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- PDB-4o8y: Zinc-free Rpn11 in complex with Rpn8 -

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Basic information

Entry
Database: PDB / ID: 4o8y
TitleZinc-free Rpn11 in complex with Rpn8
Components
  • 26S proteasome regulatory subunit RPN11
  • 26S proteasome regulatory subunit RPN8
KeywordsHYDROLASE / MPN JAMM / deubiquitinase
Function / homology
Function and homology information


Metalloprotease DUBs / proteasome storage granule assembly / peroxisome fission / mitochondrial fission / proteasome regulatory particle, lid subcomplex / metal-dependent deubiquitinase activity / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / TNFR2 non-canonical NF-kB pathway / Ubiquitin-Mediated Degradation of Phosphorylated Cdc25A ...Metalloprotease DUBs / proteasome storage granule assembly / peroxisome fission / mitochondrial fission / proteasome regulatory particle, lid subcomplex / metal-dependent deubiquitinase activity / Proteasome assembly / 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 / proteasome binding / Orc1 removal from chromatin / MAPK6/MAPK4 signaling / proteasome storage granule / Antigen processing: Ubiquitination & Proteasome degradation / protein deubiquitination / Ub-specific processing proteases / 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 / : / 26S proteasome regulatory subunit RPN11 C-terminal domain / Rpn11/EIF3F, C-terminal / Maintenance of mitochondrial structure and function / : / JAB1/Mov34/MPN/PAD-1 ubiquitin protease / JAB/MPN domain ...Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / 26S Proteasome non-ATPase regulatory subunit 7/8 / : / 26S proteasome regulatory subunit RPN11 C-terminal domain / 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 / molecular replacement / Resolution: 1.95 Å
AuthorsWorden, E.J. / Padovani, C. / Martin, A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2014
Title: Structure of the Rpn11-Rpn8 dimer reveals mechanisms of substrate deubiquitination during proteasomal degradation.
Authors: Worden, E.J. / Padovani, C. / Martin, A.
History
DepositionDec 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2014Group: Database references
Revision 1.2Mar 19, 2014Group: Database references
Revision 1.3Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: 26S proteasome regulatory subunit RPN11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,23823
Polymers47,9352
Non-polymers1,30321
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint11 kcal/mol
Surface area16930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.405, 70.405, 198.887
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein 26S proteasome regulatory subunit RPN8


Mass: 21040.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RPN8, YOR261C, O5360 / Production host: Escherichia coli (E. coli) / References: UniProt: Q08723
#2: Protein 26S proteasome regulatory subunit RPN11


Mass: 26893.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: RPN11, MPR1, YFR004W / Production host: Escherichia coli (E. coli) / References: UniProt: P43588
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 271 / 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: 2.57 Å3/Da / Density % sol: 52.16 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG8000, 30% ethylene glycol, and 100 mM HEPES (pH7.5), VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 4, 2013
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 37562 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 11.9 % / Biso Wilson estimate: 20.33 Å2 / Rmerge(I) obs: 0.075 / Χ2: 0.986 / Net I/σ(I): 9.3
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
1.95-1.981218090.9041100
1.98-2.0212.118440.91411000.807
2.02-2.0612.118380.94211000.646
2.06-2.11218300.9711000.531
2.1-2.1512.118340.96811000.464
2.15-2.212.118640.99211000.401
2.2-2.2512.118291.06711000.336
2.25-2.3112.118511.0411000.282
2.31-2.3812.118421.01911000.264
2.38-2.4612.118591.04511000.227
2.46-2.541218591.02911000.181
2.54-2.6512.118651.01511000.148
2.65-2.771218741.01111000.122
2.77-2.9112.118771.01811000.099
2.91-3.11218840.97911000.076
3.1-3.3311.918920.95511000.058
3.33-3.6711.919051.18411000.056
3.67-4.211.819281.2411000.05
4.2-5.2911.519580.83611000.036
5.29-5010.821200.595199.80.03

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
CBASSdata collection
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4F70, 2O95

4f70

2o95


Resolution: 1.95→40.615 Å / Occupancy max: 1 / Occupancy min: 0.38 / FOM work R set: 0.8841 / SU ML: 0.17 / σ(F): 0.1 / Phase error: 18.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2094 2000 5.76 %Random 10% of observed
Rwork0.1626 ---
obs0.1652 34734 92.71 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 135.71 Å2 / Biso mean: 30.8519 Å2 / Biso min: 5.89 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2697 0 84 271 3052
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0132826
X-RAY DIFFRACTIONf_angle_d1.3853779
X-RAY DIFFRACTIONf_chiral_restr0.062429
X-RAY DIFFRACTIONf_plane_restr0.007477
X-RAY DIFFRACTIONf_dihedral_angle_d16.8841049
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9502-1.9990.2198890.1891455154459
1.999-2.0530.27951270.18512077220485
2.053-2.11340.20261410.17972307244893
2.1134-2.18160.2221440.16862369251395
2.1816-2.25960.21841440.16342347249195
2.2596-2.35010.21851440.15812346249094
2.3501-2.4570.19451400.16782304244493
2.457-2.58650.22251450.16532371251695
2.5865-2.74850.27381470.1682394254195
2.7485-2.96070.19451460.16532420256696
2.9607-3.25850.21651510.15422467261898
3.2585-3.72980.20331560.149925552711100
3.7298-4.6980.18581590.13942581274099
4.698-40.62330.19521670.18312741290899

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