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- PDB-3bu8: Crystal Structure of TRF2 TRFH domain and TIN2 peptide complex -

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Basic information

Entry
Database: PDB / ID: 3bu8
TitleCrystal Structure of TRF2 TRFH domain and TIN2 peptide complex
Components
  • TERF1-interacting nuclear factor 2
  • Telomeric repeat-binding factor 2
KeywordsDNA BINDING PROTEIN / TRF2 TRFH domain TRF2 dimerization domain TIN2 peptide / Alternative splicing / Cell cycle / Chromosomal protein / DNA-binding / Nucleus / Phosphoprotein / Telomere
Function / homology
Function and homology information


regulation of telomere maintenance via telomere lengthening / perinucleolar chromocenter / 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 / telomere assembly / negative regulation of telomere maintenance / negative regulation of telomere maintenance via semi-conservative replication ...regulation of telomere maintenance via telomere lengthening / perinucleolar chromocenter / 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 / telomere assembly / 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 / negative regulation of protein ADP-ribosylation / 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 / regulation of telomere maintenance via telomerase / Telomere C-strand (Lagging Strand) Synthesis / 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 / negative regulation of telomere maintenance via telomerase / 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 / 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 / nuclear matrix / negative regulation of epithelial cell proliferation / 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
TERF1-interacting nuclear factor 2, N-terminal domain / TERF1-interacting nuclear factor 2 / TERF1-interacting nuclear factor 2 N-terminus / Telomere repeat-binding factor, dimerisation 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 ...TERF1-interacting nuclear factor 2, N-terminal domain / TERF1-interacting nuclear factor 2 / TERF1-interacting nuclear factor 2 N-terminus / Telomere repeat-binding factor, dimerisation 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 / Homeobox-like domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Telomeric repeat-binding factor 2 / TERF1-interacting nuclear factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsChen, Y. / Yang, Y. / van Overbeek, M. / Donigian, J.R. / Baciu, P. / de Lange, T. / Lei, M.
CitationJournal: Science / Year: 2008
Title: A shared docking motif in TRF1 and TRF2 used for differential recruitment of telomeric proteins.
Authors: Chen, Y. / Yang, Y. / van Overbeek, M. / Donigian, J.R. / Baciu, P. / de Lange, T. / Lei, M.
History
DepositionJan 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Telomeric repeat-binding factor 2
B: Telomeric repeat-binding factor 2
C: TERF1-interacting nuclear factor 2
D: TERF1-interacting nuclear factor 2


Theoretical massNumber of molelcules
Total (without water)58,2694
Polymers58,2694
Non-polymers00
Water3,783210
1
A: Telomeric repeat-binding factor 2
B: Telomeric repeat-binding factor 2
C: TERF1-interacting nuclear factor 2
D: TERF1-interacting nuclear factor 2

A: Telomeric repeat-binding factor 2
B: Telomeric repeat-binding factor 2
C: TERF1-interacting nuclear factor 2
D: TERF1-interacting nuclear factor 2


Theoretical massNumber of molelcules
Total (without water)116,5398
Polymers116,5398
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
2
A: Telomeric repeat-binding factor 2
C: TERF1-interacting nuclear factor 2

B: Telomeric repeat-binding factor 2
D: TERF1-interacting nuclear factor 2


Theoretical massNumber of molelcules
Total (without water)58,2694
Polymers58,2694
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_454y-1/2,-x+1/2,z-1/41
Buried area5820 Å2
MethodPISA
3
A: Telomeric repeat-binding factor 2
C: TERF1-interacting nuclear factor 2


Theoretical massNumber of molelcules
Total (without water)29,1352
Polymers29,1352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
MethodPISA
4
B: Telomeric repeat-binding factor 2
D: TERF1-interacting nuclear factor 2


Theoretical massNumber of molelcules
Total (without water)29,1352
Polymers29,1352
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.235, 75.235, 181.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Telomeric repeat-binding factor 2 / / TTAGGG repeat-binding factor 2 / Telomeric DNA-binding protein


Mass: 26957.195 Da / Num. of mol.: 2 / Fragment: TRFH domain, Dimerization domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TERF2, TRBF2, TRF2 / Plasmid: PET28B-sumo / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q15554
#2: Protein/peptide TERF1-interacting nuclear factor 2 / TRF1-interacting nuclear protein 2


Mass: 2177.446 Da / Num. of mol.: 2 / Fragment: UNP residues 2-19
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TINF2, TIN2 / Plasmid: PET28b-sumo / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9BSI4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE SER 257 C AND SER 257 D CAME FROM A PROTEASE SPECIFIC DIGESTION. IT IS A RESIDUAL ...THE RESIDUE SER 257 C AND SER 257 D CAME FROM A PROTEASE SPECIFIC DIGESTION. IT IS A RESIDUAL RESIDUE AFTER DIGESTION.

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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: 2.21 Å3/Da / Density % sol: 44.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG550 MME 14%, HEPES.Na 50 mM Tris.HCl 40 mM, MgCl2 5 mM, DTT 2 mM, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 6, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.15→500 Å / Num. all: 28812 / Num. obs: 28753 / % possible obs: 99.4 % / Redundancy: 13.6 % / Biso Wilson estimate: 47.07 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 41.78
Reflection shellResolution: 2.15→2.23 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.437 / Mean I/σ(I) obs: 5.63 / Num. unique all: 2828 / % possible all: 99.9

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Processing

Software
NameVersionClassification
Blu-IceGUI interface to EPICS controldata collection
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H6P

1h6p


Resolution: 2.15→500 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2564 2700 -
Rwork0.2381 --
all-29251 -
obs-27266 93.2 %
Displacement parametersBiso mean: 51.83 Å2
Refinement stepCycle: LAST / Resolution: 2.15→500 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3554 0 0 210 3764
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007356
X-RAY DIFFRACTIONc_angle_deg1.56759
X-RAY DIFFRACTIONc_dihedral_angle_d20.8295
X-RAY DIFFRACTIONc_improper_angle_d0.90318

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