / Breast cancer-associated protein SGA-113M / Phosphonoformate immuno-associated protein 4 / Proteasome regulatory particle subunit p44S10 / p42A


Mass: 45592.285 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q15008
#27: Protein/peptide 26S proteasome non-ATPase regulatory subunit 7 / 26S proteasome regulatory subunit RPN8 / 26S proteasome regulatory subunit S12 / Mov34 protein homolog / Proteasome subunit p40


Mass: 37086.441 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P51665
#28: Protein/peptide 26S proteasome non-ATPase regulatory subunit 13 / 26S proteasome regulatory subunit RPN9 / 26S proteasome regulatory subunit S11 / 26S proteasome regulatory subunit p40.5


Mass: 42995.359 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UNM6
#29: Protein/peptide 26S proteasome non-ATPase regulatory subunit 4 / 26S proteasome regulatory subunit RPN10 / 26S proteasome regulatory subunit S5A / Antisecretory factor 1 / ASF / Multiubiquitin chain-binding protein


Mass: 40781.590 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P55036
#30: Protein/peptide 26S proteasome non-ATPase regulatory subunit 14 / 26S proteasome regulatory subunit RPN11 / 26S proteasome-associated PAD1 homolog 1


Mass: 34488.824 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
References: UniProt: O00487, Hydrolases, Acting on peptide bonds (peptidases), Omega peptidases
#31: Protein/peptide 26S proteasome non-ATPase regulatory subunit 8 / 26S proteasome regulatory subunit RPN12 / 26S proteasome regulatory subunit S14 / p31


Mass: 39536.676 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P48556

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Proteasome subunit alpha type- ... , 7 types, 7 molecules GHIJKLM

#2: Protein/peptide Proteasome subunit alpha type-6 / / 27 kDa prosomal protein / p27K / Macropain iota chain / Multicatalytic endopeptidase complex iota chain / Proteasome iota chain


Mass: 27301.262 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
References: UniProt: P60900, proteasome endopeptidase complex
#3: Protein/peptide Proteasome subunit alpha type-2 / / Macropain subunit C3 / Multicatalytic endopeptidase complex subunit C3 / Proteasome component C3


Mass: 25796.338 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
References: UniProt: P25787, proteasome endopeptidase complex
#4: Protein/peptide Proteasome subunit alpha type-4 / / Macropain subunit C9 / Multicatalytic endopeptidase complex subunit C9 / Proteasome component C9 / Proteasome subunit L


Mass: 29394.648 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
References: UniProt: P25789, proteasome endopeptidase complex
#5: Protein/peptide Proteasome subunit alpha type-7 / / Proteasome subunit RC6-1 / Proteasome subunit XAPC7


Mass: 27798.695 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
References: UniProt: O14818, proteasome endopeptidase complex
#6: Protein/peptide Proteasome subunit alpha type-5 / / Macropain zeta chain / Multicatalytic endopeptidase complex zeta chain / Proteasome zeta chain


Mass: 26304.779 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
References: UniProt: P28066, proteasome endopeptidase complex
#7: Protein/peptide Proteasome subunit alpha type-1 / / 30 kDa prosomal protein / PROS-30 / Macropain subunit C2 / Multicatalytic endopeptidase complex subunit C2 / Proteasome component C2 / Proteasome nu chain


Mass: 30150.277 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
References: UniProt: P25786, proteasome endopeptidase complex
#8: Protein/peptide Proteasome subunit alpha type-3 / / Macropain subunit C8 / Multicatalytic endopeptidase complex subunit C8 / Proteasome component C8


Mass: 28338.057 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
References: UniProt: P25788, proteasome endopeptidase complex

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Proteasome subunit beta type- ... , 7 types, 7 molecules NOPQRST

#9: Protein/peptide Proteasome subunit beta type-6 / / Macropain delta chain / Multicatalytic endopeptidase complex delta chain / Proteasome delta chain / Proteasome subunit Y


Mass: 25246.455 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
References: UniProt: P28072, proteasome endopeptidase complex
#10: Protein/peptide Proteasome subunit beta type-7 / / Macropain chain Z / Multicatalytic endopeptidase complex chain Z / Proteasome subunit Z


Mass: 29869.223 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
References: UniProt: Q99436, proteasome endopeptidase complex
#11: Protein/peptide Proteasome subunit beta type-3 / PSMB3 / Proteasome chain 13 / Proteasome component C10-II / Proteasome theta chain


Mass: 22841.701 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
References: UniProt: P49720, proteasome endopeptidase complex
#12: Protein/peptide Proteasome subunit beta type-2 / PSMB2 / Macropain subunit C7-I / Multicatalytic endopeptidase complex subunit C7-I / Proteasome component C7-I


Mass: 22864.277 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
References: UniProt: P49721, proteasome endopeptidase complex
#13: Protein/peptide Proteasome subunit beta type-5 / PSMB5 / Macropain epsilon chain / Multicatalytic endopeptidase complex epsilon chain / Proteasome chain 6 / Proteasome epsilon chain / Proteasome subunit MB1 / Proteasome subunit X


Mass: 28379.053 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
References: UniProt: P28074, proteasome endopeptidase complex
#14: Protein/peptide Proteasome subunit beta type-1 / PSMB1 / Macropain subunit C5 / Multicatalytic endopeptidase complex subunit C5 / Proteasome component C5 / Proteasome gamma chain


Mass: 26391.201 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
References: UniProt: P20618, proteasome endopeptidase complex
#15: Protein/peptide Proteasome subunit beta type-4 / PSMB4 / 26 kDa prosomal protein / PROS-26 / Macropain beta chain / Multicatalytic endopeptidase complex beta chain / Proteasome beta chain / Proteasome chain 3 / HsN3


Mass: 29099.986 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human)
References: UniProt: P28070, proteasome endopeptidase complex

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26S protease regulatory subunit ... , 6 types, 6 molecules ABDEFC

#16: Protein/peptide 26S protease regulatory subunit 7 / 26S proteasome AAA-ATPase subunit RPT1 / Proteasome 26S subunit ATPase 2 / Protein MSS1


Mass: 48700.805 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P35998
#17: Protein/peptide 26S protease regulatory subunit 4 / P26s4 / 26S proteasome AAA-ATPase subunit RPT2 / Proteasome 26S subunit ATPase 1


Mass: 49260.504 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P62191
#18: Protein/peptide 26S protease regulatory subunit 6B / 26S proteasome AAA-ATPase subunit RPT3 / MB67-interacting protein / MIP224 / Proteasome 26S subunit ATPase 4 / Tat-binding protein 7 / TBP-7


Mass: 47426.141 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P43686
#19: Protein/peptide 26S protease regulatory subunit 10B


Mass: 45867.027 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: A0A087X2I1, UniProt: P62333*PLUS
#20: Protein/peptide 26S protease regulatory subunit 6A / 26S proteasome AAA-ATPase subunit RPT5 / Proteasome 26S subunit ATPase 3 / Proteasome subunit P50 / Tat-binding protein 1 / TBP-1


Mass: 49266.457 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P17980
#21: Protein/peptide 26S protease regulatory subunit 8 / 26S proteasome AAA-ATPase subunit RPT6 / Proteasome 26S subunit ATPase 5 / Proteasome subunit p45 / Thyroid hormone receptor-interacting protein 1 / TRIP1 / p45/SUG


Mass: 44852.121 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P62195

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Protein/peptide , 1 types, 1 molecules e

#32: Protein/peptide 26S proteasome complex subunit DSS1 / Deleted in split hand/split foot protein 1 / Split hand/foot deleted protein 1 / Split hand/foot malformation type 1 protein


Mass: 8284.611 Da / Num. of mol.: 1 / Source: (natural) Homo sapiens (human) / References: UniProt: P60896

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Non-polymers , 2 types, 5 molecules

#33: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#34: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Formula: Zn / Zinc

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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

ComponentName: Human 26S proteasome holoenzyme / Type: COMPLEX
Entity ID: 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32
Source: MULTIPLE SOURCES
Molecular weightValue: 2.5 MDa / Experimental value: YES
Buffer solutionpH: 7.5
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 30 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: 8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 14382 / Symmetry type: POINT

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