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- PDB-4ocn: Crystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, cryst... -

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Basic information

Entry
Database: PDB / ID: 4ocn
TitleCrystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form II
Components
  • 26S proteasome regulatory subunit RPN11
  • 26S proteasome regulatory subunit RPN8
  • Nb1
KeywordsHYDROLASE / PROTEIN BINDING / 26S proteasome / isopeptidase activity / regulatory particle / lid / ubiquitin
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. / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / 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)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.25 Å
AuthorsPathare, G.R. / Bracher, A.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Crystal structure of the proteasomal deubiquitylation module Rpn8-Rpn11.
Authors: Pathare, G.R. / Nagy, I. / Sledz, P. / Anderson, D.J. / Zhou, H.J. / Pardon, E. / Steyaert, J. / Forster, F. / Bracher, A. / Baumeister, W.
History
DepositionJan 9, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Category: pdbx_database_related
Revision 1.3Sep 20, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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
C: Nb1
D: 26S proteasome regulatory subunit RPN8
E: 26S proteasome regulatory subunit RPN11
F: Nb1


Theoretical massNumber of molelcules
Total (without water)120,5186
Polymers120,5186
Non-polymers00
Water2,432135
1
A: 26S proteasome regulatory subunit RPN8
B: 26S proteasome regulatory subunit RPN11
C: Nb1


Theoretical massNumber of molelcules
Total (without water)60,2593
Polymers60,2593
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 26S proteasome regulatory subunit RPN8
E: 26S proteasome regulatory subunit RPN11
F: Nb1


Theoretical massNumber of molelcules
Total (without water)60,2593
Polymers60,2593
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.042, 80.042, 386.205
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein 26S proteasome regulatory subunit RPN8


Mass: 20838.512 Da / Num. of mol.: 2 / Fragment: UNP residues 1-176
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: pRSFDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q08723
#2: Protein 26S proteasome regulatory subunit RPN11 / Protein MPR1


Mass: 24566.283 Da / Num. of mol.: 2 / Fragment: UNP residues 1-220
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: pRSFDuet / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P43588
#3: Antibody Nb1 / nanobody 1


Mass: 14854.423 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pMESy4 / Production host: Escherichia coli (E. coli) / Strain (production host): WK6 Su
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRPN8 AND RPN11 WERE EXPRESSED AS A FUSION PROTEIN CONNECTED BY A GSGGSGGSG LINKER. THEY HAVE BEEN ...RPN8 AND RPN11 WERE EXPRESSED AS A FUSION PROTEIN CONNECTED BY A GSGGSGGSG LINKER. THEY HAVE BEEN REPRESENTED AS TWO CHAINS BECAUSE THE LINKER IS DISORDERED AND IT IS UNCERTAIN WHETHER IT HAS BEEN CLEAVED.

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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: 52.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM MES, pH 6.0, 100 mM magnesium chloride, 21% PEG3350, VAPOR DIFFUSION, HANGING DROPS, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 27, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.249→48.276 Å / Num. all: 61223 / Num. obs: 61223 / % possible obs: 99.8 % / Observed criterion σ(F): -100 / Observed criterion σ(I): -100 / Redundancy: 7.8 % / Biso Wilson estimate: 56.699 Å2 / Rmerge(I) obs: 0.058 / Rsym value: 0.058 / Net I/σ(I): 20.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.249-2.3780.80616968787210.80699.2
2.37-2.5180.5231.56640683120.52399.9
2.51-2.697.70.2712.86034778180.271100
2.69-2.98.20.1644.65972673270.164100
2.9-3.187.70.0997.45200067650.099100
3.18-3.5680.05712.14913261620.057100
3.56-4.117.80.03817.34252754740.03899.9
4.11-5.037.70.02921.53633547060.02999.9
5.03-7.117.40.029222745637240.02999.7
7.11-48.8276.90.02223.61527322140.02299.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å48.89 Å
Translation3 Å48.89 Å

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Processing

Software
NameVersionClassificationNB
SCALA3.3.16data scaling
MOLREPphasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4OCL

4ocl


Resolution: 2.25→30 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.915 / WRfactor Rfree: 0.2613 / WRfactor Rwork: 0.2156 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8051 / SU B: 16.267 / SU ML: 0.18 / SU R Cruickshank DPI: 0.2698 / SU Rfree: 0.2293 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2811 3108 5.1 %RANDOM
Rwork0.2321 ---
all0.2346 61002 --
obs0.2346 61002 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 121.37 Å2 / Biso mean: 54.6609 Å2 / Biso min: 27.08 Å2
Baniso -1Baniso -2Baniso -3
1-1.97 Å20 Å20 Å2
2--1.97 Å20 Å2
3----3.94 Å2
Refinement stepCycle: LAST / Resolution: 2.25→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7206 0 0 135 7341
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0227352
X-RAY DIFFRACTIONr_angle_refined_deg1.1781.9459943
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0835906
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.44324.26331
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.167151270
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.4741537
X-RAY DIFFRACTIONr_chiral_restr0.0830.21114
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215488
X-RAY DIFFRACTIONr_mcbond_it0.5631.54537
X-RAY DIFFRACTIONr_mcangle_it1.06427299
X-RAY DIFFRACTIONr_scbond_it1.44532815
X-RAY DIFFRACTIONr_scangle_it2.3064.52644
LS refinement shellResolution: 2.249→2.307 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.423 221 -
Rwork0.387 4158 -
all-4379 -
obs--98.34 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.6799-0.80321.1662.5132-1.17684.07810.04530.0376-0.12510.03270.007-0.10920.28690.2431-0.05230.1681-0.02980.00710.0426-0.01720.092239.6815-31.440245.1613
22.4106-0.3140.8472.33020.03033.3947-0.00420.0585-0.0454-0.0349-0.03420.17630.0529-0.22370.03840.0936-0.02750.02790.0273-0.01130.037522.8318-17.890226.8163
32.4615-0.70460.6834.78711.94224.9458-0.0889-0.22340.34050.06120.0261-0.1745-0.49570.15480.06280.251-0.0761-0.03680.0589-0.01870.104234.33285.714442.5776
42.68131.7037-1.66352.8563-1.75812.04230.0556-0.18810.05180.1579-0.0594-0.0938-0.17180.12620.00380.3479-0.0337-0.05430.159-0.01340.12238.315-54.212576.5237
52.27910.2468-0.99782.1170.19974.179-0.04630.02770.0126-0.0576-0.04060.1939-0.1741-0.39310.0870.14610.0033-0.0370.1166-0.01410.065119.8169-66.526692.4041
62.5614-0.8821-1.12075.82792.97415.01230.02240.1629-0.31090.1489-0.06340.00440.35730.11210.0410.2504-0.00370.05950.1142-0.01520.121831.4115-90.902678.4148
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 176
2X-RAY DIFFRACTION1A501 - 547
3X-RAY DIFFRACTION2B23 - 217
4X-RAY DIFFRACTION2B501 - 523
5X-RAY DIFFRACTION3C3 - 127
6X-RAY DIFFRACTION3C501 - 520
7X-RAY DIFFRACTION4D5 - 176
8X-RAY DIFFRACTION4D501 - 516
9X-RAY DIFFRACTION5E22 - 217
10X-RAY DIFFRACTION5E501 - 529
11X-RAY DIFFRACTION6F3 - 126

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