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- PDB-4o8x: Zinc-bound Rpn11 in complex with Rpn8 -

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Basic information

Entry
Database: PDB / ID: 4o8x
TitleZinc-bound 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 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. / 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: 1.991 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 / 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_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.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_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_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

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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)49,92434
Polymers47,9352
Non-polymers1,99032
Water4,594255
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9930 Å2
ΔGint-1 kcal/mol
Surface area16550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.296, 70.296, 198.912
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: 21040.904 Da / Num. of mol.: 1 / Fragment: UNP residues 2-178
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 / Fragment: UNP residues 2-239
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.: 31 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 255 / 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: 2.56 Å3/Da / Density % sol: 52.01 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG8000, 12% ethylene glycol and 100 mM HEPES (pH 7.5), VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 25, 2013
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 1.99→49.67 Å / Num. obs: 34967 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 29.69 Å2 / Rmerge(I) obs: 0.076 / Χ2: 1.098 / Net I/σ(I): 9.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.99-2.028.30.7117010.878198.7
2.02-2.068.20.57716940.896198.7
2.06-2.18.20.49716810.904198.8
2.1-2.148.20.42217100.884198.9
2.14-2.198.20.35917160.886198.8
2.19-2.248.20.29217040.93199.1
2.24-2.38.20.26517130.997199.1
2.3-2.368.20.23417140.899199.1
2.36-2.438.20.20817330.894199.1
2.43-2.518.10.17917390.954199.4
2.51-2.68.20.14417010.954199.3
2.6-2.78.10.12517470.988199.4
2.7-2.828.10.10317390.97199.5
2.82-2.978.10.08717471.009199.5
2.97-3.168.10.07317591.192199.7
3.16-3.480.06717611.633199.8
3.4-3.747.90.0617951.995199.7
3.74-4.297.70.04517981.721199.8
4.29-5.47.50.03418441.212199.4
5.4-49.677.30.0319711.188199.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.3phasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.14data extraction
Blu-IceIcedata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4O8Y

4o8y


Resolution: 1.991→48.234 Å / Occupancy max: 1 / Occupancy min: 0.38 / SU ML: 0.18 / σ(F): 1.34 / Phase error: 18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1951 3493 10.01 %random 10% of observed data
Rwork0.1613 ---
obs0.1647 34908 99.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 117.76 Å2 / Biso mean: 40.3663 Å2 / Biso min: 15.4 Å2
Refinement stepCycle: LAST / Resolution: 1.991→48.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2677 0 125 255 3057
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122845
X-RAY DIFFRACTIONf_angle_d1.3273789
X-RAY DIFFRACTIONf_chiral_restr0.053430
X-RAY DIFFRACTIONf_plane_restr0.007476
X-RAY DIFFRACTIONf_dihedral_angle_d15.9791047
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9912-2.01850.2531250.22561213133898
2.0185-2.04740.25151280.21421213134199
2.0474-2.07790.26541440.20531254139899
2.0779-2.11040.26841360.19591171130799
2.1104-2.1450.21631190.18531265138499
2.145-2.1820.19931360.18491234137099
2.182-2.22160.22261450.17661214135999
2.2216-2.26440.21841470.16871257140499
2.2644-2.31060.1841250.15471214133999
2.3106-2.36080.18471410.15521230137199
2.3608-2.41570.1731500.161246139699
2.4157-2.47620.21881370.15981220135799
2.4762-2.54310.1991640.16251235139999
2.5431-2.61790.22181490.14831248139799
2.6179-2.70240.23451180.161412651383100
2.7024-2.7990.20681490.157912321381100
2.799-2.91110.19771620.156312371399100
2.9111-3.04350.20211240.158212731397100
3.0435-3.2040.17831430.150112911434100
3.204-3.40460.18661440.14912401384100
3.4046-3.66740.17511640.150112781442100
3.6674-4.03630.18421240.149213041428100
4.0363-4.620.1541290.140413221451100
4.62-5.81910.17481360.146113411477100
5.8191-48.24770.21551540.19841418157299

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