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- PDB-4b0z: Crystal structure of S. pombe Rpn12 -

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Basic information

Entry
Database: PDB / ID: 4b0z
TitleCrystal structure of S. pombe Rpn12
Components26S PROTEASOME REGULATORY SUBUNIT RPN12
KeywordsPROTEIN BINDING / PROTEASOME UBITQUITIN
Function / homology
Function and homology information


Cross-presentation of soluble exogenous antigens (endosomes) / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / MAPK6/MAPK4 signaling / UCH proteinases / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis ...Cross-presentation of soluble exogenous antigens (endosomes) / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / MAPK6/MAPK4 signaling / UCH proteinases / Orc1 removal from chromatin / CDK-mediated phosphorylation and removal of Cdc6 / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / KEAP1-NFE2L2 pathway / Neddylation / Ub-specific processing proteases / Regulation of PTEN stability and activity / Antigen processing: Ubiquitination & Proteasome degradation / proteasome regulatory particle, lid subcomplex / nuclear periphery / proteasome-mediated ubiquitin-dependent protein catabolic process / chromatin / nucleus / cytosol
Similarity search - Function
Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat - #990 / 26S proteasome non-ATPase regulatory subunit Rpn12 / CSN8/PSMD8/EIF3K / CSN8/PSMD8/EIF3K family / Proteasome component (PCI) domain / PCI domain profile. / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
NITRATE ION / MONOTHIOGLYCEROL / 26S proteasome regulatory subunit rpn12
Similarity search - Component
Biological speciesSCHIZOSACCHAROMYCES POMBE (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.585 Å
AuthorsBoehringer, J. / Riedinger, C. / Paraskevopoulos, K. / Johnson, E.O.D. / Lowe, E.D. / Khoudian, C. / Smith, D. / Noble, M.E.M. / Gordon, C. / Endicott, J.A.
CitationJournal: Biochem.J. / Year: 2012
Title: Structural and Functional Characterisation of Rpn12 Identifies Residues Required for Rpn10 Proteasome Incorporation.
Authors: Boehringer, J. / Riedinger, C. / Paraskevopoulos, K. / Johnson, E.O.D. / Lowe, E.D. / Khoudian, C. / Smith, D. / Noble, M.E.M. / Gordon, C. / Endicott, J.A.
History
DepositionJul 6, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 12, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 7, 2012Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: 26S PROTEASOME REGULATORY SUBUNIT RPN12
B: 26S PROTEASOME REGULATORY SUBUNIT RPN12
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,19311
Polymers52,4522
Non-polymers7419
Water6,557364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2590 Å2
ΔGint-11.2 kcal/mol
Surface area23520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.780, 91.380, 143.340
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein 26S PROTEASOME REGULATORY SUBUNIT RPN12 / RPN12


Mass: 26225.963 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-224
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast)
Plasmid: PGEX-6P-1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P50524
#2: Chemical
ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-SGM / MONOTHIOGLYCEROL


Mass: 108.159 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 364 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Nonpolymer detailsMONOTHIOGLYCEROL (SGM) IS BOUND TO CYS 65 BY A DISULPHIDE BRIDGE

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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: 2.67 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2 M NA NO3, 0.1 M BIS-TRIS PROPANE PH 7.5, 22.5% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.9791
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 17, 2008 / Details: TOROIDAL ZERODUR MIRROR
RadiationMonochromator: ASYMMETRIC LAUE 001 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.59→42.34 Å / Num. obs: 74706 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 22.86 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 17.1
Reflection shellResolution: 1.59→1.67 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.5 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.585→40.111 Å / SU ML: 0.17 / σ(F): 0 / Phase error: 18.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2248 3719 5.1 %
Rwork0.188 --
obs0.1898 73328 97.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.509 Å2 / ksol: 0.455 e/Å3
Displacement parametersBiso mean: 32.38 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.585→40.111 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3606 0 46 364 4016
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0153876
X-RAY DIFFRACTIONf_angle_d1.5255251
X-RAY DIFFRACTIONf_dihedral_angle_d13.5431464
X-RAY DIFFRACTIONf_chiral_restr0.081575
X-RAY DIFFRACTIONf_plane_restr0.007679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.585-1.64170.26643220.21026416X-RAY DIFFRACTION91
1.6417-1.70740.22483470.17536613X-RAY DIFFRACTION93
1.7074-1.78510.20293730.15196792X-RAY DIFFRACTION96
1.7851-1.87920.20053980.15226859X-RAY DIFFRACTION97
1.8792-1.99690.20983820.16036997X-RAY DIFFRACTION98
1.9969-2.15110.18873890.15677048X-RAY DIFFRACTION99
2.1511-2.36760.20893800.1487113X-RAY DIFFRACTION100
2.3676-2.71010.19333860.1557158X-RAY DIFFRACTION100
2.7101-3.41420.21813690.17657184X-RAY DIFFRACTION99
3.4142-40.12370.26253730.23857429X-RAY DIFFRACTION98

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