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

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Basic information

Entry
Database: PDB / ID: 2dwz
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
KeywordsONCOPROTEIN / ANKYRIN REPEATS / A-HELICAL DOMAIN / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


Cross-presentation of soluble exogenous antigens (endosomes) / Proteasome assembly / Regulation of ornithine decarboxylase (ODC) / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Autodegradation of Cdh1 by Cdh1:APC/C / SCF-beta-TrCP mediated degradation of Emi1 / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 ...Cross-presentation of soluble exogenous antigens (endosomes) / Proteasome assembly / Regulation of ornithine decarboxylase (ODC) / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Autodegradation of Cdh1 by Cdh1:APC/C / SCF-beta-TrCP mediated degradation of Emi1 / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins / Degradation of DVL / Hedgehog ligand biogenesis / Dectin-1 mediated noncanonical NF-kB signaling / Degradation of GLI1 by the proteasome / Hedgehog 'on' state / TNFR2 non-canonical NF-kB pathway / NIK-->noncanonical NF-kB signaling / Assembly of the pre-replicative complex / CDK-mediated phosphorylation and removal of Cdc6 / G2/M Checkpoints / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Ubiquitin-dependent degradation of Cyclin D / The role of GTSE1 in G2/M progression after G2 checkpoint / FBXL7 down-regulates AURKA during mitotic entry and in early mitosis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Regulation of RUNX3 expression and activity / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / GLI3 is processed to GLI3R by the proteasome / Activation of NF-kappaB in B cells / Degradation of beta-catenin by the destruction complex / Degradation of AXIN / UCH proteinases / Regulation of RAS by GAPs / Orc1 removal from chromatin / Neddylation / AUF1 (hnRNP D0) binds and destabilizes mRNA / MAPK6/MAPK4 signaling / Regulation of PTEN stability and activity / Proteasome assembly / KEAP1-NFE2L2 pathway / Separation of Sister Chromatids / Antigen processing: Ubiquitination & Proteasome degradation / ABC-family proteins mediated transport / Ub-specific processing proteases / proteasome regulatory particle assembly / cytosolic proteasome complex / proteasome accessory complex / positive regulation of cyclin-dependent protein serine/threonine kinase activity / proteasome-activating activity / proteasome regulatory particle, base subcomplex / 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 / inclusion body / proteasome complex / positive regulation of protein ubiquitination / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / microtubule cytoskeleton / positive regulation of cell growth / proteasome-mediated ubiquitin-dependent protein catabolic process / cilium / apoptotic process / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / ATP binding / nucleus / 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)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsPadmanabhan, B. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Structure of the Oncoprotein Gankyrin in Complex with S6 ATPase of the 26S Proteasome
Authors: Nakamura, Y. / Nakano, K. / Umehara, T. / Tanaka, A. / Padmanabhan, B. / Yokoyama, S.
History
DepositionAug 22, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 28, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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
B: 26S protease regulatory subunit 6B
C: 26S proteasome non-ATPase regulatory subunit 10
D: 26S protease regulatory subunit 6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,0005
Polymers69,7614
Non-polymers2381
Water4,197233
1
A: 26S proteasome non-ATPase regulatory subunit 10
B: 26S protease regulatory subunit 6B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1193
Polymers34,8812
Non-polymers2381
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 26S proteasome non-ATPase regulatory subunit 10
D: 26S protease regulatory subunit 6B


Theoretical massNumber of molelcules
Total (without water)34,8812
Polymers34,8812
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.991, 92.319, 167.191
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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Z2X2
#2: Protein 26S protease regulatory subunit 6B / TAT-BINDING PROTEIN-7 / TBP-7


Mass: 9793.156 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: Q63570
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 233 / 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: 2.32 Å3/Da / Density % sol: 47.03 %
Crystal growDetails: VAPOR DIFFUSION

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 25, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 24356 / % possible obs: 92.6 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.073
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.313 / % possible all: 85.3

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Processing

Software
NameVersionClassification
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→20 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.268 2268 -RANDOM
Rwork0.194 ---
obs0.194 23168 88.2 %-
Displacement parametersBiso mean: 31.9 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4616 0 15 233 4864
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
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: 2.4→2.55 Å / Rfactor Rfree error: 0.017
RfactorNum. reflection% reflection
Rfree0.292 346 -
Rwork0.215 --
obs--77.2 %

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