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- PDB-1h1j: The SAP domain is a DNA-Binding Domain Capable of Binding S/MAR DNA -

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Basic information

Entry
Database: PDB / ID: 1h1j
TitleThe SAP domain is a DNA-Binding Domain Capable of Binding S/MAR DNA
ComponentsTHO1 PROTEIN
KeywordsDNA BINDING / SAP DOMAIN
Function / homology
Function and homology information


poly(A)+ mRNA export from nucleus / protein-RNA complex assembly / transcription elongation by RNA polymerase II / double-stranded DNA binding / chromatin binding / RNA binding / nucleus
Similarity search - Function
THO1_MOS11, C-terminal domain / : / Tho1/MOS11 C-terminal domain / SAP domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / SAP domain superfamily / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain ...THO1_MOS11, C-terminal domain / : / Tho1/MOS11 C-terminal domain / SAP domain / Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 / SAP domain superfamily / SAP domain / SAP motif profile. / Putative DNA-binding (bihelical) motif predicted to be involved in chromosomal organisation / SAP domain / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesSACCHAROMYCES CEREVISIAE (brewer's yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsJacobsen, J.O.B. / Freund, S.M.V. / Bycroft, M.
Citation
Journal: To be Published
Title: The Sap Domain is a DNA-Binding Domain Capable of Binding S/Mar DNA
Authors: Jacobsen, J.O.B. / Freund, S.M.V. / Bycroft, M.
#1: Journal: Trends Biochem.Sci. / Year: 2000
Title: Sap - a Putative DNA-Binding Motif Involved in Chromosomal Organization
Authors: Aravind, L. / Koonin, E.V.
#2: Journal: Embo J. / Year: 1998
Title: A Novel Yeast Gene, Tho2, is Involved in RNA Pol II Transcription and Provides New Evidence for Transcriptional Elongation-Associated Recombination.
Authors: Piruat, J.I. / Aguilera, A.
History
DepositionJul 16, 2002Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 8, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 15, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
S: THO1 PROTEIN


Theoretical massNumber of molelcules
Total (without water)5,5821
Polymers5,5821
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 / 50LOWEST NOE ENERGIES
RepresentativeModel #1

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Components

#1: Protein THO1 PROTEIN


Mass: 5582.212 Da / Num. of mol.: 1 / Fragment: SAP DOMAIN, RESIDUES 2-50
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SACCHAROMYCES CEREVISIAE (brewer's yeast)
Plasmid: PGRO / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: P40040
Sequence detailsGLY 1, THROMBIN CLEAVAGE SITE INSERTION SER 2, THROMBIN CLEAVAGE SITE INSERTION

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11113C-FILTERED NOESY
121TOCSY
NMR detailsText: STRUCTURE DETERMINED USING STANDARD TRIPLE-RESONANCE AND 3D 1H,13C- NOESY/TOCSY EXPERIMENTS ON 13C, 15N-LABELED PROTEIN.

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Sample preparation

DetailsContents: 1.5MM
Sample conditionsIonic strength: 150 mM / pH: 6.8 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

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

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Processing

NMR software
NameVersionDeveloperClassification
X-PLOR3.8BRUNGERrefinement
Felixstructure solution
Sparkystructure solution
X-PLOR3.8structure solution
RefinementMethod: simulated annealing / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE. RESIDUES 45-51 ARE DISORDERED WITH NO DEFINED STRUCTURE AND NOT INCLUDED IN THE COORDINATES.
NMR ensembleConformer selection criteria: LOWEST NOE ENERGIES / Conformers calculated total number: 50 / Conformers submitted total number: 20

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