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- PDB-5ci8: Crystal structure of human Tob in complex with inhibitor fragment 1 -

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Basic information

Entry
Database: PDB / ID: 5ci8
TitleCrystal structure of human Tob in complex with inhibitor fragment 1
ComponentsProtein Tob1
KeywordsTRANSCRIPTION/INHIBITOR / Tob/BTG family / inhibitor / complex / 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
pyrrolo[1,2-a]quinoxalin-4(5H)-one / Protein Tob1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.328 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein Tob1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,6492
Polymers38,4651
Non-polymers1841
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6870 Å2
Unit cell
Length a, b, c (Å)64.975, 64.975, 163.677
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: 38465.062 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-53Y / pyrrolo[1,2-a]quinoxalin-4(5H)-one


Mass: 184.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8N2O

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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: 1.296461 Å3/Da / Density % sol: 5.126324 %
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: 2.31→50 Å / Num. obs: 8867 / % possible obs: 94.4 % / Redundancy: 12.5 % / Net I/σ(I): 52.6

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.328→39.17 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 35.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2847 880 9.97 %Random selection
Rwork0.2324 ---
obs0.2379 8828 93.98 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.328→39.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms968 0 14 0 982
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081011
X-RAY DIFFRACTIONf_angle_d1.0441365
X-RAY DIFFRACTIONf_dihedral_angle_d17.163381
X-RAY DIFFRACTIONf_chiral_restr0.039139
X-RAY DIFFRACTIONf_plane_restr0.005175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3282-2.47410.35121320.34861193X-RAY DIFFRACTION88
2.4741-2.66510.37621470.30611319X-RAY DIFFRACTION97
2.6651-2.93320.28831510.2651352X-RAY DIFFRACTION98
2.9332-3.35740.34091470.25461350X-RAY DIFFRACTION97
3.3574-4.22920.25561450.24481312X-RAY DIFFRACTION92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.64192.1206-0.67513.91683.35755.3109-0.5536-0.0591-0.25540.42570.60150.2057-0.11440.6006-0.07780.5443-0.05560.04070.8046-0.01970.860427.8126-23.72657.6836
26.12353.83830.43646.97611.23992.5116-0.376-0.17510.06390.26530.6896-0.4402-0.13210.4536-0.23460.5243-0.03720.08020.84820.0380.863633.7609-23.15921.9332
32.16611.9164-0.10982.32670.71722.68020.9974-0.51411.4486-0.3879-0.21350.7979-1.4867-1.2577-0.12810.86120.0733-0.09730.9298-0.03661.915713.2127-12.66592.6165
43.3453-1.9185-1.2043.6769-1.34938.62950.32911.2489-0.0042-0.5147-0.6460.38070.6265-0.1034-0.0690.74620.03560.03691.0014-0.03970.91428.3811-25.1811-6.5811
53.1932.7348-2.79293.2237-0.16738.17-0.17951.4858-2.8762-1.65740.478-1.3030.6654-0.24450.06640.77270.0204-0.02890.9115-0.27961.332835.4566-34.7016-6.4
64.70120.462-0.52189.4039-1.32193.24270.3520.3985-0.289-0.3812-0.22310.93160.2053-0.29650.20560.5296-0.0181-0.15190.7437-0.13521.008519.7038-28.05191.6066
73.30561.37182.15219.53550.81847.790.31070.8042-0.2832-0.63870.02720.72990.18680.28520.34760.4937-0.0107-0.04830.9769-0.12381.100815.7382-29.76785.3734
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 45 )
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 52 )
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 75 )
5X-RAY DIFFRACTION5chain 'A' and (resid 76 through 85 )
6X-RAY DIFFRACTION6chain 'A' and (resid 86 through 103 )
7X-RAY DIFFRACTION7chain 'A' and (resid 104 through 115 )

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