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- PDB-7qo4: 26S proteasome WT-Ubp6-UbVS complex in the si state (ATPases, Rpn... -

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Basic information

Entry
Database: PDB / ID: 7qo4
Title26S proteasome WT-Ubp6-UbVS complex in the si state (ATPases, Rpn1, Ubp6, and UbVS)
Components
  • 26S proteasome regulatory subunit RPN1
  • Polyubiquitin-B
  • RPT1 isoform 1
  • RPT2 isoform 1
  • RPT3 isoform 1
  • RPT4 isoform 1
  • RPT5 isoform 1
  • RPT6 isoform 1
  • Ubiquitin carboxyl-terminal hydrolase
KeywordsMOTOR PROTEIN / Proteasome / UBP6 / Ubiquitin / Allostery
Function / homology
Function and homology information


proteasome regulatory particle assembly / proteasome-activating activity / proteasome regulatory particle, base subcomplex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway ...proteasome regulatory particle assembly / proteasome-activating activity / proteasome regulatory particle, base subcomplex / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A / Regulation of PTEN stability and activity / CDK-mediated phosphorylation and removal of Cdc6 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / regulation of protein catabolic process / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / protein deubiquitination / Ub-specific processing proteases / enzyme regulator activity / Neutrophil degranulation / proteasome complex / ubiquitin-dependent protein catabolic process / protein-macromolecule adaptor activity / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / endoplasmic reticulum / ATP hydrolysis activity / ATP binding / nucleus / cytoplasm
Similarity search - Function
26S Proteasome regulatory subunit 7 / 26S Proteasome regulatory subunit 6A / 26S proteasome regulatory subunit P45-like / 26S Proteasome regulatory subunit 6B / 26S proteasome regulatory subunit 8 / Ubiquitin carboxyl-terminal hydrolase 14-like / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / RPN1, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / RPN1 N-terminal domain ...26S Proteasome regulatory subunit 7 / 26S Proteasome regulatory subunit 6A / 26S proteasome regulatory subunit P45-like / 26S Proteasome regulatory subunit 6B / 26S proteasome regulatory subunit 8 / Ubiquitin carboxyl-terminal hydrolase 14-like / 26S proteasome regulatory complex, non-ATPase subcomplex, Rpn1 subunit / RPN1, N-terminal / 26S proteasome non-ATPase regulatory subunit RPN1, C-terminal / RPN1 N-terminal domain / 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal / Proteasome/cyclosome repeat / Proteasome/cyclosome repeat / Ubiquitin specific protease (USP) domain signature 2. / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Ubiquitin specific protease (USP) domain signature 1. / Ubiquitin specific protease, conserved site / Peptidase C19, ubiquitin carboxyl-terminal hydrolase / Ubiquitin carboxyl-terminal hydrolase / Ubiquitin specific protease domain / Ubiquitin specific protease (USP) domain profile. / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Papain-like cysteine peptidase superfamily / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Armadillo-like helical / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Armadillo-type fold / Ubiquitin-like domain superfamily / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / RPT1 isoform 1 / RPT6 isoform 1 / Ubiquitin carboxyl-terminal hydrolase / RPT3 isoform 1 / RPT2 isoform 1 / RPT5 isoform 1 / RPT4 isoform 1 / Ubiquitin B / 26S proteasome regulatory subunit RPN1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 Å
AuthorsHung, K.Y.S. / Klumpe, S. / Eisele, M.R. / Elsasser, S. / Geng, T.T. / Cheng, C. / Joshi, T. / Rudack, T. / Sakata, E. / Finley, D.
Funding support Germany, 5items
OrganizationGrant numberCountry
German Research Foundation (DFG)EXC 2067/1- 390729940 Germany
German Research Foundation (DFG)SFB1035/Project A01 Germany
German Research Foundation (DFG)CRC889/Project A11 Germany
Other governmentFoundation for the National Institutes of Health R01 GM043601
Other governmentMarie Curie Career Integration grant (PCIG14-GA-2013-631577)
CitationJournal: Nat Commun / Year: 2022
Title: Allosteric control of Ubp6 and the proteasome via a bidirectional switch.
Authors: Hung, K.Y.S. / Klumpe, S. / Eisele, M.R. / Elsasser, S. / Tian, G. / Sun, S. / Moroco, J.A. / Cheng, T.C. / Joshi, T. / Seibel, T. / Van Dalen, D. / Feng, X.H. / Lu, Y. / Ovaa, H. / Engen, J. ...Authors: Hung, K.Y.S. / Klumpe, S. / Eisele, M.R. / Elsasser, S. / Tian, G. / Sun, S. / Moroco, J.A. / Cheng, T.C. / Joshi, T. / Seibel, T. / Van Dalen, D. / Feng, X.H. / Lu, Y. / Ovaa, H. / Engen, J.R. / Lee, B.H. / Rudack, T. / Sakata, E. / Finley, D.
History
DepositionDec 23, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Z: 26S proteasome regulatory subunit RPN1
H: RPT1 isoform 1
I: RPT2 isoform 1
K: RPT3 isoform 1
L: RPT4 isoform 1
M: RPT5 isoform 1
J: RPT6 isoform 1
8: Ubiquitin carboxyl-terminal hydrolase
9: Polyubiquitin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)470,50621
Polymers467,3979
Non-polymers3,10912
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 9 types, 9 molecules ZHIKLMJ89

#1: 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 (brewer's yeast) / Strain: ATCC 204508 / S288c / References: UniProt: P38764
#2: Protein RPT1 isoform 1


Mass: 52054.891 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PV22
#3: Protein RPT2 isoform 1


Mass: 48898.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q382
#4: Protein RPT3 isoform 1


Mass: 47953.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PYF7
#5: Protein RPT4 isoform 1


Mass: 49480.137 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q8D3
#6: Protein RPT5 isoform 1


Mass: 48315.727 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5Q672
#7: Protein RPT6 isoform 1


Mass: 45342.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: A0A6A5PWS2
#8: Protein Ubiquitin carboxyl-terminal hydrolase


Mass: 57188.648 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: UBP6, GI527_G0002094 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6A5PXS0, ubiquitinyl hydrolase 1
#9: Protein Polyubiquitin-B


Mass: 8560.831 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: J3QS39

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Non-polymers , 3 types, 12 molecules

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


Mass: 507.181 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#11: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
#12: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Details

Has ligand of interestN

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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

Component
IDNameTypeEntity IDParent-IDSource
126S proteasome WT-Ubp6-UbVS complex in the si stateCOMPLEX#1-#90MULTIPLE SOURCES
2yeast WT 26S proteasome body2 (ATPase, Rpn1)COMPLEX#1-#71NATURAL
3Ubp6-UbVSCOMPLEX#8-#91RECOMBINANT
Molecular weightValue: 2.5 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Saccharomyces cerevisiae (brewer's yeast)4932
23Saccharomyces cerevisiae (brewer's yeast)4932
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / 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 FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 88243 / Symmetry type: POINT

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