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- PDB-2l42: The solution structure of Rap1 BRCT domain from Saccharomyces cer... -

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Basic information

Entry
Database: PDB / ID: 2l42
TitleThe solution structure of Rap1 BRCT domain from Saccharomyces cerevisiae
ComponentsDNA-binding protein RAP1
KeywordsPROTEIN BINDING / Rap1 / BRCT domain / DNA BINDING PROTEIN
Function / homology
Function and homology information


positive regulation of ribosomal protein gene transcription by RNA polymerase II / G-quadruplex DNA formation / telomeric G-quadruplex DNA binding / protection from non-homologous end joining at telomere / establishment of protein localization to telomere / shelterin complex / telomere maintenance via telomere lengthening / establishment of protein localization to chromatin / double-stranded telomeric DNA binding / G-quadruplex DNA binding ...positive regulation of ribosomal protein gene transcription by RNA polymerase II / G-quadruplex DNA formation / telomeric G-quadruplex DNA binding / protection from non-homologous end joining at telomere / establishment of protein localization to telomere / shelterin complex / telomere maintenance via telomere lengthening / establishment of protein localization to chromatin / double-stranded telomeric DNA binding / G-quadruplex DNA binding / DNA binding, bending / silent mating-type cassette heterochromatin formation / regulation of glycolytic process / nucleosomal DNA binding / nuclear chromosome / telomeric DNA binding / TFIID-class transcription factor complex binding / subtelomeric heterochromatin formation / cis-regulatory region sequence-specific DNA binding / TBP-class protein binding / telomere maintenance / protein-DNA complex / transcription regulator complex / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / histone binding / DNA-binding transcription factor activity, RNA polymerase II-specific / chromosome, telomeric region / DNA-binding transcription factor activity / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus / cytosol
Similarity search - Function
Rap1, DNA-binding domain / Rap1, DNA-binding / 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 / Myb-type HTH DNA-binding domain profile. / Myb domain ...Rap1, DNA-binding domain / Rap1, DNA-binding / 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 / Myb-type HTH DNA-binding domain profile. / Myb domain / Myb-like DNA-binding domain / breast cancer carboxy-terminal domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Homeobox-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA-binding protein RAP1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
Model detailsclosest to the average, model 1
AuthorsZhang, W. / Zhang, J. / Tu, X.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: Solution structure of Rap1 BRCT domain from Saccharomyces cerevisiae reveals a novel fold
Authors: Zhang, W. / Zhang, J. / Zhang, X. / Xu, C. / Tu, X.
History
DepositionSep 29, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 26, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding protein RAP1


Theoretical massNumber of molelcules
Total (without water)12,1861
Polymers12,1861
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 #1closest to the average

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Components

#1: Protein DNA-binding protein RAP1 / Repressor/activator site-binding protein / SBF-E / TUF


Mass: 12185.600 Da / Num. of mol.: 1 / Fragment: BRCT domain, UNP residues 116-212
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: RAP1, GRF1, TUF1, YNL216W, N1310 / Production host: Escherichia coli (E. coli) / References: UniProt: P11938

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D CBCA(CO)NH
1313D C(CO)NH
1413D HNCO
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D H(CCO)NH
1813D 1H-15N NOESY
1923D (H)CCH-COSY
11023D (H)CCH-TOCSY
11123D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
120 mM sodium phosphate-1, 100 mM sodium chloride-2, 90% H2O/10% D2O90% H2O/10% D2O
220 mM sodium phosphate-3, 100 mM sodium chloride-4, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentSolution-ID
20 mMsodium phosphate-11
100 mMsodium chloride-21
20 mMsodium phosphate-32
100 mMsodium chloride-42
Sample conditionsIonic strength: 0.12 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 500 MHz

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Processing

NMR software
NameDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readchemical shift calculation
CNSBrunger, Adams, Clore, Gros, Nilges and Readdata analysis
SparkyGoddardcollection
SparkyGoddardchemical shift assignment
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 150 / Conformers submitted total number: 20 / Representative conformer: 1

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