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- PDB-5w83: Rpn8/Rpn11 dimer complex -

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Basic information

Entry
Database: PDB / ID: 5w83
TitleRpn8/Rpn11 dimer complex
Components
  • 26S proteasome regulatory subunit RPN8
  • Ubiquitin carboxyl-terminal hydrolase RPN11
KeywordsHYDROLASE / Protease
Function / homology
Function and homology information


peroxisome fission / proteasome storage granule assembly / proteasome regulatory particle, lid subcomplex / mitochondrial fission / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ub-specific processing proteases / proteasome binding / protein deubiquitination / proteasome storage granule ...peroxisome fission / proteasome storage granule assembly / proteasome regulatory particle, lid subcomplex / mitochondrial fission / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ub-specific processing proteases / proteasome binding / protein deubiquitination / proteasome storage granule / proteasome assembly / Neutrophil degranulation / proteasome complex / metallopeptidase activity / ubiquitin-dependent protein catabolic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ubiquitinyl hydrolase 1 / cysteine-type deubiquitinase activity / mitochondrion / metal ion binding / nucleus / cytosol
Similarity search - Function
Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / 26S Proteasome non-ATPase regulatory subunit 7/8 / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. ...Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / 26S Proteasome non-ATPase regulatory subunit 7/8 / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain / JAB1/MPN/MOV34 metalloenzyme domain / MPN domain / MPN domain profile. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome regulatory subunit RPN8
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.554 Å
AuthorsDong, K.C. / Worden, E.J. / Martin, A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
National Science Foundation (NSF, United States) United States
CitationJournal: Mol. Cell / Year: 2017
Title: An AAA Motor-Driven Mechanical Switch in Rpn11 Controls Deubiquitination at the 26S Proteasome.
Authors: Worden, E.J. / Dong, K.C. / Martin, A.
History
DepositionJun 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 6, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 23, 2022Group: Advisory / Author supporting evidence / Database references
Category: database_2 / pdbx_audit_support / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 26S proteasome regulatory subunit RPN8
B: Ubiquitin carboxyl-terminal hydrolase RPN11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,3123
Polymers63,2462
Non-polymers651
Water3,729207
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-67 kcal/mol
Surface area15490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.720, 74.990, 82.470
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 26S proteasome regulatory subunit RPN8


Mass: 38365.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPN8, YOR261C, O5360 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08723
#2: Protein Ubiquitin carboxyl-terminal hydrolase RPN11 / 26S proteasome regulatory subunit RPN11 / Protein MPR1


Mass: 24880.621 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c / Gene: RPN11, MPR1, YFR004W / Production host: Escherichia coli (E. coli) / References: UniProt: P43588, ubiquitinyl hydrolase 1
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 207 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.44 Å3/Da / Density % sol: 14.31 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: 1.5 M ammonium tartrate pH 6.8

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.55→55.482 Å / Num. obs: 52965 / % possible obs: 99 % / Redundancy: 2 % / Net I/σ(I): 13.1

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O8X

4o8x


Resolution: 1.554→55.482 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2344 1990 3.77 %
Rwork0.2135 --
obs0.2143 52719 99.3 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.554→55.482 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2601 0 1 207 2809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072718
X-RAY DIFFRACTIONf_angle_d0.983687
X-RAY DIFFRACTIONf_dihedral_angle_d23.2171000
X-RAY DIFFRACTIONf_chiral_restr0.066420
X-RAY DIFFRACTIONf_plane_restr0.006473
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5545-1.59340.4121300.38523302X-RAY DIFFRACTION92
1.5934-1.63650.38131410.35333581X-RAY DIFFRACTION100
1.6365-1.68460.33311410.3313584X-RAY DIFFRACTION100
1.6846-1.7390.32421410.31053600X-RAY DIFFRACTION100
1.739-1.80110.30391420.28483614X-RAY DIFFRACTION100
1.8011-1.87330.28781410.25923616X-RAY DIFFRACTION100
1.8733-1.95850.21951410.2293607X-RAY DIFFRACTION100
1.9585-2.06180.24171430.21393630X-RAY DIFFRACTION100
2.0618-2.1910.20481420.21023622X-RAY DIFFRACTION100
2.191-2.36010.21981440.1973649X-RAY DIFFRACTION100
2.3601-2.59760.19571430.20873665X-RAY DIFFRACTION100
2.5976-2.97350.25161440.20973682X-RAY DIFFRACTION100
2.9735-3.74620.20181460.19763719X-RAY DIFFRACTION100
3.7462-55.51770.23561510.19113858X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 11.1005 Å / Origin y: 18.6694 Å / Origin z: 19.6081 Å
111213212223313233
T0.1504 Å20.0007 Å2-0.0029 Å2-0.1915 Å20.059 Å2--0.199 Å2
L1.6671 °2-1.1175 °2-1.2655 °2-2.6119 °21.6948 °2--3.1439 °2
S-0.1141 Å °-0.187 Å °-0.0199 Å °0.1912 Å °0.0799 Å °0.0261 Å °0.1121 Å °0.0877 Å °0.0269 Å °
Refinement TLS groupSelection details: all

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