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- PDB-2dvw: Structure of the Oncoprotein Gankyrin in Complex with S6 ATPase o... -

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Basic information

Entry
Database: PDB / ID: 2dvw
TitleStructure of the Oncoprotein Gankyrin in Complex with S6 ATPase of the 26S Proteasome
Components
  • 26S protease regulatory subunit 6B
  • 26S proteasome non-ATPase regulatory subunit 10
KeywordsCELL CYCLE/PROTEIN-BINDING / ANKYRIN REPEATS / A-HELICAL DOMAIN / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI / CELL CYCLE-PROTEIN-BINDING COMPLEX
Function / homology
Function and homology information


Proteasome assembly / proteasome regulatory particle assembly / proteasome accessory complex / positive regulation of cyclin-dependent protein serine/threonine kinase activity / proteasome-activating activity / proteasome regulatory particle, base subcomplex / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis ...Proteasome assembly / proteasome regulatory particle assembly / proteasome accessory complex / positive regulation of cyclin-dependent protein serine/threonine kinase activity / proteasome-activating activity / proteasome regulatory particle, base subcomplex / Regulation of ornithine decarboxylase (ODC) / Proteasome assembly / Cross-presentation of soluble exogenous antigens (endosomes) / Somitogenesis / 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 / blastocyst development / negative regulation of MAPK cascade / proteasome complex / Regulation of activated PAK-2p34 by proteasome mediated degradation / positive regulation of protein ubiquitination / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / Asymmetric localization of PCP proteins / Ubiquitin-dependent degradation of Cyclin D / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / AUF1 (hnRNP D0) binds and destabilizes mRNA / Vpu mediated degradation of CD4 / Assembly of the pre-replicative complex / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Degradation of DVL / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of AXIN / Hh mutants are degraded by ERAD / Activation of NF-kappaB in B cells / Degradation of GLI1 by the proteasome / Hedgehog ligand biogenesis / G2/M Checkpoints / Defective CFTR causes cystic fibrosis / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Autodegradation of the E3 ubiquitin ligase COP1 / Negative regulation of NOTCH4 signaling / Vif-mediated degradation of APOBEC3G / Regulation of RUNX3 expression and activity / Hedgehog 'on' state / 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 / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / MAPK6/MAPK4 signaling / Degradation of beta-catenin by the destruction complex / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / ABC-family proteins mediated transport / 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 / Regulation of RUNX2 expression and activity / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / UCH proteinases / KEAP1-NFE2L2 pathway / Antigen processing: Ubiquitination & Proteasome degradation / Downstream TCR signaling / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Neddylation / microtubule cytoskeleton / ER-Phagosome pathway / positive regulation of cell growth / proteasome-mediated ubiquitin-dependent protein catabolic process / Ub-specific processing proteases / ciliary basal body / cilium / apoptotic process / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / proteolysis / nucleoplasm / ATP binding / nucleus / membrane / cytosol
Similarity search - Function
: / : / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Helicase, Ruva Protein; domain 3 - #60 / Ankyrin repeat-containing domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. ...: / : / Proteasomal ATPase OB C-terminal domain / Proteasomal ATPase OB C-terminal domain / Helicase, Ruva Protein; domain 3 - #60 / Ankyrin repeat-containing domain / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / Ankyrin repeat / Helicase, Ruva Protein; domain 3 / Ankyrin repeats (3 copies) / ATPase family associated with various cellular activities (AAA) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / ATPase, AAA-type, core / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
26S proteasome regulatory subunit 6B / 26S proteasome non-ATPase regulatory subunit 10
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsYokoyama, S. / Padmanabhan, B. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Structure / Year: 2007
Title: Structure of the Oncoprotein Gankyrin in Complex with S6 ATPase of the 26S Proteasome
Authors: Nakamura, Y. / Nakano, K. / Umehara, T. / Kimura, M. / Hayashizaki, Y. / Tanaka, A. / Horikoshi, M. / Padmanabhan, B. / Yokoyama, S.
History
DepositionAug 1, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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

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Assembly

Deposited unit
A: 26S proteasome non-ATPase regulatory subunit 10
B: 26S protease regulatory subunit 6B


Theoretical massNumber of molelcules
Total (without water)34,8812
Polymers34,8812
Non-polymers00
Water5,134285
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.398, 67.886, 107.767
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: 25087.549 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Psmd10 / Plasmid: PETDUET1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z2X2
#2: Protein 26S protease regulatory subunit 6B / S6 ATPASE / MIP224 / MB67-interacting protein / TAT-binding protein 7 / TBP-7


Mass: 9793.156 Da / Num. of mol.: 1 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSMC4, TBP7 / Plasmid: PETDUET1 / Production host: Escherichia coli (E. coli) / References: UniProt: P43686
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.38 Å3/Da / Density % sol: 48.32 %

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Dec 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 14844 / % possible obs: 96.5 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.069
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.182 / % possible all: 83.9

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: gankyrin(PDB entry:1IXV)

1ixv


Resolution: 2.3→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.238 1464 -RANDOM
Rwork0.169 ---
obs0.169 14299 93.1 %-
Displacement parametersBiso mean: 24.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.24 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2327 0 0 285 2612
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.01
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018
RfactorNum. reflection% reflection
Rfree0.251 204 -
Rwork0.19 --
obs--79.5 %

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