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- PDB-2k7f: HADDOCK calculated model of the complex between the BRCT region o... -

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Basic information

Entry
Database: PDB / ID: 2k7f
TitleHADDOCK calculated model of the complex between the BRCT region of RFC p140 and dsDNA
Components
  • 5'-D(P*DCP*DGP*DAP*DCP*DCP*DTP*DCP*DGP*DAP*DGP*DAP*DTP*DCP*DA)-3'
  • 5'-D(P*DCP*DTP*DCP*DGP*DAP*DGP*DGP*DTP*DCP*DG)-3'
  • Replication factor C subunit 1
KeywordsREPLICATION/DNA / BRCT / DNA / HADDOCK / model / complex / protein / Activator / ATP-binding / DNA replication / DNA-binding / Metal-binding / Nucleotide-binding / Nucleus / Phosphoprotein / Transcription / Transcription regulation / Zinc-finger / REPLICATION-DNA COMPLEX
Function / homology
Function and homology information


DNA clamp unloader activity / DNA replication factor C complex / Elg1 RFC-like complex / Polymerase switching / DNA clamp loader activity / Polymerase switching on the C-strand of the telomere / telomere maintenance via telomerase / PCNA-Dependent Long Patch Base Excision Repair / enzyme activator activity / Translesion synthesis by REV1 ...DNA clamp unloader activity / DNA replication factor C complex / Elg1 RFC-like complex / Polymerase switching / DNA clamp loader activity / Polymerase switching on the C-strand of the telomere / telomere maintenance via telomerase / PCNA-Dependent Long Patch Base Excision Repair / enzyme activator activity / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / DNA-templated DNA replication / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / double-stranded DNA binding / DNA-binding transcription factor binding / sequence-specific DNA binding / protein domain specific binding / DNA repair / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / extracellular exosome / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Replication factor C subunit 1 / DNA replication factor RFC1, C-terminal / Replication factor RFC1 C terminal domain / BRCT domain / : / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain ...Replication factor C subunit 1 / DNA replication factor RFC1, C-terminal / Replication factor RFC1 C terminal domain / BRCT domain / : / DNA polymerase III, clamp loader complex, gamma/delta/delta subunit, C-terminal / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Replication factor C subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / HADDOCK
AuthorsKobayashi, M. / Ab, E. / Bonvin, A. / Siegal, G.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Structure of the DNA-bound BRCA1 C-terminal region from human replication factor C p140 and model of the protein-DNA complex.
Authors: Kobayashi, M. / Ab, E. / Bonvin, A.M. / Siegal, G.
History
DepositionAug 10, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 8, 2009Provider: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Replication factor C subunit 1
B: 5'-D(P*DCP*DGP*DAP*DCP*DCP*DTP*DCP*DGP*DAP*DGP*DAP*DTP*DCP*DA)-3'
C: 5'-D(P*DCP*DTP*DCP*DGP*DAP*DGP*DGP*DTP*DCP*DG)-3'


Theoretical massNumber of molelcules
Total (without water)19,3063
Polymers19,3063
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)4 / 200back calculated data agree with experimental NOESY spectrum
RepresentativeModel #1fewest violations

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Components

#1: Protein Replication factor C subunit 1 / Activator 1 subunit 1 / Replication factor C large subunit / RF-C 140 kDa subunit / Activator 1 140 ...Activator 1 subunit 1 / Replication factor C large subunit / RF-C 140 kDa subunit / Activator 1 140 kDa subunit / A1 140 kDa subunit / Activator 1 large subunit / DNA-binding protein PO-GA


Mass: 11995.629 Da / Num. of mol.: 1 / Fragment: BRCT domain (UNP residues 375-480)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RFC1, RFC140 / Plasmid: pET20b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P35251
#2: DNA chain 5'-D(P*DCP*DGP*DAP*DCP*DCP*DTP*DCP*DGP*DAP*DGP*DAP*DTP*DCP*DA)-3'


Mass: 4249.781 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA strand
#3: DNA chain 5'-D(P*DCP*DTP*DCP*DGP*DAP*DGP*DGP*DTP*DCP*DG)-3'


Mass: 3061.004 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA strand primer

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
121f1 isotope filtered 2D NOESY
131f1,f2 isotope filtered 2D NOESY

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Sample preparation

DetailsContents: 0.3 mM [U-98% 13C; U-98% 15N] BRCT region RFC p140, 0.3 mM DNA strand, 0.3 mM DNA strand primer, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.3 mMBRCT region RFC p140[U-98% 13C; U-98% 15N]1
0.3 mMDNA strand1
0.3 mMDNA strand primer1
Sample conditionsIonic strength: 5 / pH: 7.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 900 MHz

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Processing

NMR software
NameVersionDeveloperClassification
HADDOCK2Dominguez C., Boelens R and Bonvin AMJJ., JACS 125, 1731 (2003)structure solution
HADDOCK2Dominguez C., Boelens R and Bonvin AMJJ., JACS 125, 1731 (2003)refinement
RefinementMethod: HADDOCK / Software ordinal: 1
Details: The refinement method can be found in Dominguez C., Boelens R and Bonvin AMJJ., JACS 125, 1731 (2003)
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: back calculated data agree with experimental NOESY spectrum
Conformers calculated total number: 200 / Conformers submitted total number: 4

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