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- PDB-2xnh: Structure and function of the Rad9-binding region of the DNA dama... -

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Basic information

Entry
Database: PDB / ID: 2xnh
TitleStructure and function of the Rad9-binding region of the DNA damage checkpoint adaptor TopBP1
ComponentsDNA TOPOISOMERASE 2-BINDING PROTEIN 1
KeywordsISOMERASE / PHOSPHORYLATION / PROTEIN-PROTEIN INTERACTION / DNA REPAIR
Function / homology
Function and homology information


BRCA1-B complex / phosphorylation-dependent protein binding / chromatin-protein adaptor activity / homologous recombination / protein localization to site of double-strand break / DNA replication checkpoint signaling / double-strand break repair via alternative nonhomologous end joining / double-strand break repair via classical nonhomologous end joining / mitotic DNA replication checkpoint signaling / HDR through Single Strand Annealing (SSA) ...BRCA1-B complex / phosphorylation-dependent protein binding / chromatin-protein adaptor activity / homologous recombination / protein localization to site of double-strand break / DNA replication checkpoint signaling / double-strand break repair via alternative nonhomologous end joining / double-strand break repair via classical nonhomologous end joining / mitotic DNA replication checkpoint signaling / HDR through Single Strand Annealing (SSA) / DNA metabolic process / Impaired BRCA2 binding to RAD51 / response to ionizing radiation / site of DNA damage / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / DNA replication initiation / chromosome organization / protein serine/threonine kinase activator activity / DNA damage checkpoint signaling / condensed nuclear chromosome / male germ cell nucleus / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / PML body / spindle pole / actin cytoskeleton / site of double-strand break / chromosome / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / nuclear body / DNA repair / centrosome / DNA damage response / DNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
: / TopBP1, BRCT0 domain / TopBP1, first BRCT domain / Secretoglobin superfamily / twin BRCT domain / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain ...: / TopBP1, BRCT0 domain / TopBP1, first BRCT domain / Secretoglobin superfamily / twin BRCT domain / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IODIDE ION / DNA topoisomerase 2-binding protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.8 Å
AuthorsRappas, M. / Oliver, A.W. / Pearl, L.H.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: Structure and Function of the Rad9-Binding Region of the DNA-Damage Checkpoint Adaptor Topbp1.
Authors: Rappas, M. / Oliver, A.W. / Pearl, L.H.
History
DepositionAug 2, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA TOPOISOMERASE 2-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,01918
Polymers33,8621
Non-polymers2,15717
Water1,27971
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)115.770, 115.770, 115.770
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Space group name H-MP213
Components on special symmetry positions
IDModelComponents
11A-1293-

IOD

21A-1302-

IOD

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Components

#1: Protein DNA TOPOISOMERASE 2-BINDING PROTEIN 1 / DNA TOPOISOMERASE II-BINDING PROTEIN 1 / DNA TOPOISOMERASE II-BETA-BINDING PROTEIN 1 / TOPBP1


Mass: 33861.984 Da / Num. of mol.: 1 / Fragment: BRCT 0,1 AND 2, RESIDUES 1-287
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPINH8, PGEX6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2(DE3)PLYSS / References: UniProt: Q92547
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.84 Å3/Da / Density % sol: 0.68 % / Description: NONE
Crystal growpH: 6.8
Details: 0.1M TRIS-HCL PH 6.8, 0.5M KI, 5% (V/V) GLYCEROL, 22.5% (W/V), 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 20, 2009 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.6→51.77 Å / Num. obs: 13035 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5.93 % / Biso Wilson estimate: 54.82 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.9
Reflection shellResolution: 2.8→2.95 Å / Redundancy: 6.09 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.52 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 2.8→47.263 Å / SU ML: 1.16 / σ(F): 1.44 / Phase error: 23.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2513 1254 5.1 %
Rwork0.2318 --
obs0.2327 24687 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.687 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso mean: 58.7 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.8→47.263 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2280 0 17 71 2368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0032330
X-RAY DIFFRACTIONf_angle_d0.6033135
X-RAY DIFFRACTIONf_dihedral_angle_d14.706875
X-RAY DIFFRACTIONf_chiral_restr0.041342
X-RAY DIFFRACTIONf_plane_restr0.002395
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8004-2.91250.29231470.28372648X-RAY DIFFRACTION100
2.9125-3.04510.3071500.27332592X-RAY DIFFRACTION100
3.0451-3.20560.30631280.26482606X-RAY DIFFRACTION100
3.2056-3.40640.28211240.24332609X-RAY DIFFRACTION100
3.4064-3.66930.24991410.21412584X-RAY DIFFRACTION100
3.6693-4.03840.23381500.19362596X-RAY DIFFRACTION100
4.0384-4.62230.21281440.17682605X-RAY DIFFRACTION100
4.6223-5.82190.17021340.19742603X-RAY DIFFRACTION100
5.8219-47.26960.25621360.24982590X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.2581-1.43521.33632.2667-2.49321.83480.1374-0.1004-0.4722-0.1710.30790.50650.1832-0.2714-0.38690.26010.021-0.1510.20270.0840.486536.792267.445576.9068
22.0077-2.15880.38812.7689-0.15280.1099-0.01980.2025-0.2981-0.1590.0630.12710.0064-0.1-0.00870.21740.0376-0.06740.2115-0.05680.128437.616889.142762.3073
30.7715-1.87931.29282.7296-0.66650.71230.18820.31530.0594-0.7324-0.26370.04430.0151-0.05270.04780.45330.1007-0.02330.32670.07930.18333.6415115.511850.837
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 6:103
2X-RAY DIFFRACTION2CHAIN A AND RESID 104:198
3X-RAY DIFFRACTION3CHAIN A AND RESID 199:287

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