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- PDB-3bua: Crystal Structure of TRF2 TRFH domain and APOLLO peptide complex -

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Basic information

Entry
Database: PDB / ID: 3bua
TitleCrystal Structure of TRF2 TRFH domain and APOLLO peptide complex
Components
  • DNA cross-link repair 1B protein
  • Telomeric repeat-binding factor 2
KeywordsDNA BINDING PROTEIN / TRF2 TRFH domain Dimerization domain APOLLO peptide / Alternative splicing / Cell cycle / Chromosomal protein / DNA-binding / Nucleus / Phosphoprotein / Telomere / DNA damage / DNA repair / Polymorphism
Function / homology
Function and homology information


telomeric 3' overhang formation / 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 via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / negative regulation of telomere capping ...telomeric 3' overhang formation / 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 via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / negative regulation of telomere capping / protection from non-homologous end joining at telomere / negative regulation of t-circle formation / telomerase activity / telomere maintenance via telomere lengthening / 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 / 5'-3' exonuclease activity / positive regulation of telomere maintenance / nuclear telomere cap complex / 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 / anterograde axonal transport / G-rich strand telomeric DNA binding / telomere capping / regulation of telomere maintenance / 5'-3' DNA exonuclease activity / negative regulation of telomere maintenance via telomere lengthening / protein localization to chromosome, telomeric region / telomeric DNA binding / negative regulation of cellular senescence / negative regulation of telomere maintenance via telomerase / Telomere Extension By Telomerase / interstrand cross-link repair / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / axon cytoplasm / 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 / positive regulation of nitric-oxide synthase activity / male germ cell nucleus / Fanconi Anemia Pathway / DNA Damage/Telomere Stress Induced Senescence / double-strand break repair via nonhomologous end joining / beta-lactamase activity / beta-lactamase / cellular senescence / in utero embryonic development / chromosome, telomeric region / damaged DNA binding / Hydrolases; Acting on ester bonds / nuclear body / cell cycle / negative regulation of gene expression / centrosome / protein-containing complex binding / positive regulation of gene expression / enzyme binding / protein homodimerization activity / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
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 ...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 / DNA repair metallo-beta-lactamase / DNA repair metallo-beta-lactamase / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / Homeobox-like domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Mainly Alpha
Similarity search - Domain/homology
Telomeric repeat-binding factor 2 / 5' exonuclease Apollo
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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

Downloads & links

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Assembly

Deposited unit
A: Telomeric repeat-binding factor 2
B: Telomeric repeat-binding factor 2
C: Telomeric repeat-binding factor 2
D: Telomeric repeat-binding factor 2
E: DNA cross-link repair 1B protein
F: DNA cross-link repair 1B protein
G: DNA cross-link repair 1B protein
H: DNA cross-link repair 1B protein


Theoretical massNumber of molelcules
Total (without water)112,2268
Polymers112,2268
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Telomeric repeat-binding factor 2
E: DNA cross-link repair 1B protein


Theoretical massNumber of molelcules
Total (without water)28,0572
Polymers28,0572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
MethodPISA
3
B: Telomeric repeat-binding factor 2
F: DNA cross-link repair 1B protein


Theoretical massNumber of molelcules
Total (without water)28,0572
Polymers28,0572
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
MethodPISA
4
C: Telomeric repeat-binding factor 2
G: DNA cross-link repair 1B protein


Theoretical massNumber of molelcules
Total (without water)28,0572
Polymers28,0572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
MethodPISA
5
D: Telomeric repeat-binding factor 2
H: DNA cross-link repair 1B protein


Theoretical massNumber of molelcules
Total (without water)28,0572
Polymers28,0572
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.947, 109.947, 130.830
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 23724.646 Da / Num. of mol.: 4 / Fragment: TRFH domain, dimerization domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TERF2, TRBF2, TRF2 / Plasmid: PET 28B-sumo / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q15554
#2: Protein/peptide
DNA cross-link repair 1B protein / hSNM1B


Mass: 4331.907 Da / Num. of mol.: 4 / Fragment: UNP residues 495-530
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DCLRE1B, SNM1B / Plasmid: PET 28B-sumo / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q9H816
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE RESIDUE SER 495 IN CHAIN E,F,G,H CAME FROM A PROTEASE SPECIFIC DIGESTION. IT IS A RESIDUAL ...THE RESIDUE SER 495 IN CHAIN E,F,G,H 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

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Sample preparation

CrystalDensity Matthews: 2.03 Å3/Da / Density % sol: 39.53 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: (NH4)2SO4 2.6 M DTT 1 mM MES 0.05 M pH 5.6 MgAc2 10 mM, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97869 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 8, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97869 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 31918 / Num. obs: 31885 / % possible obs: 99.9 % / Redundancy: 10.8 % / Biso Wilson estimate: 57.3 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 30
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 8 % / Rmerge(I) obs: 0.61 / Mean I/σ(I) obs: 2.51 / Num. unique all: 3110 / % possible all: 99.2

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Processing

Software
NameVersionClassification
Locallymodified Blu-Ice GUI 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: 2.5→50 Å / σ(F): 0
RfactorNum. reflection% reflection
Rfree0.2544 3069 -
Rwork0.2294 --
all-32152 -
obs-30645 95.3 %
Displacement parametersBiso mean: 40.2 Å2
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7042 0 0 111 7153
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006472
X-RAY DIFFRACTIONc_angle_deg1.62791
X-RAY DIFFRACTIONc_dihedral_angle_d22.25072
X-RAY DIFFRACTIONc_improper_angle_d0.98572

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