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

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Basic information

Entry
Database: PDB / ID: 4ocm
TitleCrystal Structure of the Rpn8-Rpn11 MPN domain heterodimer, crystal form Ib
Components
  • (26S proteasome regulatory subunit ...) x 2
  • 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 regulatory subunit RPN11 C-terminal domain / 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 ...Cytidine Deaminase, domain 2 / Cytidine Deaminase; domain 2 / : / 26S proteasome regulatory subunit RPN11 C-terminal domain / 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: 1.99 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 ...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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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 1.4Nov 27, 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)120,6889
Polymers120,5186
Non-polymers1703
Water3,531196
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)60,3645
Polymers60,2593
Non-polymers1052
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.401, 44.970, 200.043
Angle α, β, γ (deg.)90.000, 98.400, 90.000
Int Tables number3
Space group name H-MP121

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Components

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26S proteasome regulatory subunit ... , 2 types, 4 molecules ADBE

#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

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Antibody , 1 types, 2 molecules CF

#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

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Non-polymers , 3 types, 199 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 196 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 47.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM MES, pH 6.0, 200 mM calcium acetate, 22% 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: 1.99→197.898 Å / Num. all: 74800 / Num. obs: 74800 / % possible obs: 96.8 % / Observed criterion σ(F): -100 / Observed criterion σ(I): -100 / Redundancy: 3.2 % / Biso Wilson estimate: 32.52 Å2 / Rmerge(I) obs: 0.078 / Rsym value: 0.078 / Net I/σ(I): 9.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.99-2.13.20.61.33186998160.688
2.1-2.223.10.4371.732727104000.43798.2
2.22-2.383.40.3252.23325598730.32599
2.38-2.573.30.2382.93080192240.23899.1
2.57-2.813.20.1644.12704384740.16498.5
2.81-3.153.30.0937.42564976750.09399
3.15-3.633.10.05611.92044566420.05696.7
3.63-4.453.20.03914.71810956990.03997.8
4.45-6.2930.03514.61339644450.03597.2
6.29-44.9730.0316.4771725520.0397.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3 Å44.97 Å
Translation3 Å44.97 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: 1.99→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.2556 / WRfactor Rwork: 0.2075 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.7657 / SU B: 11.894 / SU ML: 0.144 / SU R Cruickshank DPI: 0.1898 / SU Rfree: 0.175 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.19 / ESU R Free: 0.175 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2623 3757 5 %RANDOM
Rwork0.2158 ---
all0.2181 74685 --
obs0.2181 74685 96.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 138.7 Å2 / Biso mean: 40.609 Å2 / Biso min: 11.36 Å2
Baniso -1Baniso -2Baniso -3
1--1.19 Å20 Å20.06 Å2
2--0.66 Å20 Å2
3---0.56 Å2
Refinement stepCycle: LAST / Resolution: 1.99→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7299 0 3 196 7498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0227476
X-RAY DIFFRACTIONr_angle_refined_deg1.9331.94210134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4865936
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.14424.316329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.697151251
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8961534
X-RAY DIFFRACTIONr_chiral_restr0.1560.21146
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215604
X-RAY DIFFRACTIONr_mcbond_it1.5091.54669
X-RAY DIFFRACTIONr_mcangle_it2.61327494
X-RAY DIFFRACTIONr_scbond_it4.32932807
X-RAY DIFFRACTIONr_scangle_it6.4644.52640
LS refinement shellResolution: 1.99→2.042 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 242 -
Rwork0.369 4219 -
all-4461 -
obs--78.33 %
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)
13.27120.78810.72322.64610.61062.8997-0.0403-0.00090.2647-0.10720.0036-0.0584-0.23510.18350.03670.2383-0.018-0.01070.20660.050.1459.7837.83477.894
22.1290.1630.53962.85920.50361.71410.03090.1952-0.1516-0.3106-0.04380.05760.1148-0.020.01290.2660.01170.00640.19030.04560.1267-5.624-9.2162.575
34.1804-0.1543-2.33121.72850.07884.22380.035-0.08970.21360.11530.04860.0327-0.1264-0.0861-0.08360.1970.0253-0.02470.235-0.01990.0976-25.5532.51882.759
43.361-0.59160.90622.6809-0.45293.138-0.05320.03290.26740.08870.0270.0908-0.2246-0.18160.02620.0540.02750.00040.0845-0.02230.1818-56.48313.1120.649
52.3592-0.23280.51913.6309-0.90322.46190.0436-0.1711-0.25560.408-0.0323-0.00410.19750.0177-0.01130.1123-0.0130.00290.0823-0.01520.1431-40.772-5.83535.725
64.41620.1371-2.23551.6358-0.23544.5526-0.02630.0840.1687-0.06970.0721-0.038-0.12470.1241-0.04590.011-0.0239-0.00780.12120.02570.1226-20.7587.42716.32
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 177
2X-RAY DIFFRACTION1A501 - 523
3X-RAY DIFFRACTION2B23 - 217
4X-RAY DIFFRACTION2B401
5X-RAY DIFFRACTION2B501 - 531
6X-RAY DIFFRACTION3C3 - 127
7X-RAY DIFFRACTION3C501 - 523
8X-RAY DIFFRACTION4D5 - 176
9X-RAY DIFFRACTION4D301
10X-RAY DIFFRACTION4D501 - 533
11X-RAY DIFFRACTION5E23 - 218
12X-RAY DIFFRACTION5E401
13X-RAY DIFFRACTION5E501 - 543
14X-RAY DIFFRACTION6F3 - 127
15X-RAY DIFFRACTION6F501 - 543

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