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- PDB-8x6d: Crystal structure of the C-terminal TBF1 -

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Basic information

Entry
Database: PDB / ID: 8x6d
TitleCrystal structure of the C-terminal TBF1
Components
  • DNA (5'-D(P*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*C)-3')
  • DNA (5'-D(P*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')
  • Protein TBF1
KeywordsDNA BINDING PROTEIN / telomere / DNA damage response / gene transcription
Function / homology
Function and homology information


snoRNA transcription by RNA polymerase II / chromatin insulator sequence binding / telomere maintenance via telomere lengthening / double-stranded telomeric DNA binding / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / DNA-binding transcription factor activity, RNA polymerase II-specific / chromosome, telomeric region / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling ...snoRNA transcription by RNA polymerase II / chromatin insulator sequence binding / telomere maintenance via telomere lengthening / double-stranded telomeric DNA binding / telomeric DNA binding / negative regulation of telomere maintenance via telomerase / DNA-binding transcription factor activity, RNA polymerase II-specific / chromosome, telomeric region / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin remodeling / protein homodimerization activity / nucleus
Similarity search - Function
: / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
DNA / DNA (> 10) / Protein TBF1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
DNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGao, Y. / Niu, L.W.
Funding support China, 1items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Structural study of yeast TBF1 protein
Authors: Gao, Y. / Niu, L.W.
History
DepositionNov 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 27, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Protein TBF1
C: DNA (5'-D(P*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')
D: DNA (5'-D(P*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*C)-3')
E: Protein TBF1
F: Protein TBF1


Theoretical massNumber of molelcules
Total (without water)49,2505
Polymers49,2505
Non-polymers00
Water2,504139
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.794, 72.103, 63.132
Angle α, β, γ (deg.)90.000, 99.570, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Protein TBF1


Mass: 11709.684 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C (yeast) / Gene: TBF1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q02457
#2: DNA chain DNA (5'-D(P*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')


Mass: 7262.677 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#3: DNA chain DNA (5'-D(P*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*C)-3')


Mass: 6858.467 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 139 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.59 Å3/Da / Density % sol: 52.47 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Bis-Tris, pH 5.7, 20% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97849 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97849 Å / Relative weight: 1
ReflectionResolution: 2→30.31 Å / Num. obs: 33979 / % possible obs: 99.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 39.24 Å2 / CC1/2: 0.999 / Net I/σ(I): 19.2
Reflection shellResolution: 2→2.071 Å / Num. unique obs: 3354 / CC1/2: 0.928

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→30.31 Å / SU ML: 0.2622 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.6665
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2374 1711 5.06 %
Rwork0.2042 32112 -
obs0.2058 33823 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 48.55 Å2
Refinement stepCycle: LAST / Resolution: 2→30.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1951 943 0 139 3033
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00363044
X-RAY DIFFRACTIONf_angle_d0.60344296
X-RAY DIFFRACTIONf_chiral_restr0.0325470
X-RAY DIFFRACTIONf_plane_restr0.0033379
X-RAY DIFFRACTIONf_dihedral_angle_d23.34641243
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.060.36291230.30982637X-RAY DIFFRACTION98.75
2.06-2.130.32861380.28042698X-RAY DIFFRACTION99.2
2.13-2.20.26481480.27842616X-RAY DIFFRACTION99.21
2.2-2.290.32921410.25512679X-RAY DIFFRACTION99.58
2.29-2.390.29861440.24692660X-RAY DIFFRACTION99.64
2.39-2.520.26791500.24352681X-RAY DIFFRACTION99.54
2.52-2.680.30571380.25782675X-RAY DIFFRACTION99.89
2.68-2.880.33761530.25512680X-RAY DIFFRACTION99.72
2.88-3.170.28411470.24542680X-RAY DIFFRACTION99.58
3.17-3.630.25531460.21542649X-RAY DIFFRACTION98.21
3.63-4.570.16871300.15772725X-RAY DIFFRACTION99.76
4.57-30.310.17481530.14982732X-RAY DIFFRACTION99.31

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