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- PDB-1qym: X-ray structure of human gankyrin -

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Basic information

Entry
Database: PDB / ID: 1qym
TitleX-ray structure of human gankyrin
Components26S proteasome non-ATPase regulatory subunit 10
KeywordsONCOPROTEIN / ankyrin repeat / structural genomics
Function / homology
Function and homology information


cytoplasmic sequestering of NF-kappaB / proteasome regulatory particle assembly / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / intermediate filament cytoskeleton / Somitogenesis / negative regulation of MAPK cascade / negative regulation of NF-kappaB transcription factor activity / negative regulation of release of cytochrome c from mitochondria / negative regulation of DNA damage response, signal transduction by p53 class mediator ...cytoplasmic sequestering of NF-kappaB / proteasome regulatory particle assembly / Regulation of ornithine decarboxylase (ODC) / Cross-presentation of soluble exogenous antigens (endosomes) / intermediate filament cytoskeleton / Somitogenesis / negative regulation of MAPK cascade / negative regulation of NF-kappaB transcription factor activity / negative regulation of release of cytochrome c from mitochondria / negative regulation of DNA damage response, signal transduction by p53 class mediator / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / cytoskeletal protein binding / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / positive regulation of protein ubiquitination / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / AUF1 (hnRNP D0) binds and destabilizes mRNA / TNFR2 non-canonical NF-kB pathway / Assembly of the pre-replicative complex / Vpu mediated degradation of CD4 / Degradation of DVL / protein localization to plasma membrane / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Hh mutants are degraded by ERAD / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Degradation of AXIN / Defective CFTR causes cystic fibrosis / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / Activation of NF-kappaB in B cells / Negative regulation of NOTCH4 signaling / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / G2/M Checkpoints / Vif-mediated degradation of APOBEC3G / Autodegradation of the E3 ubiquitin ligase COP1 / Hedgehog 'on' state / Regulation of RUNX3 expression and activity / Degradation of GLI2 by the proteasome / GLI3 is processed to GLI3R by the proteasome / MAPK6/MAPK4 signaling / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / ABC-family proteins mediated transport / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / CDK-mediated phosphorylation and removal of Cdc6 / CLEC7A (Dectin-1) signaling / SCF(Skp2)-mediated degradation of p27/p21 / Regulation of expression of SLITs and ROBOs / FCERI mediated NF-kB activation / Regulation of PTEN stability and activity / Interleukin-1 signaling / Orc1 removal from chromatin / Regulation of RAS by GAPs / Separation of Sister Chromatids / Regulation of RUNX2 expression and activity / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / protein-macromolecule adaptor activity / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / Neddylation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / ER-Phagosome pathway / positive regulation of cell growth / RNA polymerase II-specific DNA-binding transcription factor binding / transmembrane transporter binding / cytoskeleton / Ub-specific processing proteases / neuron projection / apoptotic process / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / plasma membrane / 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 / 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: 2.8 Å
AuthorsManjasetty, B.A. / Quedenau, C. / Sievert, V. / Buessow, K. / Niesen, F. / Delbrueck, H. / Heinemann, U.
CitationJournal: Proteins / Year: 2004
Title: X-ray structure of human gankyrin, the product of a gene linked to hepatocellular carcinoma.
Authors: Manjasetty, B.A. / Quedenau, C. / Sievert, V. / Buessow, K. / Niesen, F. / Delbrueck, H. / Heinemann, U.
History
DepositionSep 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 26S proteasome non-ATPase regulatory subunit 10


Theoretical massNumber of molelcules
Total (without water)24,4731
Polymers24,4731
Non-polymers00
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)116.373, 116.373, 74.399
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-246-

HOH

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Components

#1: Protein 26S proteasome non-ATPase regulatory subunit 10 / 26S proteasome regulatory subunit p28 / Gankyrin


Mass: 24472.789 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMD10 / Plasmid: PSFEP250A062 / Cellular location (production host): cytoplasm / Production host: Escherichia coli (E. coli) / Strain (production host): SCS1 / References: UniProt: O75832
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 5.15 Å3/Da / Density % sol: 76.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 3.5M Na Formate , pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
118.3 mg/mlprotein1drop
23.5 Msodium formate1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 19, 2003 / Details: mirrors
RadiationMonochromator: Si111-DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 12978 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 13 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 35.4
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 4 / Rsym value: 0.62 / % possible all: 99.3
Reflection
*PLUS
Num. measured all: 169487
Reflection shell
*PLUS
% possible obs: 99.3 %

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SWISS-MODEL (PDB ENTRIES 1N1I, 1N0R, 1MJ0, 1N0Q)

1n1i

1n0r

1mj0

1n0q


Resolution: 2.8→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 10.54 / SU ML: 0.191 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.31 / ESU R Free: 0.253 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS TLS RESTRAINED REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.23349 632 4.9 %RANDOM
Rwork0.18748 ---
obs-12144 98.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 27.566 Å2
Baniso -1Baniso -2Baniso -3
1--1.74 Å20 Å20 Å2
2---1.74 Å20 Å2
3---3.48 Å2
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1680 0 0 53 1733
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0211705
X-RAY DIFFRACTIONr_bond_other_d0.0020.021554
X-RAY DIFFRACTIONr_angle_refined_deg1.2811.962308
X-RAY DIFFRACTIONr_angle_other_deg1.03733629
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8975222
X-RAY DIFFRACTIONr_chiral_restr0.0670.2267
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021916
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02301
X-RAY DIFFRACTIONr_nbd_refined0.2080.2415
X-RAY DIFFRACTIONr_nbd_other0.2430.21834
X-RAY DIFFRACTIONr_nbtor_other0.0820.21031
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.242
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.190.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.290.218
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.230.21
X-RAY DIFFRACTIONr_mcbond_it0.3751.51103
X-RAY DIFFRACTIONr_mcangle_it0.72921752
X-RAY DIFFRACTIONr_scbond_it1.2243602
X-RAY DIFFRACTIONr_scangle_it2.2054.5556
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.389 54
Rwork0.343 795
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)
18.3737-0.86741.548110.34830.979212.51460.38741.14320.2328-1.30360.3792-1.50180.1551.869-0.76670.51690.260.22520.7380.07870.213651.1853.16518.977
210.0123-4.1997-2.15178.58691.995410.8910.48891.12560.1512-1.0495-0.2865-0.34430.3460.4538-0.20240.66920.2594-0.0780.525-0.01180.299843.59850.24424.909
310.9095-1.8271-1.40695.30653.196411.46290.02910.0796-0.029-0.2945-0.1297-0.07610.5746-0.13970.10060.63490.2093-0.16610.3387-0.04360.351736.54551.15531.65
49.3388-3.5612-3.18934.13171.439210.2952-0.0186-0.1969-0.0159-0.16470.01590.35660.2387-0.11350.00270.5350.1611-0.15960.3432-0.02760.438529.66954.21138.005
57.2145-2.18141.57577.28334.317611.2555-0.0169-0.06950.0470.21950.08090.46630.09560.081-0.0640.42440.0357-0.02610.4342-0.06890.495323.5858.0644.026
67.7416-2.6589-2.16635.42673.716314.8177-0.0282-0.46190.40790.26090.14330.5893-0.03480.3261-0.11510.33330.04930.0350.3658-0.12620.528119.04864.96150.302
77.2799-1.0086-5.99154.20385.63917.62560.2866-0.70730.98520.4898-0.03290.1715-0.17210.0341-0.25370.45920.00520.12680.3435-0.15870.670813.61169.74654.737
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 39
2X-RAY DIFFRACTION2A40 - 71
3X-RAY DIFFRACTION3A72 - 104
4X-RAY DIFFRACTION4A105 - 137
5X-RAY DIFFRACTION5A138 - 170
6X-RAY DIFFRACTION6A171 - 203
7X-RAY DIFFRACTION7A204 - 226
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.233 / Rfactor Rwork: 0.187
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.011
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.281

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