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- PDB-5b7j: Structure model of Sap1-DNA complex -

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Basic information

Entry
Database: PDB / ID: 5b7j
TitleStructure model of Sap1-DNA complex
Components
  • DNA (5'-D(*AP*AP*TP*AP*TP*TP*GP*TP*TP*TP*TP*G)-3')
  • DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*AP*TP*AP*TP*T)-3')
  • Switch-activating protein 1
KeywordsDNA BINDING PROTEIN/DNA / protein / DNA / interaction / complex / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


site-specific DNA replication termination / mitotic pre-replicative complex assembly / replication fork arrest at rDNA repeats / rDNA spacer replication fork barrier binding / gene conversion at mating-type locus / DNA binding, bending / chromosome segregation / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / chromatin ...site-specific DNA replication termination / mitotic pre-replicative complex assembly / replication fork arrest at rDNA repeats / rDNA spacer replication fork barrier binding / gene conversion at mating-type locus / DNA binding, bending / chromosome segregation / sequence-specific double-stranded DNA binding / sequence-specific DNA binding / chromatin / DNA binding / nucleus
Similarity search - Function
: / Switch activating protein 1, N-terminal
Similarity search - Domain/homology
DNA / DNA (> 10) / Switch-activating protein 1
Similarity search - Component
Biological speciesSchizosaccharomyces pombe (fission yeast)
MethodSOLUTION NMR / simulated annealing
AuthorsJin, C. / Hu, Y. / Ding, J. / Zhang, Y.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Sap1 is a replication-initiation factor essential for the assembly of pre-replicative complex in the fission yeast Schizosaccharomyces pombe
Authors: Guan, L. / He, P. / Yang, F. / Zhang, Y. / Hu, Y. / Ding, J. / Hua, Y. / Zhang, Y. / Ye, Q. / Hu, J. / Wang, T. / Jin, C. / Kong, D.
History
DepositionJun 7, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Switch-activating protein 1
B: DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*AP*TP*AP*TP*T)-3')
C: DNA (5'-D(*AP*AP*TP*AP*TP*TP*GP*TP*TP*TP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)20,5693
Polymers20,5693
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3380 Å2
ΔGint-24 kcal/mol
Surface area10790 Å2
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Switch-activating protein 1


Mass: 13248.225 Da / Num. of mol.: 1 / Fragment: UNP residues 25-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Schizosaccharomyces pombe (strain 972 / ATCC 24843) (yeast)
Strain: 972 / ATCC 24843 / Gene: sap1, SPCC1672.02c / Production host: Escherichia coli (E. coli) / References: UniProt: P40847
#2: DNA chain DNA (5'-D(*CP*AP*AP*AP*AP*CP*AP*AP*TP*AP*TP*T)-3')


Mass: 3638.432 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast)
#3: DNA chain DNA (5'-D(*AP*AP*TP*AP*TP*TP*GP*TP*TP*TP*TP*G)-3')


Mass: 3682.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Schizosaccharomyces pombe (fission yeast)

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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
171isotropic13D CBCA(CO)NH
181isotropic13D HN(CA)CB
1121isotropic13D HNCO
192isotropic12D 1H-15N HSQC
152isotropic13D CBCA(CO)NH
162isotropic13D HN(CA)CB
1102isotropic13D HNCO
1112isotropic13D HNCA
122isotropic33D 1H-15N NOESY
132isotropic33D 1H-13C NOESY
1132isotropic33D filtered NOESY
143isotropic32D 1H-1H NOESY

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Sample preparation

Details
TypeSolution-IDContentsLabelSolvent system
solution10.5 mM [U-99% 15N][U-99% 13C; U-99% 15N] Sap1, 20 mM sodium phosphate, 90% H2O/10% D2O15N/13C_sap190% H2O/10% D2O
solution30.5 mM DNA (5'-CAAAACAATATT-3'), 20 mM sodium phosphate, 90% H2O/10% D2O1H_DNA90% H2O/10% D2O
solution20.5 mM [U-99% 13C; U-99% 15N] Sap1, 0.7 mM DNA (5'-CAAAACAATATT-3'), 20 mM sodium phosphate, 90% H2O/10% D2O15N/13C_complex90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMSap1[U-99% 15N][U-99% 13C; U-99% 15N]1
20 mMsodium phosphatenatural abundance1
0.5 mMDNA (5'-CAAAACAATATT-3')natural abundance3
20 mMsodium phosphatenatural abundance3
0.5 mMSap1[U-99% 13C; U-99% 15N]2
0.7 mMDNA (5'-CAAAACAATATT-3')natural abundance2
20 mMsodium phosphatenatural abundance2
Sample conditionsIonic strength: 60 mM / Label: conditions_1 / pH: 6.0 / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance5001
Bruker AvanceBrukerAvance8002
Bruker AvanceBrukerAvance9503

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Processing

NMR software
NameDeveloperClassification
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 2
Details: The structure model of the Sap1-DNA complex was derived based on the crystal structure of Sap1, the B-form DNA model based on the 3D-DART server, and the experimentally obtained inter- ...Details: The structure model of the Sap1-DNA complex was derived based on the crystal structure of Sap1, the B-form DNA model based on the 3D-DART server, and the experimentally obtained inter-molecular distance restraints from NMR NOESY spectra.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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