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

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Basic information

Entry
Database: PDB / ID: 4ocl
TitleCrystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ia
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


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. / 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: 2.4 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 1.2Sep 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,6498
Polymers120,5186
Non-polymers1312
Water1,69394
1
A: 26S proteasome regulatory subunit RPN8
B: 26S proteasome regulatory subunit RPN11
C: Nb1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3254
Polymers60,2593
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 26S proteasome regulatory subunit RPN8
E: 26S proteasome regulatory subunit RPN11
F: Nb1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,3254
Polymers60,2593
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.258, 63.431, 100.111
Angle α, β, γ (deg.)100.080, 92.750, 90.620
Int Tables number1
Space group name H-MP1

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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: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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: 2.35 Å3/Da / Density % sol: 47.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 50 mM MES, pH 6.0, 200 mM calcium acetate, 22% PEG3350, VAPOR DIFFUSION, SITTING DROPS, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.00753 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: May 25, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00753 Å / Relative weight: 1
ReflectionResolution: 2.392→98.44 Å / Num. all: 41691 / Num. obs: 41691 / % possible obs: 96.4 % / Observed criterion σ(F): -100 / Observed criterion σ(I): -100 / Redundancy: 3.5 % / Biso Wilson estimate: 54.346 Å2 / Rmerge(I) obs: 0.081 / Rsym value: 0.081 / Net I/σ(I): 10.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
2.392-2.523.40.6341.21920157200.63490.4
2.52-2.673.60.421.72069658000.4297
2.67-2.863.50.2582.71945754860.25897.8
2.86-3.093.30.1614.21709551030.16198
3.09-3.383.70.0987.11736747480.09898.2
3.38-3.783.60.0719.71534942570.07197.9
3.78-4.373.30.05911.31226336850.05996.6
4.37-5.353.40.04913.11077031360.04996.6
5.35-7.563.50.05112.4844624390.05197.1
7.56-48.9783.40.04314.1445513170.04396.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å48.98 Å
Translation3 Å48.98 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 ENTRIES 2X1P AND 2O95

2x1p

2o95


Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.914 / WRfactor Rfree: 0.253 / WRfactor Rwork: 0.1946 / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.8174 / SU B: 19.64 / SU ML: 0.206 / SU R Cruickshank DPI: 0.4107 / SU Rfree: 0.2683 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.411 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2522 2089 5 %RANDOM
Rwork0.1951 ---
all0.198 41609 --
obs0.198 41609 97.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 150.67 Å2 / Biso mean: 47.387 Å2 / Biso min: 18.54 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å20.26 Å20.56 Å2
2---1.53 Å2-0.5 Å2
3----0.81 Å2
Refinement stepCycle: LAST / Resolution: 2.4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7263 0 2 94 7359
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0227413
X-RAY DIFFRACTIONr_angle_refined_deg1.7331.94210050
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1955932
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25524.107319
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.967151224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.4621535
X-RAY DIFFRACTIONr_chiral_restr0.1190.21142
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0215547
X-RAY DIFFRACTIONr_mcbond_it0.8881.54655
X-RAY DIFFRACTIONr_mcangle_it1.71927457
X-RAY DIFFRACTIONr_scbond_it2.71332758
X-RAY DIFFRACTIONr_scangle_it4.2864.52593
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.442 145 -
Rwork0.354 2835 -
all-2980 -
obs--94.42 %
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)
13.2277-0.88061.01094.1128-1.0344.6690.00190.128-0.07810.0675-0.0668-0.26740.48680.44560.0650.1940.09350.06450.18140.00840.156410.3708-5.72846.6598
23.1688-0.61350.58683.4766-0.6463.2822-0.06640.33530.1073-0.32030.07640.278-0.0052-0.2379-0.00990.0835-0.01540.03620.22060.00590.1548-6.98989.795-8.8469
32.0136-0.3408-0.46136.49023.05517.46760.1314-0.1951-0.0006-0.1097-0.0688-0.2485-0.56620.2756-0.06250.2279-0.0589-0.03790.0851-0.01460.09814.876529.738711.3265
42.84770.6602-0.19564.5719-0.95123.7428-0.0395-0.06880.0556-0.1263-0.0428-0.2865-0.22060.22810.08230.0347-0.0184-0.01740.1485-0.01420.193815.7759-2.5364-50.2733
54.65010.3539-1.2413.1259-0.89883.1138-0.0768-0.30460.05710.17030.12770.29310.0916-0.2101-0.05090.03410.0153-0.01720.1708-0.00350.1091-3.3752-18.4013-35.2831
62.5044-0.3152-0.43186.32172.55865.94860.17840.1754-0.0513-0.179-0.1513-0.33090.12540.0917-0.0270.13640.06010.03360.0375-0.00010.0910.6429-38.1125-54.6759
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 176
2X-RAY DIFFRACTION1A501 - 511
3X-RAY DIFFRACTION2B23 - 217
4X-RAY DIFFRACTION2B401
5X-RAY DIFFRACTION2B501 - 521
6X-RAY DIFFRACTION3C3 - 127
7X-RAY DIFFRACTION3C501 - 514
8X-RAY DIFFRACTION4D5 - 176
9X-RAY DIFFRACTION4D501 - 517
10X-RAY DIFFRACTION5E23 - 217
11X-RAY DIFFRACTION5E401
12X-RAY DIFFRACTION5E501 - 511
13X-RAY DIFFRACTION6F3 - 127
14X-RAY DIFFRACTION6F501 - 520

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