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- PDB-1uoh: HUMAN GANKYRIN -

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Basic information

Entry
Database: PDB / ID: 1uoh
TitleHUMAN GANKYRIN
Components26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 10
KeywordsONCOPROTEIN / ANKYRIN REPEAT / 26S PROTEASOME
Function / homology
Function and homology information


proteasome regulatory particle assembly / positive regulation of cyclin-dependent protein serine/threonine kinase activity / Proteasome assembly / transcription factor binding / negative regulation of release of cytochrome c from mitochondria / negative regulation of NF-kappaB transcription factor activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of MAPK cascade / proteasome complex / positive regulation of protein ubiquitination ...proteasome regulatory particle assembly / positive regulation of cyclin-dependent protein serine/threonine kinase activity / Proteasome assembly / transcription factor binding / negative regulation of release of cytochrome c from mitochondria / negative regulation of NF-kappaB transcription factor activity / negative regulation of DNA damage response, signal transduction by p53 class mediator / negative regulation of MAPK cascade / proteasome complex / positive regulation of protein ubiquitination / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / microtubule cytoskeleton / positive regulation of cell growth / RNA polymerase II-specific DNA-binding transcription factor binding / cytoskeleton / cilium / apoptotic process / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / nucleus / cytosol / cytoplasm
Similarity search - Function
: / Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ...: / Ankyrin repeat-containing domain / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
26S proteasome non-ATPase regulatory subunit 10
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKrzywda, S. / Brzozowski, A.M. / Wilkinson, A.J.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: The Crystal Structure of Gankyrin, an Oncoprotein Found in Complexes with Cyclin-Dependent Kinase 4, a 19 S Proteasomal ATPase Regulator, and the Tumor Suppressors Rb and P53
Authors: Krzywda, S. / Brzozowski, A.M. / Higashitsuji, H. / Fujita, J. / Welchman, R. / Dawson, S. / Mayer, R.J. / Wilkinson, A.J.
History
DepositionSep 17, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2003Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 26S PROTEASOME NON-ATPASE REGULATORY SUBUNIT 10


Theoretical massNumber of molelcules
Total (without water)24,4601
Polymers24,4601
Non-polymers00
Water2,072115
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)37.606, 64.622, 74.696
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 NON-ATPASE REGULATORY SUBUNIT 10 / 26S PROTEASOME REGULATORY SUBUNIT P28 / GANKYRIN


Mass: 24459.855 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA BLUE / References: UniProt: O75832
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTIONS AS A REGULATORY SUBUNIT OF THE 26S PROTEASOME INVOLVED IN THE ATP-DEPENDENT DEGRADATION ...FUNCTIONS AS A REGULATORY SUBUNIT OF THE 26S PROTEASOME INVOLVED IN THE ATP-DEPENDENT DEGRADATION OF UBIQUITINATED PROTEINS. A PA700 COMPLEX COMPONENT WITH 5 ANKYRIN REPEATS

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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: 1.8 Å3/Da / Density % sol: 32.6 %
Crystal growpH: 6.4 / Details: 24% PEG 5000 MONOMETHYL ETHER, 0.1 M MES PH 6.4
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop / Details: Krzywda, S., (2003) Acta Crystallogr., D59, 1294.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mMTris-HCl1droppH7.5
210 mg/mlprotein1drop
324 %(w/v)PEG5000 MME1reservoir
40.1 MMES1reservoirpH6.4

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9756
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9756 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 12405 / % possible obs: 95.6 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 10.13
Reflection shellResolution: 2→2.07 Å / Redundancy: 2 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 1.79 / % possible all: 88.6
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / Num. obs: 12976 / Redundancy: 2.2 % / Num. measured all: 194568 / Rmerge(I) obs: 0.076
Reflection shell
*PLUS
Highest resolution: 2.04 Å / % possible obs: 88.6 % / Rmerge(I) obs: 0.583 / Mean I/σ(I) obs: 1.79

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MJ0

1mj0


Resolution: 2→32.44 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.908 / SU B: 4.934 / SU ML: 0.141 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.241 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THIS ENTRY CONTAINS RESIDUES WITH ZERO OCCUPANCY. THESE RESIDUES ARE A24, A30, A38, A87, A171, A189, A215, A221, A222, A224 AND A226
RfactorNum. reflection% reflectionSelection details
Rfree0.253 612 4.9 %RANDOM
Rwork0.191 ---
obs0.194 11860 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 17.58 Å2
Baniso -1Baniso -2Baniso -3
1--1.7 Å20 Å20 Å2
2--0.54 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 2→32.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1689 0 0 115 1804
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211691
X-RAY DIFFRACTIONr_bond_other_d0.0020.021545
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.962288
X-RAY DIFFRACTIONr_angle_other_deg1.67533599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6475221
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.10.2266
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021897
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02300
X-RAY DIFFRACTIONr_nbd_refined0.2280.2384
X-RAY DIFFRACTIONr_nbd_other0.2380.21898
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0930.21053
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.20.269
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.211
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.861.51099
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.43821745
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.4743592
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it3.6464.5543
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.25 48
Rwork0.19 779
Refinement TLS params.Method: refined / Origin x: 15.7268 Å / Origin y: 28.4851 Å / Origin z: 3.9409 Å
111213212223313233
T0.0899 Å20.0136 Å2-0.0501 Å2-0.0193 Å2-0.0057 Å2--0.0281 Å2
L4.7521 °22.2157 °2-2.1731 °2-1.9624 °2-1.1195 °2--1.5922 °2
S0.0695 Å °0.0119 Å °-0.2378 Å °0.0852 Å °-0.0446 Å °-0.0717 Å °0.003 Å °0.0115 Å °-0.0249 Å °
Refinement
*PLUS
Num. reflection Rfree: 622 / % reflection Rfree: 5 % / Rfactor Rfree: 0.252
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.018
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.658

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