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- PDB-1fex: SOLUTION STRUCTURE OF MYB-DOMAIN OF HUMAN RAP1 -

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Entry
Database: PDB / ID: 1fex
TitleSOLUTION STRUCTURE OF MYB-DOMAIN OF HUMAN RAP1
ComponentsTRF2-INTERACTING TELOMERIC RAP1 PROTEIN
KeywordsSTRUCTURAL PROTEIN / HELIX TURN HELIX / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
Function / homology
Function and homology information


negative regulation of DNA recombination at telomere / negative regulation of telomere maintenance / protection from non-homologous end joining at telomere / telomere maintenance via telomere lengthening / shelterin complex / Telomere C-strand synthesis initiation / Telomere C-strand (Lagging Strand) Synthesis / positive regulation of telomere maintenance / nuclear telomere cap complex / Processive synthesis on the C-strand of the telomere ...negative regulation of DNA recombination at telomere / negative regulation of telomere maintenance / protection from non-homologous end joining at telomere / telomere maintenance via telomere lengthening / shelterin complex / Telomere C-strand synthesis initiation / 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 / 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 / regulation of double-strand break repair via homologous recombination / nuclear chromosome / telomeric DNA binding / Telomere Extension By Telomerase / telomere maintenance via telomerase / phosphatase binding / 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 / negative regulation of protein phosphorylation / male germ cell nucleus / DNA Damage/Telomere Stress Induced Senescence / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / chromosome, telomeric region / nuclear body / intracellular signal transduction / regulation of DNA-templated transcription / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Rap1 Myb domain / Rap1 Myb domain / TRF2-interacting telomeric protein/Rap1, C-terminal / TRF2-interacting telomeric protein/Rap1, C-terminal domain superfamily / TRF2-interacting telomeric protein/Rap1 - C terminal domain / TE2IP/Rap1 / BRCT domain, a BRCA1 C-terminus domain / Homeodomain-like / BRCT domain / BRCT domain superfamily ...Rap1 Myb domain / Rap1 Myb domain / TRF2-interacting telomeric protein/Rap1, C-terminal / TRF2-interacting telomeric protein/Rap1, C-terminal domain superfamily / TRF2-interacting telomeric protein/Rap1 - C terminal domain / TE2IP/Rap1 / BRCT domain, a BRCA1 C-terminus domain / Homeodomain-like / BRCT domain / BRCT domain superfamily / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Telomeric repeat-binding factor 2-interacting protein 1
Similarity search - Component
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsHanaoka, S. / Nishimura, Y. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.Mol.Biol. / Year: 2001
Title: NMR structure of the hRap1 Myb motif reveals a canonical three-helix bundle lacking the positive surface charge typical of Myb DNA-binding domains.
Authors: Hanaoka, S. / Nagadoi, A. / Yoshimura, S. / Aimoto, S. / Li, B. / de Lange, T. / Nishimura, Y.
History
DepositionJul 24, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 19, 2001Provider: 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 1.4May 22, 2024Group: 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: TRF2-INTERACTING TELOMERIC RAP1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)6,6611
Polymers6,6611
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)25 / 100The submitted conformer models are 25 structure with the lowest energy in those with the fewest number of constraint violations.
Representative

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Components

#1: Protein TRF2-INTERACTING TELOMERIC RAP1 PROTEIN


Mass: 6660.511 Da / Num. of mol.: 1 / Fragment: MYB-DOMAIN / Mutation: 25MDR / Source method: obtained synthetically
Details: THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THIS PEPTIDE OCCURS NATURALLY IN HUMANS (HOMO SAPIENS).
References: UniProt: Q9NYB0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121DQF-COSY
NMR detailsText: This structure was determined using standard 2D homonuclear techniques.

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Sample preparation

DetailsContents: 1.0mM protein concentration in 100mM potassium phosphate buffer pH5.5, 1mM NaN3 ; 90%H2O, 10%D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 5.5 / Pressure: 1 atm / 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 spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe4.2.5Delaglio, F., Grzesiek, S., Vuister, G.W., Zhu,G., Pfeifer, J. and Bax,A.processing
X-PLOR3.851Brnger,A.T.structure solution
X-PLOR3.851Brnger,A.T.refinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 884 restraints, 838 are NOE-derived distance constraints, 39 dihedral angle restraints, 7 distance restraints from hydrogen bonds.
NMR ensembleConformer selection criteria: The submitted conformer models are 25 structure with the lowest energy in those with the fewest number of constraint violations.
Conformers calculated total number: 100 / Conformers submitted total number: 25

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