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- PDB-2csw: Solution structure of the FHA domain of human ubiquitin ligase pr... -

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Basic information

Entry
Database: PDB / ID: 2csw
TitleSolution structure of the FHA domain of human ubiquitin ligase protein RNF8
ComponentsUbiquitin ligase protein RNF8
KeywordsLIGASE / 11-stranded beta sandwich / RING finger protein 8 / Structural Genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


sperm DNA condensation / protein K6-linked ubiquitination / isotype switching / response to ionizing radiation / DNA repair-dependent chromatin remodeling / negative regulation of transcription elongation by RNA polymerase II / protein K63-linked ubiquitination / signal transduction in response to DNA damage / ubiquitin ligase complex / positive regulation of double-strand break repair via homologous recombination ...sperm DNA condensation / protein K6-linked ubiquitination / isotype switching / response to ionizing radiation / DNA repair-dependent chromatin remodeling / negative regulation of transcription elongation by RNA polymerase II / protein K63-linked ubiquitination / signal transduction in response to DNA damage / ubiquitin ligase complex / positive regulation of double-strand break repair via homologous recombination / interstrand cross-link repair / protein K48-linked ubiquitination / protein autoubiquitination / positive regulation of DNA repair / epigenetic regulation of gene expression / ubiquitin binding / Nonhomologous End-Joining (NHEJ) / G2/M DNA damage checkpoint / RING-type E3 ubiquitin transferase / double-strand break repair via nonhomologous end joining / ubiquitin protein ligase activity / double-strand break repair / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / Processing of DNA double-strand break ends / midbody / ubiquitin-dependent protein catabolic process / histone binding / chromosome, telomeric region / cell division / ubiquitin protein ligase binding / DNA damage response / chromatin binding / protein homodimerization activity / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
E3 ubiquitin-protein ligase RNF8 / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Zinc finger, C3HC4 type (RING finger) / SMAD/FHA domain superfamily / Zinc finger, RING-type, conserved site ...E3 ubiquitin-protein ligase RNF8 / Tumour Suppressor Smad4 - #20 / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / Zinc finger, C3HC4 type (RING finger) / SMAD/FHA domain superfamily / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type / Sandwich / Mainly Beta
Similarity search - Domain/homology
E3 ubiquitin-protein ligase RNF8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsHayashi, F. / Nagashima, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the FHA domain of human ubiquitin ligase protein RNF8
Authors: Hayashi, F. / Nagashima, T. / Yokoyama, S.
History
DepositionMay 23, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 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 1.4May 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: Ubiquitin ligase protein RNF8


Theoretical massNumber of molelcules
Total (without water)16,0561
Polymers16,0561
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 / 100target function, structures with the lowest energy, structures with the least restraint violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Ubiquitin ligase protein RNF8 / RING finger protein 8


Mass: 16056.050 Da / Num. of mol.: 1 / Fragment: FHA domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: RNF8 / Plasmid: P040322-86
References: UniProt: O76064, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY
NMR detailsText: The structure was determined using triple-resonance NMR spectroscopy.

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Sample preparation

DetailsContents: 1.1mM 13C,15N-labeled protein; 20mM d-TrisHCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120mM / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA8001
Varian INOVAVarianINOVA9002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR6.1CVariancollection
NMRPipe20031121Delaglio, F.processing
NMRView5.0.4Johnson, B. A.data analysis
KUJIRA0.9297Kobayashi, N.data analysis
CYANA2Guntert, P.structure solution
CYANA2Guntert, P.refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: target function, structures with the lowest energy, structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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