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- PDB-7oz0: Solution structure of the N-terminal domain of human telomeric Re... -

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Basic information

Entry
Database: PDB / ID: 7oz0
TitleSolution structure of the N-terminal domain of human telomeric Repeat-binding factor 2-interacting protein 1 (hRap1): implication for Rap1-TRF2 interaction in Human.
ComponentsTelomeric repeat-binding factor 2-interacting protein 1
KeywordsTRANSCRIPTION / Telomere Integrity
Function / homology
Function and homology information


negative regulation of DNA recombination at telomere / protection from non-homologous end joining at telomere / negative regulation of telomere maintenance / shelterin complex / telomere maintenance via telomere lengthening / Telomere C-strand synthesis initiation / Telomere C-strand (Lagging Strand) Synthesis / nuclear telomere cap complex / G-rich strand telomeric DNA binding / telomere capping ...negative regulation of DNA recombination at telomere / protection from non-homologous end joining at telomere / negative regulation of telomere maintenance / shelterin complex / telomere maintenance via telomere lengthening / Telomere C-strand synthesis initiation / 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 / regulation of telomere maintenance / protein localization to chromosome, telomeric region / regulation of double-strand break repair via homologous recombination / nuclear chromosome / telomeric DNA binding / positive regulation of telomere maintenance / negative regulation of protein phosphorylation / 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 / male germ cell nucleus / positive regulation of non-canonical NF-kappaB signal transduction / DNA Damage/Telomere Stress Induced Senescence / positive regulation of NF-kappaB transcription factor activity / positive regulation of canonical NF-kappaB signal transduction / chromosome, telomeric region / intracellular signal transduction / nuclear body / 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 / BRCT domain / BRCT domain superfamily / Homeobox-like domain superfamily
Similarity search - Domain/homology
Telomeric repeat-binding factor 2-interacting protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsMiron, S. / LeDU, M.H. / Gaullier, G. / Zinn-justin, S. / Cuniasse, P.
Funding support France, 2items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)Teloloop : ANR-1582-30020690 France
French Infrastructure for Integrated Structural Biology (FRISBI) France
CitationJournal: To Be Published
Title: Solution structure of the N-terminal domain of human telomeric Repeat-binding factor 2-interacting protein 1 (hRap1): implication for Rap1-TRF2 interaction in Human.
Authors: Miron, S. / LeDU, M.H. / Gaullier, G. / Zinn-justin, S. / Cuniasse, P.
History
DepositionJun 25, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Telomeric repeat-binding factor 2-interacting protein 1


Theoretical massNumber of molelcules
Total (without water)12,1391
Polymers12,1391
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8520 Å2
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100target function
RepresentativeModel #1closest to the average

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Components

#1: Protein Telomeric repeat-binding factor 2-interacting protein 1 / TERF2-interacting telomeric protein 1 / TRF2-interacting telomeric protein 1 / Dopamine receptor- ...TERF2-interacting telomeric protein 1 / TRF2-interacting telomeric protein 1 / Dopamine receptor-interacting protein 5 / Repressor/activator protein 1 homolog / RAP1 homolog / hRap1


Mass: 12138.556 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TERF2IP, DRIP5, RAP1, PP8000 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NYB0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
131isotropic13D HN(CA)CB
141isotropic13D HNCO
151isotropic13D HN(CA)CO
181isotropic13D (H)CCH-TOSCY
1131isotropic13D 1H-15N NOESY
191isotropic13D 1H-15N TOCSY
1101isotropic23D 15N NOESY-HSQC
1111isotropic23D 13C (aromatic)NOESY-HSQC
1121isotropic23D 13C(aliphatic)NOESY-HSQC

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Sample preparation

DetailsType: solution
Contents: 100 uM [U-100% 13C; U-100% 15N] human Telomeric Repeat-binding factor 2-interacting protein 1 (hRAP1), 90% H2O/10% D2O
Details: 50 mM MES Buffer / Label: 15N_13C_Sample / Solvent system: 90% H2O/10% D2O
SampleConc.: 100 uM
Component: human Telomeric Repeat-binding factor 2-interacting protein 1 (hRAP1)
Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 150 mM NaCl Not defined / Label: 15N_13C / pH: 6.5 / Pressure: 1 atm / Temperature: 293 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIBrukerAVANCE II7001
Bruker AVANCE IIIBrukerAVANCE III9502

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Processing

NMR software
NameVersionDeveloperClassification
TopSpin4.0.7Bruker Biospinprocessing
CcpNmr Analysis2.4.2CCPNchemical shift assignment
CcpNmr Analysis2.4.2CCPNpeak picking
CYANA3.98.5Guntert, Mumenthaler and Wuthrichstructure calculation
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 5 / Details: Explicit Water
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 20

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