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- PDB-1xg1: Solution structure of Myb-domain of human TRF2 -

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Basic information

Entry
Database: PDB / ID: 1xg1
TitleSolution structure of Myb-domain of human TRF2
ComponentsTelomeric repeat binding factor 2
KeywordsDNA BINDING PROTEIN / helix-turn-helix
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 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 ...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 / 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 / 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 / anterograde axonal transport / Removal of the Flap Intermediate from the C-strand / G-rich strand telomeric DNA binding / 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 / 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 / DNA Damage/Telomere Stress Induced Senescence / cellular senescence / in utero embryonic development / chromosome, telomeric region / nuclear body / negative regulation of gene expression / positive regulation of gene expression / protein-containing complex binding / 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
Telomeric repeat-binding factor 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Automated assignment of ambiguous nuclear overhauser effects with ARIA, NMR structure calculation
AuthorsPaquet, F. / Meudal, H. / Amiard, S. / Doudeau, M. / Paoletti, J. / Giraud-Panis, M.J. / Lancelot, G.
CitationJournal: C.R.Chimie / Year: 2006
Title: NMR studies of telomeric nucleoprotein complexes involving the Myb-like domain of the human telomeric protein TRF2
Authors: Bilbille, Y. / Paquet, F. / Meudal, H. / Giraud-Panis, M.J. / Lancelot, G.
History
DepositionSep 16, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 27, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Telomeric repeat binding factor 2


Theoretical massNumber of molelcules
Total (without water)7,8341
Polymers7,8341
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 150structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Telomeric repeat binding factor 2 / hTRF2 / TTAGGG repeat binding factor 2 / Telomeric DNA binding protein


Mass: 7833.939 Da / Num. of mol.: 1 / Fragment: C-terminal Myb domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET-14b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 STAR (DE3) / References: UniProt: Q15554

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
131TOCSY

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Sample preparation

DetailsContents: 2mM myb, 2mM phosphate buffer pH6, 50mM NaCl / Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50mM NaCl / pH: 5.3 / Pressure: ambient / Temperature: 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeLinuxDelaglioprocessing
ARIA1.1Lingestructure solution
ARIA1.1Lingerefinement
RefinementMethod: Automated assignment of ambiguous nuclear overhauser effects with ARIA, NMR structure calculation
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 20

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