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- PDB-2k6g: Solution structure of the DNA binding BRCT domain from the large ... -

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Basic information

Entry
Database: PDB / ID: 2k6g
TitleSolution structure of the DNA binding BRCT domain from the large subunit of human Replication Factor C
ComponentsReplication factor C subunit 1
KeywordsDNA BINDING PROTEIN / Protein / BRCT / DNA binding / replication factor C / Activator / Alternative splicing / ATP-binding / DNA replication / DNA-binding / Metal-binding / Nucleotide-binding / Nucleus / Phosphoprotein / Polymorphism / Transcription / Transcription regulation / Zinc / Zinc-finger
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
Replication factor C subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailsIt binds specifically to 5' end phosphorylated dsDNA
AuthorsKobayashi, M. / Siegal, G. / Ab, E. / Bonvin, A.M.J.J.
CitationJournal: To be Published
Title: Solution structure of the DNA bound BRCT domain from human Replication Factor C p140
Authors: Kobayashi, M. / Ab, E. / Bonvin, A.M.J.J. / Siegal, G.
History
DepositionJul 9, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Replication factor C subunit 1


Theoretical massNumber of molelcules
Total (without water)11,9961
Polymers11,9961
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)24 / 180bb conformation Z-score (whatif)
RepresentativeModel #1lowest bb conformation z-scores

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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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RFC1, RFC140 / Production host: Escherichia coli (E. coli) / References: UniProt: P35251

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
Details: It binds specifically to 5' end phosphorylated dsDNA
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D CBCA(CO)NH
1413D HNCA
1513D HN(CA)CB
161CCH-TOCSY
1713D 1H-15N NOESY
1813D 1H-13C NOESY
1912D 1H-1H NOESY

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Sample preparation

DetailsContents: 0.5 mM [U-15N; U-13C] RFC p140 BRCT region, 0.5 mM self - annealing hairpin - dsDNA, 20 mM Tris-HCl, 5 mM NaCl, 1 mM DTT, 95% H2O/5% D2O
Solvent system: 95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMRFC p140 BRCT region[U-15N; U-13C]1
0.5 mMself - annealing hairpin - dsDNA1
20 mMTris-HCl1
5 mMNaCl1
1 mMDTT1
Sample conditionspH: 7.5 / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CNSBrunger, Adams, Clore, Gros, Nilges and Readrefinement
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: RECOORD scripts using CNS
NMR constraintsNOE constraints total: 1812
NMR representativeSelection criteria: lowest bb conformation z-scores
NMR ensembleConformer selection criteria: bb conformation Z-score (whatif)
Conformers calculated total number: 180 / Conformers submitted total number: 24

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