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- PDB-2x5n: Crystal Structure of the SpRpn10 VWA domain -

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Basic information

Entry
Database: PDB / ID: 2x5n
TitleCrystal Structure of the SpRpn10 VWA domain
Components26S PROTEASOME REGULATORY SUBUNIT RPN10
KeywordsNUCLEAR PROTEIN / NUCLEUS / UBIQUITIN / PROTEASOME
Function / homology
Function and homology information


Cross-presentation of soluble exogenous antigens (endosomes) / Regulation of ornithine decarboxylase (ODC) / : / UCH proteinases / Ub-specific processing proteases / positive regulation of mitotic metaphase/anaphase transition / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / K48-linked polyubiquitin modification-dependent protein binding / polyubiquitin modification-dependent protein binding ...Cross-presentation of soluble exogenous antigens (endosomes) / Regulation of ornithine decarboxylase (ODC) / : / UCH proteinases / Ub-specific processing proteases / positive regulation of mitotic metaphase/anaphase transition / proteasome regulatory particle, lid subcomplex / proteasome regulatory particle, base subcomplex / K48-linked polyubiquitin modification-dependent protein binding / polyubiquitin modification-dependent protein binding / proteasome assembly / ubiquitin binding / proteasome-mediated ubiquitin-dependent protein catabolic process / nucleus / cytosol
Similarity search - Function
Proteasome subunit Rpn10 / von Willebrand factor type A domain / von Willebrand factor, type A domain / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Rossmann fold ...Proteasome subunit Rpn10 / von Willebrand factor type A domain / von Willebrand factor, type A domain / Ubiquitin interacting motif / Ubiquitin-interacting motif (UIM) domain profile. / von Willebrand factor (vWF) type A domain / VWFA domain profile. / von Willebrand factor, type A / von Willebrand factor A-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
26S proteasome regulatory subunit rpn10
Similarity search - Component
Biological speciesSCHIZOSACCHAROMYCES POMBE (fission yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsRiedinger, C. / Boehringer, J. / Trempe, J.-F. / Lowe, E.D. / Brown, N.R. / Gehring, K. / Noble, M.E.M. / Gordon, C. / Endicott, J.A.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The Structure of Rpn10 and its Interactions with Polyubiquitin Chains and the Proteasome Subunit Rpn12.
Authors: Riedinger, C. / Boehringer, J. / Trempe, J.F. / Lowe, E.D. / Brown, N.R. / Gehring, K. / Noble, M.E. / Gordon, C. / Endicott, J.A.
History
DepositionFeb 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 26S PROTEASOME REGULATORY SUBUNIT RPN10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6534
Polymers21,3641
Non-polymers2883
Water4,882271
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.990, 35.230, 60.140
Angle α, β, γ (deg.)90.00, 111.20, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2001-

HOH

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Components

#1: Protein 26S PROTEASOME REGULATORY SUBUNIT RPN10 / SPRPN10


Mass: 21364.439 Da / Num. of mol.: 1 / Fragment: VWA DOMAIN, RESIDUES 2-193
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SCHIZOSACCHAROMYCES POMBE (fission yeast)
Plasmid: PET21D / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O94444
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 271 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHIS DEPOSITION CONTAINS ONLY THE VWA DOMAIN OF SPRPN10, RESIDUES 2-193

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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: 1.82 Å3/Da / Density % sol: 32 % / Description: NONE
Crystal growpH: 8.5
Details: 0.1 M TRIS/HCL PH 8.5, 1.5 M (NH4)2SO4, 25 MM MGSO4,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 22, 2007 / Details: TOROIDAL ZERODUR MIRROR
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.27→56.1 Å / Num. obs: 38709 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 8.23 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.37
Reflection shellResolution: 1.27→1.4 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.16 / Mean I/σ(I) obs: 7.34 / % possible all: 98.7

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Processing

Software
NameClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXDphasing
SHELXEphasing
PHENIXrefinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.3→27.738 Å / SU ML: 0.11 / Phase error: 13.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1646 1887 5 %
Rwork0.1228 --
obs0.1248 37864 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.953 Å2 / ksol: 0.458 e/Å3
Displacement parametersBiso mean: 15.73 Å2
Baniso -1Baniso -2Baniso -3
1-0.7849 Å2-0 Å20.4916 Å2
2--0.1402 Å20 Å2
3----0.9251 Å2
Refinement stepCycle: LAST / Resolution: 1.3→27.738 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1469 0 15 271 1755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011637
X-RAY DIFFRACTIONf_angle_d1.5872237
X-RAY DIFFRACTIONf_dihedral_angle_d16.794627
X-RAY DIFFRACTIONf_chiral_restr0.215254
X-RAY DIFFRACTIONf_plane_restr0.007299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.34650.17561970.11993445X-RAY DIFFRACTION95
1.3465-1.40040.18991850.12323542X-RAY DIFFRACTION96
1.4004-1.46410.1731650.11393546X-RAY DIFFRACTION97
1.4641-1.54130.17082020.1043567X-RAY DIFFRACTION98
1.5413-1.63790.15141940.10343570X-RAY DIFFRACTION98
1.6379-1.76430.15182050.10373621X-RAY DIFFRACTION99
1.7643-1.94180.17831950.11093546X-RAY DIFFRACTION97
1.9418-2.22270.14441690.10553663X-RAY DIFFRACTION99
2.2227-2.79990.15211700.11793700X-RAY DIFFRACTION99
2.7999-27.74470.16512050.14173777X-RAY DIFFRACTION100

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