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

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Entry
Database: PDB / ID: 2xnk
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


broken chromosome clustering / BRCA1-B complex / phosphorylation-dependent protein binding / homologous recombination / DNA replication checkpoint signaling / double-strand break repair via alternative nonhomologous end joining / double-strand break repair via classical nonhomologous end joining / chromatin-protein adaptor activity / mitotic DNA replication checkpoint signaling / protein localization to site of double-strand break ...broken chromosome clustering / BRCA1-B complex / phosphorylation-dependent protein binding / homologous recombination / DNA replication checkpoint signaling / double-strand break repair via alternative nonhomologous end joining / double-strand break repair via classical nonhomologous end joining / chromatin-protein adaptor activity / mitotic DNA replication checkpoint signaling / protein localization to site of double-strand break / HDR through Single Strand Annealing (SSA) / DNA metabolic process / response to ionizing radiation / Impaired BRCA2 binding to RAD51 / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / site of DNA damage / DNA replication initiation / chromosome organization / DNA damage checkpoint signaling / protein serine/threonine kinase activator activity / condensed nuclear chromosome / male germ cell nucleus / double-strand break repair via homologous recombination / PML body / G2/M DNA damage checkpoint / spindle pole / actin cytoskeleton / chromosome / site of double-strand break / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / nuclear body / DNA repair / DNA damage response / centrosome / DNA binding / nucleoplasm / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
: / TopBP1, BRCT0 domain / TopBP1, first BRCT domain / : / TopBP1/SLF1, BRCT domain / Secretoglobin superfamily / twin BRCT domain / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain ...: / TopBP1, BRCT0 domain / TopBP1, first BRCT domain / : / TopBP1/SLF1, 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
DNA topoisomerase 2-binding protein 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 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 3, 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
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
B: DNA TOPOISOMERASE 2-BINDING PROTEIN 1
C: DNA TOPOISOMERASE 2-BINDING PROTEIN 1
D: DNA TOPOISOMERASE 2-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,26715
Polymers137,2544
Non-polymers1,01311
Water6,125340
1
A: DNA TOPOISOMERASE 2-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4983
Polymers34,3131
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: DNA TOPOISOMERASE 2-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5904
Polymers34,3131
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: DNA TOPOISOMERASE 2-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5904
Polymers34,3131
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: DNA TOPOISOMERASE 2-BINDING PROTEIN 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5904
Polymers34,3131
Non-polymers2763
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.490, 290.280, 60.580
Angle α, β, γ (deg.)90.00, 89.85, 90.00
Int Tables number4
Space group name H-MP1211

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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: 34313.457 Da / Num. of mol.: 4 / Fragment: BRCT 0,1 AND 2, RESIDUES 1-290
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: POPINH8 AND PGEX6P1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): ROSETTA2(DE3)PLYSS / References: UniProt: Q92547
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 340 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 0.52 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M TRIS-HCL PH 7.5, 0.4 M MGCL2, 25% PEG 4000, 4% GLYCEROL, 0.01 M SPERMIDINE TETRA-HCL

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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 21, 2009 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.47→55.91 Å / Num. obs: 40485 / % possible obs: 97.2 % / Observed criterion σ(I): 0 / Redundancy: 2.63 % / Biso Wilson estimate: 45.09 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 4.96
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 2.57 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.99 / % possible all: 98.8

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XNH

2xnh


Resolution: 2.6→51.347 Å / SU ML: 0.92 / σ(F): 0.98 / Phase error: 29.4 / Stereochemistry target values: ML
Details: DURING REFINEMENT UNMERGED REFLECTIONS (APPROXIMATELY DOUBLE THE NUMBER OF THE MERGED REFLECTIONS) IN ORDE TO TAKE INTO ACCOUNT THE ANOMALOUS CONTRIBUTIONS OF THE SEMET AT THE WAVELENGTH AT ...Details: DURING REFINEMENT UNMERGED REFLECTIONS (APPROXIMATELY DOUBLE THE NUMBER OF THE MERGED REFLECTIONS) IN ORDE TO TAKE INTO ACCOUNT THE ANOMALOUS CONTRIBUTIONS OF THE SEMET AT THE WAVELENGTH AT WHICH THE DATA SET WAS COLLECTED (WHICH HAPPENS TO BE THE INFLECTION POINT OF THE SE ANOMALOUS PEAK)
RfactorNum. reflection% reflection
Rfree0.2663 3850 5.1 %
Rwork0.2048 --
obs0.2079 76051 91.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.145 Å2 / ksol: 0.352 e/Å3
Displacement parametersBiso mean: 57.5 Å2
Baniso -1Baniso -2Baniso -3
1-14.329 Å2-0 Å20.887 Å2
2---15.2878 Å2-0 Å2
3---0.9588 Å2
Refinement stepCycle: LAST / Resolution: 2.6→51.347 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9418 0 66 340 9824
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0059705
X-RAY DIFFRACTIONf_angle_d0.80613037
X-RAY DIFFRACTIONf_dihedral_angle_d15.2683687
X-RAY DIFFRACTIONf_chiral_restr0.0521404
X-RAY DIFFRACTIONf_plane_restr0.0031646
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.63170.36891340.29922619X-RAY DIFFRACTION93
2.6317-2.6650.34681110.28622576X-RAY DIFFRACTION92
2.665-2.70010.36221310.28022504X-RAY DIFFRACTION92
2.7001-2.73710.35061690.28182537X-RAY DIFFRACTION91
2.7371-2.77620.31681310.26872735X-RAY DIFFRACTION93
2.7762-2.81760.31681230.26892567X-RAY DIFFRACTION93
2.8176-2.86160.40021650.27882502X-RAY DIFFRACTION93
2.8616-2.90860.36641540.2782593X-RAY DIFFRACTION92
2.9086-2.95870.31871550.26382517X-RAY DIFFRACTION92
2.9587-3.01250.33181490.25742751X-RAY DIFFRACTION93
3.0125-3.07040.29591030.22812534X-RAY DIFFRACTION93
3.0704-3.13310.29591090.22992598X-RAY DIFFRACTION92
3.1331-3.20120.27851230.22122620X-RAY DIFFRACTION92
3.2012-3.27570.29891510.21182638X-RAY DIFFRACTION93
3.2757-3.35760.26311480.19642551X-RAY DIFFRACTION93
3.3576-3.44830.24691400.18312614X-RAY DIFFRACTION92
3.4483-3.54980.28751300.17582624X-RAY DIFFRACTION93
3.5498-3.66430.21571500.172527X-RAY DIFFRACTION93
3.6643-3.79530.2231410.15472619X-RAY DIFFRACTION92
3.7953-3.94720.20651550.15642592X-RAY DIFFRACTION92
3.9472-4.12670.17921340.1482513X-RAY DIFFRACTION92
4.1267-4.34420.23421270.15152625X-RAY DIFFRACTION92
4.3442-4.61620.21091330.14672528X-RAY DIFFRACTION92
4.6162-4.97240.19151250.14932616X-RAY DIFFRACTION91
4.9724-5.47220.27551570.16192522X-RAY DIFFRACTION91
5.4722-6.26290.23281280.18712489X-RAY DIFFRACTION89
6.2629-7.8860.24161220.18212508X-RAY DIFFRACTION88
7.886-51.35670.20951520.17582582X-RAY DIFFRACTION93
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)
11.3322-0.57041.98782.40190.5450.9719-0.06070.09950.3312-0.1346-0.0356-0.29890.0333-0.0441-0.00120.12280.01240.02210.25520.12460.633121.8709-9.70492.0541
21.5104-0.3814-0.90122.1985-1.14640.60750.04450.01440.0430.1735-0.2202-0.41740.2957-0.06230.01050.0818-0.0123-0.01920.23040.07850.30767.2311-30.1428.9676
30.3790.02320.59042.2277-0.61311.6238-0.08270.01590.15340.05070.00080.1061-0.05290.0521-0.00010.176-0.04060.01480.2760.00290.121-2.9752-55.31918.9263
4-1.3117-0.16210.52573.11430.23131.8849-0.0486-0.27520.2108-0.2834-0.06950.238-0.16380.0572-0.00670.215-0.00170.05570.2582-0.03460.2096-23.9868-63.873952.8279
51.70890.96781.24491.863-0.86830.76040.2192-0.15680.26130.52530.06540.0941-0.39460.01640.00260.35790.00890.08420.23790.00740.1671-16.2246-41.745942.145
61.24640.362-0.27381.581-0.2890.566-0.04890.19560.2020.7474-0.1596-0.0266-0.24470.13880.00010.633-0.0641-0.05760.23440.01940.3961-1.3134-17.854835.4914
7-0.02930.9642-0.0982.0292-1.01862.5012-0.0210.0565-0.3109-0.18310.0459-0.49470.1657-0.0387-00.20280.0147-0.06630.2003-0.04860.20844.7502-80.296722.2142
81.00881.8165-0.67551.5591.54850.36450.2734-0.1212-0.23980.4260.0634-0.32730.3238-0.113400.528-0.0028-0.0480.2431-0.02130.3028-3.1595-102.337411.5727
90.85470.0694-0.67231.77-0.40120.88990.08020.1682-0.20661.0501-0.2152-0.00920.1983-0.185100.7372-0.1141-0.01740.2355-0.02610.3351-18.2152-126.155.0748
101.73370.6077-1.46921.649-0.81981.8806-0.00620.0638-0.1232-0.0846-0.02560.30820.31340.01400.1327-0.003-0.07210.1679-0.0670.5666-41.4983-134.2416-28.402
111.3454-0.37561.54311.7078-0.1683.08860.10760.0786-0.07950.1028-0.18640.4788-0.6079-0.04790.2698-0.05260.0005-0.00730.1877-0.10390.3092-26.8338-113.9304-21.486
12-0.158-1.2391-0.83581.47732.36590.25180.02870.0811-0.16550.0785-0.0726-0.0902-0.07650.0267-0.00140.2636-0.046-0.00070.27280.00170.1334-16.4566-88.7771-11.5689
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID -1:103
2X-RAY DIFFRACTION2CHAIN A AND RESID 104:198
3X-RAY DIFFRACTION3CHAIN A AND RESID 199:288
4X-RAY DIFFRACTION4CHAIN B AND RESID 0:103
5X-RAY DIFFRACTION5CHAIN B AND RESID 104:198
6X-RAY DIFFRACTION6CHAIN B AND RESID 199:287
7X-RAY DIFFRACTION7CHAIN C AND RESID 0:103
8X-RAY DIFFRACTION8CHAIN C AND RESID 104:198
9X-RAY DIFFRACTION9CHAIN C AND RESID 199:287
10X-RAY DIFFRACTION10CHAIN D AND RESID -1:103
11X-RAY DIFFRACTION11CHAIN D AND RESID 104:198
12X-RAY DIFFRACTION12CHAIN D AND RESID 199:288

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