[English] 日本語
Yorodumi
- PDB-1uoh: HUMAN GANKYRIN -

+
Open data


ID or keywords:

Loading...

-
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


cytoplasmic sequestering of NF-kappaB / proteasome regulatory particle assembly / Regulation of ornithine decarboxylase (ODC) / intermediate filament cytoskeleton / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / protein localization to chromosome, telomeric region / negative regulation of MAPK cascade / negative regulation of NF-kappaB transcription factor activity / negative regulation of release of cytochrome c from mitochondria ...cytoplasmic sequestering of NF-kappaB / proteasome regulatory particle assembly / Regulation of ornithine decarboxylase (ODC) / intermediate filament cytoskeleton / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / protein localization to chromosome, telomeric region / 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 / positive regulation of telomere capping / transcription factor binding / positive regulation of cyclin-dependent protein serine/threonine kinase activity / NAD+-protein poly-ADP-ribosyltransferase 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 / protein localization to plasma membrane / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Dectin-1 mediated noncanonical NF-kB signaling / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Hh mutants are degraded by ERAD / Degradation of AXIN / Degradation of GLI1 by the proteasome / Activation of NF-kappaB in B cells / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / 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 / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / MAPK6/MAPK4 signaling / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Degradation of beta-catenin by the destruction complex / ABC-family proteins mediated transport / 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 / Antigen processing: Ubiquitination & Proteasome degradation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / positive regulation of canonical Wnt signaling pathway / Downstream TCR signaling / protein-macromolecule adaptor activity / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / 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 / cytoplasm / cytosol
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 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more