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- PDB-2ebu: Solution structure of the BRCT domain from human replication fact... -

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Basic information

Entry
Database: PDB / ID: 2ebu
TitleSolution structure of the BRCT domain from human replication factor C large subunit 1
ComponentsReplication factor C subunit 1
KeywordsREPLICATION / a/b/a 3 layers / parallel beta-sheet / DNA replication / clamp loader / RFC1 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


DNA clamp unloader activity / Elg1 RFC-like complex / DNA replication factor C complex / Polymerase switching / Polymerase switching on the C-strand of the telomere / PCNA-Dependent Long Patch Base Excision Repair / telomere maintenance via telomerase / enzyme activator activity / Translesion synthesis by REV1 / Translesion synthesis by POLK ...DNA clamp unloader activity / Elg1 RFC-like complex / DNA replication factor C complex / Polymerase switching / Polymerase switching on the C-strand of the telomere / PCNA-Dependent Long Patch Base Excision Repair / telomere maintenance via telomerase / 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 / Termination of translesion DNA synthesis / Recognition of DNA damage by PCNA-containing replication complex / 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 / DNA clamp loader activity / 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Replication factor C subunit 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsNagashima, T. / Hayashi, F. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the BRCT domain from human replication factor C large subunit 1
Authors: Nagashima, T. / Hayashi, F. / Yokoyama, S.
History
DepositionFeb 9, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 14, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _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)11,8521
Polymers11,8521
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 / 100structures with the lowest energy, target function
RepresentativeModel #1lowest energy

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Components

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


Mass: 11852.476 Da / Num. of mol.: 1 / Fragment: BRCT domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Plasmid: P060403-02 / References: UniProt: P35251

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1.17mM uniformly 13C/15N-labeled protein, 20mM TrisHCl, 100mM NaCl, 1mM DTT, 0.02% NaN3, 10% D2O, 90% H2O
Solvent system: 10% D2O, 90% H2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20020425Delaglio, F.processing
NMRView5.0.4Johnson, B.A.data analysis
KUJIRA0.9822Kobayashi, N.data analysis
CYANA2.0.17Guntert, P.structure solution
CYANA2.0.17Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy, target function
Conformers calculated total number: 100 / Conformers submitted total number: 20

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