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- PDB-7elk: Solution structure of Terfa derived from Danio rerio -

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Basic information

Entry
Database: PDB / ID: 7elk
TitleSolution structure of Terfa derived from Danio rerio
ComponentsTerfa protein
KeywordsDNA BINDING PROTEIN / Telomere binding protein / Myb domain / human telomeric DNA / plant telomeric DNA
Function / homology
Function and homology information


negative regulation of telomere maintenance via recombination / telomeric loop formation / negative regulation of telomeric D-loop disassembly / protection from non-homologous end joining at telomere / RNA-templated DNA biosynthetic process / telomeric D-loop disassembly / shelterin complex / double-stranded telomeric DNA binding / regulation of telomere maintenance via telomerase / G-rich strand telomeric DNA binding ...negative regulation of telomere maintenance via recombination / telomeric loop formation / negative regulation of telomeric D-loop disassembly / protection from non-homologous end joining at telomere / RNA-templated DNA biosynthetic process / telomeric D-loop disassembly / shelterin complex / double-stranded telomeric DNA binding / regulation of telomere maintenance via telomerase / G-rich strand telomeric DNA binding / protein localization to chromosome, telomeric region / cell cycle / protein homodimerization activity
Similarity search - Function
Telomeric repeat-binding factor 2 / Telomere repeat-binding factor, dimerisation domain superfamily / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / Myb-like domain profile. / 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 / Homeobox-like domain superfamily
Similarity search - Domain/homology
Biological speciesDanio rerio (zebrafish)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsYun, J.H. / Kim, M. / Lee, W.
CitationJournal: To Be Published
Title: Solution structure of Terfa derived from Danio rerio
Authors: Kim, M. / Yun, J.H. / Lee, W.
History
DepositionApr 11, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1May 15, 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: Terfa protein


Theoretical massNumber of molelcules
Total (without water)7,4701
Polymers7,4701
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Terfa protein


Mass: 7469.786 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: terfa / Production host: Escherichia coli (E. coli) / References: UniProt: Q4QRH9

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111anisotropic23D-NOESY
121anisotropic23D (H)CCH-TOCSY
131anisotropic13D HN(CA)CB
141anisotropic13D CBCA(CO)NH
151anisotropic13D HNCO
162anisotropic23D 1H-15N NOESY
171anisotropic12D 1H-15N HSQC NH2 only

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution11 mM [U-13C; U-15N] Terfa, 90% H2O/10% D2O13C_15N sample90% H2O/10% D2O
solution21 mM [U-15N] Terfa, 90% H2O/10% D2O15N sample90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMTerfa[U-13C; U-15N]1
1 mMTerfa[U-15N]2
Sample conditionsIonic strength: 50 mM / Label: experimental condition / pH: 6.0 pH* / Pressure: AMBIENT Pa / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE DRXBrukerAVANCE DRX6001
Bruker AVANCE DRXBrukerAVANCE DRX8502

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.2.5Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
Sparky2.2.5Goddardchemical shift assignment
CYANAGuntert, Mumenthaler and Wuthrichstructure calculation
SparkyGoddardpeak picking
XwinNMRBruker Biospincollection
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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