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- PDB-3bqo: Crystal Structure of TRF1 TRFH domain and TIN2 peptide complex -

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Basic information

Entry
Database: PDB / ID: 3bqo
TitleCrystal Structure of TRF1 TRFH domain and TIN2 peptide complex
Components
  • TERF1-interacting nuclear factor 2
  • Telomeric repeat-binding factor 1
KeywordsDNA BINDING PROTEIN / TRF1 TRFH domain Dimerization domain TIN2 / ADP-ribosylation / Alternative splicing / Cell cycle / Cell division / Chromosomal protein / DNA-binding / Mitosis / Nucleus / Phosphoprotein / Telomere
Function / homology
Function and homology information


regulation of telomere maintenance via telomere lengthening / positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / perinucleolar chromocenter / telomere assembly / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering ...regulation of telomere maintenance via telomere lengthening / positive regulation of shelterin complex assembly / negative regulation of establishment of protein localization to telomere / negative regulation of establishment of RNA localization to telomere / negative regulation of establishment of protein-containing complex localization to telomere / perinucleolar chromocenter / telomere assembly / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering / t-circle formation / telomeric D-loop disassembly / shelterin complex / Telomere C-strand synthesis initiation / double-stranded telomeric DNA binding / ankyrin repeat binding / Telomere C-strand (Lagging Strand) Synthesis / nuclear telomere cap complex / G-rich strand telomeric DNA binding / telomere capping / Processive synthesis on the C-strand of the telomere / Polymerase switching on the C-strand of the telomere / Removal of the Flap Intermediate from the C-strand / DNA binding, bending / negative regulation of telomere maintenance via telomere lengthening / protein localization to chromosome, telomeric region / telomeric DNA binding / negative regulation of DNA replication / negative regulation of telomere maintenance via telomerase / positive regulation of telomere maintenance / Telomere Extension By Telomerase / telomere maintenance via telomerase / Packaging Of Telomere Ends / 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 / telomere maintenance / Inhibition of DNA recombination at telomere / Meiotic synapsis / DNA Damage/Telomere Stress Induced Senescence / spindle / nuclear matrix / fibrillar center / negative regulation of epithelial cell proliferation / microtubule binding / chromosome, telomeric region / nuclear body / response to xenobiotic stimulus / cell division / nucleolus / protein homodimerization activity / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
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 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. ...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 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 1 / TERF1-interacting nuclear factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionDec 20, 2007Deposition 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 1
B: TERF1-interacting nuclear factor 2


Theoretical massNumber of molelcules
Total (without water)26,6892
Polymers26,6892
Non-polymers00
Water2,540141
1
A: Telomeric repeat-binding factor 1
B: TERF1-interacting nuclear factor 2

A: Telomeric repeat-binding factor 1
B: TERF1-interacting nuclear factor 2


Theoretical massNumber of molelcules
Total (without water)53,3794
Polymers53,3794
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_654-x+y+1,y,-z-1/21
Buried area6050 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.105, 117.105, 88.018
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 Telomeric repeat-binding factor 1 / TTAGGG repeat-binding factor 1 / NIMA-interacting protein 2 / Telomeric protein Pin2/TRF1


Mass: 24216.666 Da / Num. of mol.: 1 / Fragment: TRFH domain, Dimerization domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TERF1, PIN2, TRBF1, TRF, TRF1 / Plasmid: PET 28B-sumo / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P54274
#2: Protein/peptide TERF1-interacting nuclear factor 2 / TRF1-interacting nuclear protein 2


Mass: 2472.787 Da / Num. of mol.: 1 / Fragment: Nuclear localization signal
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TINF2, TIN2 / Plasmid: PET 28B-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


Mass: 18.015 Da / Num. of mol.: 141 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE SER 256 B 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: 3.26 Å3/Da / Density % sol: 62.31 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.6
Details: NaCl 2.5 M MgCl2 0.35 M Tris 0.1 M pH 8.6 DTT 5 mM , VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 19, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 24553 / Num. obs: 24517 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 20.2 % / Biso Wilson estimate: 52 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 50.3
Reflection shellResolution: 2→2.07 Å / Redundancy: 18.7 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 7.4 / Num. unique all: 2388 / % possible all: 100

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Processing

Software
NameVersionClassification
PHASERphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1H6O

1h6o


Resolution: 2→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2369 2378 -
Rwork0.2199 --
all-24571 -
obs-23998 97.7 %
Displacement parametersBiso mean: 36.3825 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1733 0 0 141 1874
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005983
X-RAY DIFFRACTIONc_angle_deg1.2367
X-RAY DIFFRACTIONc_dihedral_angle_d17.299906
X-RAY DIFFRACTIONc_improper_angle_d0.7125

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