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- PDB-2d5r: Crystal Structure of a Tob-hCaf1 Complex -

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Basic information

Entry
Database: PDB / ID: 2d5r
TitleCrystal Structure of a Tob-hCaf1 Complex
Components
  • CCR4-NOT transcription complex subunit 7
  • Tob1 protein
KeywordsTRANSCRIPTION / poly(A) deadenylase / antiproliferative protein
Function / homology
Function and homology information


negative regulation of nuclear-transcribed mRNA poly(A) tail shortening / regulation of tyrosine phosphorylation of STAT protein / regulation of SMAD protein signal transduction / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT core complex / CCR4-NOT complex / miRNA-mediated gene silencing by mRNA destabilization / RNA exonuclease activity / positive regulation of mRNA catabolic process ...negative regulation of nuclear-transcribed mRNA poly(A) tail shortening / regulation of tyrosine phosphorylation of STAT protein / regulation of SMAD protein signal transduction / poly(A)-specific ribonuclease / poly(A)-specific ribonuclease activity / CCR4-NOT core complex / CCR4-NOT complex / miRNA-mediated gene silencing by mRNA destabilization / RNA exonuclease activity / positive regulation of mRNA catabolic process / nuclear-transcribed mRNA poly(A) tail shortening / deadenylation-dependent decapping of nuclear-transcribed mRNA / Deadenylation of mRNA / M-decay: degradation of maternal mRNAs by maternally stored factors / P-body assembly / regulatory ncRNA-mediated gene silencing / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / intracellular non-membrane-bounded organelle / negative regulation of type I interferon-mediated signaling pathway / SMAD binding / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of BMP signaling pathway / negative regulation of osteoblast differentiation / positive regulation of viral genome replication / P-body / receptor tyrosine kinase binding / transcription corepressor activity / regulation of translation / 3'-5'-RNA exonuclease activity / regulation of gene expression / defense response to virus / DNA-binding transcription factor binding / negative regulation of translation / nuclear body / nuclear speck / negative regulation of cell population proliferation / negative regulation of gene expression / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / RNA binding / membrane / nucleus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Tob1/2 / Anti-proliferative protein, N-terminal domain / BTG family signature 1. / BTG family signature 2. / Anti-proliferative protein / BTG-like domain superfamily / BTG family / tob/btg1 family / CCR4-NOT transcription complex subunit 7/8/Pop2 / Ribonuclease CAF1 ...Tob1/2 / Anti-proliferative protein, N-terminal domain / BTG family signature 1. / BTG family signature 2. / Anti-proliferative protein / BTG-like domain superfamily / BTG family / tob/btg1 family / CCR4-NOT transcription complex subunit 7/8/Pop2 / Ribonuclease CAF1 / CAF1 family ribonuclease / Actin; Chain A, domain 4 / Ribonuclease H-like superfamily/Ribonuclease H / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Protein Tob1 / CCR4-NOT transcription complex subunit 7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsHoriuchi, M. / Suzuki, N.N. / Muroya, N. / Takahasi, K. / Nishida, M. / Yoshida, Y. / Ikematsu, N. / Nakamura, T. / Kawamura-Tsuzuku, J. / Yamamoto, T. / Inagaki, F.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Structural basis for the antiproliferative activity of the Tob-hCaf1 complex.
Authors: Horiuchi, M. / Takeuchi, K. / Noda, N. / Muroya, N. / Suzuki, T. / Nakamura, T. / Kawamura-Tsuzuku, J. / Takahasi, K. / Yamamoto, T. / Inagaki, F.
History
DepositionNov 4, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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: CCR4-NOT transcription complex subunit 7
B: Tob1 protein


Theoretical massNumber of molelcules
Total (without water)42,9302
Polymers42,9302
Non-polymers00
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)151.505, 151.505, 114.181
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11A-329-

HOH

DetailsThe biological assembly is a hetero dimer generated from the dimer in the asymmetric unit.

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Components

#1: Protein CCR4-NOT transcription complex subunit 7 / CCR4-associated factor 1 / CAF1 / BTG1 binding factor 1


Mass: 29376.572 Da / Num. of mol.: 1 / Fragment: POLY(A) DEADENYLASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): BLR (DE3)/pLysS / References: UniProt: Q9UIV1
#2: Protein Tob1 protein / Transducer of erbB-2 1


Mass: 13553.520 Da / Num. of mol.: 1 / Fragment: BTG/TOB DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BLR (DE3)/pLysS / References: UniProt: P50616
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.81 Å3/Da / Density % sol: 67.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 12% PEG4000, 0.08M Tris, 0.16M sodium acetate, 0.01M dithiothreitol, 12% glycerol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: OXFORD PX210 / Detector: CCD / Date: Feb 3, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→58.27 Å / Num. all: 23275 / Num. obs: 23262 / % possible obs: 80.9 % / Biso Wilson estimate: 46.3 Å2
Reflection shellResolution: 2.5→2.64 Å / % possible all: 83.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CNSphasing
RefinementMethod to determine structure: MIR / Resolution: 2.5→58.27 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1267432.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.246 2327 10 %RANDOM
Rwork0.223 ---
all0.225 ---
obs0.225 18832 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.4297 Å2 / ksol: 0.357063 e/Å3
Displacement parametersBiso mean: 47.8 Å2
Baniso -1Baniso -2Baniso -3
1-3.62 Å20 Å20 Å2
2--3.62 Å20 Å2
3----7.24 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.5→58.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3023 0 0 90 3113
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.73
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.422
X-RAY DIFFRACTIONc_scbond_it2.22
X-RAY DIFFRACTIONc_scangle_it3.472.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.34 413 10.8 %
Rwork0.309 3403 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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