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- PDB-2htf: The solution structure of the BRCT domain from human polymerase r... -

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Basic information

Entry
Database: PDB / ID: 2htf
TitleThe solution structure of the BRCT domain from human polymerase reveals homology with the TdT BRCT domain
ComponentsDNA polymerase mu
KeywordsTRANSFERASE / BRCT domain / alpha-beta-alpha sandwich
Function / homology
Function and homology information


Nonhomologous End-Joining (NHEJ) / double-strand break repair via nonhomologous end joining / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
BRCT domain / DNA-directed DNA/RNA polymerase mu / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain ...BRCT domain / DNA-directed DNA/RNA polymerase mu / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / Torsion angle dynamics, molecular dynamics refinement in explicit water solvent
Model type detailsminimized average
AuthorsDeRose, E.F. / Clarkson, M.W. / Gilmore, S.A. / Ramsden, D.A. / Mueller, G.A. / London, R.E. / Lee, A.L.
CitationJournal: Biochemistry / Year: 2007
Title: Solution structure of polymerase mu's BRCT Domain reveals an element essential for its role in nonhomologous end joining.
Authors: DeRose, E.F. / Clarkson, M.W. / Gilmore, S.A. / Galban, C.J. / Tripathy, A. / Havener, J.M. / Mueller, G.A. / Ramsden, D.A. / London, R.E. / Lee, A.L.
History
DepositionJul 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA polymerase mu


Theoretical massNumber of molelcules
Total (without water)11,4201
Polymers11,4201
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)11 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein DNA polymerase mu / / Pol Mu


Mass: 11420.022 Da / Num. of mol.: 1 / Fragment: BRCT domain / Mutation: S20G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLM / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NP87, DNA-directed DNA polymerase

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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: 1mM polymerase mu BRCT domain, 25 mM d-Tris, 50 mM KCl, 0.02% NaN3, 5 mM DTT, pH 7.9, 90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 50 mM KCl / pH: 7.9 / Pressure: ambient / Temperature: 283 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA6001
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR1.1C, VNMRJ 1.1CVariancollection
NMRPipe2003, 2004Delaglio, Grzesiek, Vuister, Zhu, Pfeifer, and Baxprocessing
NMRView5.0.4Johnson and Blevinsprocessing
CYANA2.1Guentert, Mumenthaler, Herrmann, and Wuthrichstructure solution
ARIA2.0aHabeck, Rieping, Linge, and Nilgesrefinement
RefinementMethod: Torsion angle dynamics, molecular dynamics refinement in explicit water solvent
Software ordinal: 1
Details: The initial structures were computed using the auto noeassign feature of CYANA 2.1; 1503 NOE distance restraints were assigned, and 147 dihedral angle restraints were used in the calculation. ...Details: The initial structures were computed using the auto noeassign feature of CYANA 2.1; 1503 NOE distance restraints were assigned, and 147 dihedral angle restraints were used in the calculation. The 20 best CYANA structures were refined in explicit solvent using ARIA 2.0a with the 1506 NOE distance restraints, 147 dihedral angle restraints, 42 H-bond restraints, and 48 residual dipolar coupling restraints.
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 11

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