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- PDB-2l3n: Solution structure of Rap1-Taz1 fusion protein -

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Basic information

Entry
Database: PDB / ID: 2l3n
TitleSolution structure of Rap1-Taz1 fusion protein
ComponentsDNA-binding protein rap1,Telomere length regulator taz1
KeywordsDNA BINDING PROTEIN / RAP1 / TAZ1
Function / homology
Function and homology information


meiotic attachment of telomeric heterochromatin to spindle pole body / meiotic spindle pole body / nucleus leading edge / mitotic telomere tethering at nuclear periphery / Removal of the Flap Intermediate from the C-strand / meiotic attachment of telomere to nuclear envelope / chromosome, telomeric repeat region / protection from non-homologous end joining at telomere / telomere maintenance via telomere lengthening / mitotic telomere maintenance via semi-conservative replication ...meiotic attachment of telomeric heterochromatin to spindle pole body / meiotic spindle pole body / nucleus leading edge / mitotic telomere tethering at nuclear periphery / Removal of the Flap Intermediate from the C-strand / meiotic attachment of telomere to nuclear envelope / chromosome, telomeric repeat region / protection from non-homologous end joining at telomere / telomere maintenance via telomere lengthening / mitotic telomere maintenance via semi-conservative replication / shelterin complex / double-stranded telomeric DNA binding / nuclear telomere cap complex / telomere capping / telomeric DNA binding / telomere maintenance / nuclear periphery / molecular adaptor activity / regulation of DNA-templated transcription / chromatin / protein homodimerization activity / nucleus / cytoplasm
Similarity search - Function
Ribosomal Protein S4 Delta 41; Chain A, domain 1 - #20 / S. pombe DNA-binding protein Rap1, C-terminal / Rap1, DNA-binding domain / Rap1, DNA-binding / TE2IP/Rap1 / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains ...Ribosomal Protein S4 Delta 41; Chain A, domain 1 - #20 / S. pombe DNA-binding protein Rap1, C-terminal / Rap1, DNA-binding domain / Rap1, DNA-binding / TE2IP/Rap1 / Telomere repeat-binding factor, dimerisation domain / Telomere repeat binding factor (TRF) / Ribosomal Protein S4 Delta 41; Chain A, domain 1 / Myb-like DNA-binding domain / SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains / SANT/Myb domain / BRCT domain profile. / BRCT domain / Homeobox-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Telomere length regulator taz1 / DNA-binding protein rap1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsZhou, Z.R. / Wang, F. / Chen, Y. / Lei, M. / Hu, H.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2011
Title: A conserved motif within RAP1 has diversified roles in telomere protection and regulation in different organisms.
Authors: Chen, Y. / Rai, R. / Zhou, Z.R. / Kanoh, J. / Ribeyre, C. / Yang, Y. / Zheng, H. / Damay, P. / Wang, F. / Tsujii, H. / Hiraoka, Y. / Shore, D. / Hu, H.Y. / Chang, S. / Lei, M.
History
DepositionSep 19, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 18, 2019Group: Data collection / Database references
Category: citation / pdbx_nmr_software ...citation / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3Jan 1, 2020Group: Database references / Source and taxonomy / Structure summary
Category: entity / entity_src_gen ...entity / entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity.pdbx_description
Revision 1.4May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-binding protein rap1,Telomere length regulator taz1


Theoretical massNumber of molelcules
Total (without water)11,1171
Polymers11,1171
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 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA-binding protein rap1,Telomere length regulator taz1


Mass: 11117.336 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 639-693, 362-395
Source method: isolated from a genetically manipulated source
Details: The fusion protein of DNA-binding protein rap1 (639-693), Linker (GGSGGSKLGGSGGS) and Telomere length regulator taz1 (362-395)
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: rap1, SPBC1778.02, taz1, myb, myb1, SPAC16A10.07c / Production host: Escherichia coli (E. coli) / References: UniProt: Q96TL7, UniProt: P79005
Sequence detailsTHE FUSION PROTEIN OF DNA-BINDING PROTEIN RAP1 (639-693), LINKER (GGSGGSKLGGSGGS) AND TELOMERE ...THE FUSION PROTEIN OF DNA-BINDING PROTEIN RAP1 (639-693), LINKER (GGSGGSKLGGSGGS) AND TELOMERE LENGTH REGULATOR TAZ1 (362-395)

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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 HN(CA)CB
1313D CBCA(CO)NH
1413D HNCO
1513D HN(CA)CO
1613D C(CO)NH
1713D H(CCO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY
11113D HNHA
11222D 1H-15N IPAP HSQC
11313D CCH-COSY

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Sample preparation

Details
Solution-IDContentsSolvent system
11.1 mM [U-99% 13C; U-99% 15N] spRT6-1, 20 mM sodium phosphate-2, 50 mM sodium chloride-3, 1 mM DTT-4, 90% H2O/10% D2O90% H2O/10% D2O
20.6 mM [U-99% 15N] spRT6-5, 20 mM sodium phosphate-6, 50 mM sodium chloride-7, 1 mM DTT-8, 93% H2O/7% D2O93% H2O/7% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1.1 mMspRT6-1[U-99% 13C; U-99% 15N]1
20 mMsodium phosphate-21
50 mMsodium chloride-31
1 mMDTT-41
0.6 mMspRT6-5[U-99% 15N]2
20 mMsodium phosphate-62
50 mMsodium chloride-72
1 mMDTT-82
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10.07 6.5 ambient atm298 K
26.5 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

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Processing

NMR softwareName: Amber / Version: 9
Developer: Case, Darden, Cheatham, III, Simmerling, Wang, Duke, Luo, and Kollm
Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1

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