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- PDB-3sjm: Crystal Structure Analysis of TRF2-Dbd-DNA complex -

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Basic information

Entry
Database: PDB / ID: 3sjm
TitleCrystal Structure Analysis of TRF2-Dbd-DNA complex
Components
  • DNA (5'-D(*CP*TP*CP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')
  • DNA (5'-D(*TP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*GP*A)-3')
  • Telomeric repeat-binding factor 2
KeywordsDNA/DNA binding protein / Human Telomeric Repeat Binding Protein 2 / telomere / telomeric repeat / Homeodomain Proteins amino acid sequence / nucleic acid / DNA-DNA binding protein complex
Function / homology
Function and homology information


axonal transport of messenger ribonucleoprotein complex / negative regulation of beta-galactosidase activity / negative regulation of telomere single strand break repair / negative regulation of telomere maintenance via recombination / telomeric loop formation / negative regulation of telomere maintenance / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / protection from non-homologous end joining at telomere ...axonal transport of messenger ribonucleoprotein complex / negative regulation of beta-galactosidase activity / negative regulation of telomere single strand break repair / negative regulation of telomere maintenance via recombination / telomeric loop formation / negative regulation of telomere maintenance / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / protection from non-homologous end joining at telomere / negative regulation of telomere capping / RNA-templated DNA biosynthetic process / negative regulation of t-circle formation / telomeric D-loop disassembly / shelterin complex / Telomere C-strand synthesis initiation / double-stranded telomeric DNA binding / Telomere C-strand (Lagging Strand) Synthesis / regulation of telomere maintenance via telomerase / Processive synthesis on the C-strand of the telomere / nuclear telomere cap complex / G-rich strand telomeric DNA binding / positive regulation of telomere maintenance / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / anterograde axonal transport / telomere capping / regulation of telomere maintenance / protein localization to chromosome, telomeric region / negative regulation of telomere maintenance via telomere lengthening / telomeric DNA binding / negative regulation of cellular senescence / negative regulation of telomere maintenance via telomerase / Telomere Extension By Telomerase / Packaging Of Telomere Ends / axon cytoplasm / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere maintenance / male germ cell nucleus / positive regulation of nitric-oxide synthase activity / DNA Damage/Telomere Stress Induced Senescence / cellular senescence / in utero embryonic development / chromosome, telomeric region / nuclear body / cell cycle / negative regulation of gene expression / protein-containing complex binding / positive regulation of gene expression / enzyme binding / protein homodimerization activity / nucleoplasm / nucleus
Similarity search - Function
Telomeric repeat-binding factor 2, Rap1-binding domain / Telomeric repeat-binding factor 2 Rap1-binding motif / Telomeric repeat-binding factor 2 / Telomeric repeat-binding factor 1/2 / Telomere repeat-binding factor, dimerisation domain superfamily / 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 ...Telomeric repeat-binding factor 2, Rap1-binding domain / Telomeric repeat-binding factor 2 Rap1-binding motif / Telomeric repeat-binding factor 2 / Telomeric repeat-binding factor 1/2 / Telomere repeat-binding factor, dimerisation domain superfamily / 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 / Homeodomain-like / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / Telomeric repeat-binding factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsNair, S.K. / Sliverman, S.K. / Chen, J.H. / Xiao, Y.
CitationJournal: To be Published
Title: Crystal Structure Analysis of TRF2-Dbd-DNA complex
Authors: Nair, S.K. / Sliverman, S.K. / Chen, J.H. / Xiao, Y.
History
DepositionJun 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 28, 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

Downloads & links

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Assembly

Deposited unit
C: DNA (5'-D(*CP*TP*CP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')
D: DNA (5'-D(*TP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*GP*A)-3')
A: Telomeric repeat-binding factor 2
B: Telomeric repeat-binding factor 2


Theoretical massNumber of molelcules
Total (without water)26,0124
Polymers26,0124
Non-polymers00
Water5,368298
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-28 kcal/mol
Surface area10950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.073, 47.454, 108.172
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: DNA chain DNA (5'-D(*CP*TP*CP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*G)-3')


Mass: 5602.625 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*TP*CP*TP*AP*AP*CP*CP*CP*TP*AP*AP*CP*CP*CP*TP*AP*GP*A)-3')


Mass: 5404.533 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Telomeric repeat-binding factor 2 / / TTAGGG repeat-binding factor 2 / Telomeric DNA-binding protein


Mass: 7502.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: telomeric repeat binding factor 2, TERF2, TRBF2, TRF2 / Plasmid: pET28b/thrombin / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta / References: UniProt: Q15554
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.17 Å3/Da / Density % sol: 43.43 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 50 mM HEPES, pH 7.5, 1 mM spermine, 2 M ammonium sulfate and 40 mM Mg(OAc)2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Feb 16, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 48737 / % possible obs: 96.2 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 11.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→35.67 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.955 / SU ML: 0.044 / Cross valid method: THROUGHOUT / ESU R: 0.061 / ESU R Free: 0.059 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2081 2429 5 %RANDOM
Rwork0.17215 ---
obs0.17399 46231 96.22 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Refinement stepCycle: LAST / Resolution: 1.35→35.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms922 697 0 298 1917
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0211746
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.6232.4362507
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7425116
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.05723.33345
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46215183
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.065158
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined0.020.021089
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.351→1.386 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 127 -
Rwork0.264 2591 -
obs--73.78 %

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