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- PDB-4owp: Crystal structure of rpn11 in a heterodimer complex with rpn8, re... -

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Basic information

Entry
Database: PDB / ID: 4owp
TitleCrystal structure of rpn11 in a heterodimer complex with rpn8, representing the active portion of the proteasome lid.
Components
  • 26S proteasome regulatory subunit RPN11
  • 26S proteasome regulatory subunit RPN8
KeywordsHYDROLASE / proteasome / deubiquitination / ubiquitin / metalloprotease / zinc / MPN domain
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsYu, Z. / Mansour, W. / Nakasone, M.A. / Glickman, M.H. / Dvir, H.
Funding support Israel, United States, 2items
OrganizationGrant numberCountry
Marie Curie330879 Israel
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM095755 United States
CitationJournal: To Be Published
Title: Crystal structure of rpn11 in a heterodimer complex with rpn8, representing the active portion of the proteasome lid.In preparation.
Authors: Yu, Z. / Mansour, W. / Nakasone, M.A. / Pick, E. / Glickman, M.H. / Dvir, H.
History
DepositionFeb 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 5, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Derived calculations / Refinement description
Category: pdbx_audit_support / pdbx_struct_oper_list / software
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Dec 18, 2019Group: Database references / Structure summary / Category: citation / struct / struct_keywords
Item: _citation.title / _struct.title / _struct_keywords.text
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)47,8833
Polymers47,8182
Non-polymers651
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-69 kcal/mol
Surface area16000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.388, 70.388, 199.648
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
DetailsThe Rpn11-Rpn8 heterodimer in the assymeteric unit is also the minimal active assembly

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Components

#1: Protein 26S proteasome regulatory subunit RPN8


Mass: 21023.816 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: O5360,RPN8,YOR261C / Plasmid: pETDUET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 - Rossetta / References: UniProt: Q08723
#2: Protein 26S proteasome regulatory subunit RPN11 / Protein MPR1


Mass: 26793.693 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: MPR1,RPN11,YFR004W / Plasmid: pETDUET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 - Rossetta / References: UniProt: P43588
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / 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: 2.59 Å3/Da / Density % sol: 52.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 10% PEG 5000, 5% Tacsimate, 0.1 M Hepes pH 7.0 / PH range: 7.0 - 7.5 / Temp details: constant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS HTC / Detector: IMAGE PLATE / Date: Jan 21, 2014 / Details: Osmic Confocal Max-Flux? Cu/Cr DW
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→40 Å / Num. obs: 21697 / % possible obs: 98.6 % / Redundancy: 16.7 % / Rmerge(I) obs: 0.138 / Χ2: 1.042 / Net I/av σ(I): 21.188 / Net I/σ(I): 8.2 / Num. measured all: 362134
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
2.35-2.399.90.811.729320.92988.4
2.39-2.43110.83610580.94496.1
2.43-2.4813.20.84110170.96298.4
2.48-2.5315.30.75910730.98598.5
2.53-2.59170.70210591.0199
2.59-2.65180.67210601.00398.9
2.65-2.7118.30.60310741.05398.8
2.71-2.7918.30.51110541.07399.1
2.79-2.8718.30.43210711.08599.2
2.87-2.9618.30.37910951.09199.3
2.96-3.0718.20.29910781.09799.4
3.07-3.1918.30.21710741.10399.2
3.19-3.3318.10.18211061.08799.5
3.33-3.5118.10.15210751.0699.6
3.51-3.7317.90.11811051.05499.7
3.73-4.0217.80.10211001.00599.6
4.02-4.4217.50.08111191.02199.7
4.42-5.0617.30.0711381.013100
5.06-6.3716.80.07211571.063100
6.37-4015.10.05712521.06198.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
StructureStudio2.2.3 b2data collection
PDB_EXTRACT3.14data extraction
PHASER2.5.5phasing
REFMAC5.6.0117refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→28.763 Å / FOM work R set: 0.8092 / SU ML: 0.27 / σ(F): 1.35 / Phase error: 24.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2421 1116 5.18 %
Rwork0.1883 20416 -
obs0.191 21532 98.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 112.71 Å2 / Biso mean: 40.91 Å2 / Biso min: 19.44 Å2
Refinement stepCycle: final / Resolution: 2.35→28.763 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2676 0 1 127 2804
Biso mean--32.49 40.14 -
Num. residues----336
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082725
X-RAY DIFFRACTIONf_angle_d1.0773681
X-RAY DIFFRACTIONf_chiral_restr0.073420
X-RAY DIFFRACTIONf_plane_restr0.004466
X-RAY DIFFRACTIONf_dihedral_angle_d17.4191008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.45690.33451430.25312395253897
2.4569-2.58640.29241410.22592492263399
2.5864-2.74830.2551380.212512265099
2.7483-2.96030.29911330.21692531266499
2.9603-3.25780.27671280.2062546267499
3.2578-3.72840.19941500.179225662716100
3.7284-4.69410.22521420.16212600274299
4.6941-28.76480.22691410.178727742915100

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