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- PDB-1ity: Solution structure of the DNA binding domain of human TRF1 -

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Basic information

Entry
Database: PDB / ID: 1ity
TitleSolution structure of the DNA binding domain of human TRF1
ComponentsTRF1
KeywordsDNA BINDING PROTEIN / helix-turn-helix / telomeres / DNA binding / Myb domain / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


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 / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering / telomeric D-loop disassembly / t-circle formation ...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 / negative regulation of telomere maintenance via semi-conservative replication / negative regulation of exonuclease activity / negative regulation of telomeric D-loop disassembly / meiotic telomere clustering / telomeric D-loop disassembly / t-circle formation / shelterin complex / Telomere C-strand synthesis initiation / double-stranded telomeric DNA binding / 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 / ankyrin repeat binding / Removal of the Flap Intermediate from the C-strand / telomere capping / negative regulation of telomere maintenance via telomerase / DNA binding, bending / negative regulation of telomere maintenance via telomere lengthening / telomeric DNA binding / negative regulation of DNA replication / negative regulation of telomerase activity / 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 / Inhibition of DNA recombination at telomere / Meiotic synapsis / telomere maintenance / DNA Damage/Telomere Stress Induced Senescence / spindle / fibrillar center / microtubule binding / chromosome, telomeric region / molecular adaptor activity / nuclear body / cell division / nucleolus / protein homodimerization activity / DNA binding / nucleoplasm / identical protein binding / nucleus / cytoplasm
Similarity search - Function
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 ...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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry, simulated annealing
AuthorsNishikawa, T. / Okamura, H. / Nagadoi, A. / Konig, P. / Rhodes, D. / Nishimura, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Structure / Year: 2001
Title: Solution structure of a telomeric DNA complex of human TRF1
Authors: Nishikawa, T. / Okamura, H. / Nagadoi, A. / Konig, P. / Rhodes, D. / Nishimura, Y.
History
DepositionFeb 15, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 23, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TRF1


Theoretical massNumber of molelcules
Total (without water)8,4681
Polymers8,4681
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 100structures with the least restraint violations
RepresentativeModel #2closest to the average

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Components

#1: Protein TRF1 / / Telomeric repeat binding factor 1


Mass: 8467.753 Da / Num. of mol.: 1 / Fragment: DNA binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TRF1 / Plasmid: pET13A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P54274

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D HNHA, 3D HNHB, 3D Sequential assignment protocol, 3D 15N separated NOESY, 3D 13C separated NOESY, 2D NOESY, 2D TOCSY, 2D DQF-COSY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1.5-2.5mM TRF1 U-15N, 13C, 50mM phosphate buffer, 100mM NaCl
Solvent system: 90% H2O, 10% D2O, 100% D2O
Sample conditionspH: 6.8 / Pressure: ambient / Temperature: 300 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker DRXBrukerDRX5002
Bruker AMXBrukerAMX5003

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Processing

NMR softwareName: EMBOSS / Version: 5 / Developer: Nakai, T., Kidera, A., and Nakamura, H. / Classification: refinement
RefinementMethod: distance geometry, simulated annealing / Software ordinal: 1
Details: The structures are generated by 4D simulated annealing with EMBOSS, based on a total of 916 experimental restraints, 852 are NOE-derived distance restraints, 36 hydrogen restraints and 28 ...Details: The structures are generated by 4D simulated annealing with EMBOSS, based on a total of 916 experimental restraints, 852 are NOE-derived distance restraints, 36 hydrogen restraints and 28 dihedral restraints. 25 out of 100 structures which have the lowest violation and a low energies were selected for the final set.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 25

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