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- PDB-5ci9: Crystal structure of human Tob in complex with inhibitor fragment 6 -

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Basic information

Entry
Database: PDB / ID: 5ci9
TitleCrystal structure of human Tob in complex with inhibitor fragment 6
ComponentsProtein Tob1
KeywordsTRANSCRIPTION/INHIBITOR / Tob/BTG family / TRANSCRIPTION-INHIBITOR complex
Function / homology
Function and homology information


negative regulation of nuclear-transcribed mRNA poly(A) tail shortening / regulation of SMAD protein signal transduction / CCR4-NOT complex / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / SMAD binding / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of BMP signaling pathway / negative regulation of osteoblast differentiation / receptor tyrosine kinase binding / transcription corepressor activity ...negative regulation of nuclear-transcribed mRNA poly(A) tail shortening / regulation of SMAD protein signal transduction / CCR4-NOT complex / positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay / SMAD binding / positive regulation of nuclear-transcribed mRNA poly(A) tail shortening / negative regulation of BMP signaling pathway / negative regulation of osteoblast differentiation / receptor tyrosine kinase binding / transcription corepressor activity / regulation of gene expression / negative regulation of translation / negative regulation of cell population proliferation / nucleus / 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 / Actin; Chain A, domain 4 / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-549 / Protein Tob1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsBai, Y. / Tashiro, S. / Nagatoishi, S. / Suzuki, T. / Tsumoto, K. / Bartlam, M. / Yamamoto, T.
Funding support China, Japan, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology2014CB560709 China
Ministry of Education, Culture, Sports, Science and Technology (Japan) Japan
KAKENHI25121734 Japan
CitationJournal: Protein Cell / Year: 2015
Title: Structural basis for inhibition of the Tob-CNOT7 interaction by a fragment screening approach
Authors: Bai, Y. / Tashiro, S. / Nagatoishi, S. / Suzuki, T. / Yan, D. / Liu, R. / Tsumoto, K. / Bartlam, M. / Yamamoto, T.
History
DepositionJul 11, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 9, 2015Group: Database references
Revision 1.2Mar 20, 2024Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_audit_support / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein Tob1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,7584
Polymers38,3271
Non-polymers4313
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-7 kcal/mol
Surface area7030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.119, 65.119, 162.945
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Protein Tob1 / Transducer of erbB-2 1


Mass: 38326.918 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TOB1, TOB, TROB1 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P50616
#2: Chemical ChemComp-549 / 1-(propan-2-yl)-1H-benzimidazole-5-carboxylic acid


Mass: 204.225 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H12N2O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 1.301063 Å3/Da / Density % sol: 5.461893 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M Citric acid pH 5.0, 3.0 M Sodium chloride, 5% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 20, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 9738 / % possible obs: 99.6 % / Redundancy: 18.5 % / Net I/σ(I): 32.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 2.3→39.121 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 32.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2644 946 10.15 %Random selection
Rwork0.2141 ---
obs0.2192 9317 95.75 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.3→39.121 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms957 0 31 5 993
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071013
X-RAY DIFFRACTIONf_angle_d1.021371
X-RAY DIFFRACTIONf_dihedral_angle_d15.848393
X-RAY DIFFRACTIONf_chiral_restr0.039138
X-RAY DIFFRACTIONf_plane_restr0.004175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2998-2.42110.38531250.30471069X-RAY DIFFRACTION89
2.4211-2.57270.28861290.2321102X-RAY DIFFRACTION92
2.5727-2.77130.31971310.23381156X-RAY DIFFRACTION95
2.7713-3.05010.32511340.23861190X-RAY DIFFRACTION97
3.0501-3.49120.27791330.22611229X-RAY DIFFRACTION99
3.4912-4.39760.22841420.19251265X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 5.3695 Å / Origin y: 30.891 Å / Origin z: 80.7585 Å
111213212223313233
T0.4185 Å20.0461 Å2-0.0443 Å2-0.5825 Å20.0453 Å2--0.4916 Å2
L8.5233 °20.3117 °2-1.8978 °2-4.5357 °20.6542 °2--2.8187 °2
S-0.0398 Å °-0.4063 Å °0.166 Å °0.3315 Å °0.0373 Å °-0.0501 Å °0.0504 Å °-0.0219 Å °0.0242 Å °
Refinement TLS groupSelection details: chain 'A' and (resid 0 through 115 )

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