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- PDB-3ueo: Crystal structure of TopBP1 BRCT4/5 domains in complex with a pho... -

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Basic information

Entry
Database: PDB / ID: 3ueo
TitleCrystal structure of TopBP1 BRCT4/5 domains in complex with a phospho-peptide
Components
  • DNA topoisomerase 2-binding protein 1
  • phospho-peptide
KeywordsPEPTIDE BINDING PROTEIN / BRCT domain / phospho-peptide binding
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 / mitotic intra-S DNA damage checkpoint signaling / HDR through Single Strand Annealing (SSA) / DNA metabolic process / response to ionizing radiation / Impaired BRCA2 binding to RAD51 / mitotic G2 DNA damage checkpoint signaling / histone reader activity / Presynaptic phase of homologous DNA pairing and strand exchange / site of DNA damage / DNA replication initiation / chromosome organization / SUMOylation of DNA damage response and repair proteins / DNA damage checkpoint signaling / protein serine/threonine kinase activator activity / condensed nuclear chromosome / male germ cell nucleus / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / G2/M DNA damage checkpoint / PML body / spindle pole / actin cytoskeleton / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / site of double-strand break / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / nuclear body / focal adhesion / 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 / Regulator of Ty1 transposition protein 107 BRCT domain / twin BRCT domain / BRCT domain ...: / TopBP1, BRCT0 domain / TopBP1, first BRCT domain / : / TopBP1/SLF1, BRCT domain / : / Secretoglobin superfamily / Regulator of Ty1 transposition protein 107 BRCT domain / twin BRCT domain / BRCT domain / BRCT domain / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / FHA domain / Forkhead-associated (FHA) domain / SMAD/FHA domain superfamily / 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
Mediator of DNA damage checkpoint protein 1 / DNA topoisomerase 2-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.6 Å
AuthorsLeung, C.C. / Glover, J.N.M.
CitationJournal: Structure / Year: 2013
Title: Structural insights into recognition of MDC1 by TopBP1 in DNA replication checkpoint control.
Authors: Leung, C.C. / Sun, L. / Gong, Z. / Burkat, M. / Edwards, R. / Assmus, M. / Chen, J. / Glover, J.N.
History
DepositionOct 31, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 3, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 26, 2014Group: Database references
Revision 1.2Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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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
E: phospho-peptide
F: phospho-peptide


Theoretical massNumber of molelcules
Total (without water)91,9846
Polymers91,9846
Non-polymers00
Water4,630257
1
A: DNA topoisomerase 2-binding protein 1
C: DNA topoisomerase 2-binding protein 1
F: phospho-peptide


Theoretical massNumber of molelcules
Total (without water)45,9923
Polymers45,9923
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA topoisomerase 2-binding protein 1
D: DNA topoisomerase 2-binding protein 1
E: phospho-peptide


Theoretical massNumber of molelcules
Total (without water)45,9923
Polymers45,9923
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.810, 59.100, 78.310
Angle α, β, γ (deg.)102.050, 98.040, 114.340
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111CHAIN AA0
211CHAIN BB0
112CHAIN CC0
212CHAIN DD0

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(-0.414384, 0.910102, 0.000764), (0.9101, 0.414381, 0.002279), (0.001758, 0.00164, -0.999997)-14.7101, 9.38303, 36.336399
2given(-0.414312, 0.910131, -0.002516), (0.910134, 0.414315, 0.000429), (0.001433, -0.002112, -0.999997)-14.825, 9.54171, 36.3144

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Components

#1: Protein
DNA topoisomerase 2-binding protein 1 / DNA topoisomerase II-beta-binding protein 1 / TopBP1 / DNA topoisomerase II-binding protein 1


Mass: 22238.371 Da / Num. of mol.: 4 / Fragment: BRCT domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIAA0259, TOPBP1 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: Q92547
#2: Protein/peptide phospho-peptide


Mass: 1515.275 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: This represents a consensus sequence in humans / References: UniProt: Q14676*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 257 / 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: 2.55 Å3/Da / Density % sol: 51.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PEG 10000, Ammonium acetate, bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Feb 6, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.6→34.6 Å / Num. all: 26653 / Num. obs: 26653 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 47.8 Å2 / Rmerge(I) obs: 0.059 / Net I/σ(I): 11.89
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
2.6-2.70.4022.236058288095.2
2.7-2.80.322.825146245495.5
2.8-2.90.2493.474447211995.5
2.9-3.20.1525.5110352493295.6
3.2-3.50.0829.537160341195.9
3.5-40.04715.497547359694.9
4-50.03122.297387351894.3
5-100.02625.766887328395
100.01838.695746094.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 43.49 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å34.57 Å
Translation2.5 Å34.57 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.1.4phasing
PHENIX1.7.2_869refinement
PDB_EXTRACT3.1data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→34.566 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8071 / SU ML: 0.69 / σ(F): 1.99 / Phase error: 26.58 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.234 1330 4.99 %random
Rwork0.1898 ---
obs0.192 26637 95.33 %-
all-26637 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.676 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso max: 166.19 Å2 / Biso mean: 44.2076 Å2 / Biso min: 4.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.1003 Å23.4003 Å2-1.28 Å2
2---2.9969 Å2-3.5971 Å2
3---22.9298 Å2
Refinement stepCycle: LAST / Resolution: 2.6→34.566 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5875 0 0 257 6132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095982
X-RAY DIFFRACTIONf_angle_d1.1328111
X-RAY DIFFRACTIONf_chiral_restr0.071947
X-RAY DIFFRACTIONf_plane_restr0.0041023
X-RAY DIFFRACTIONf_dihedral_angle_d13.2782150
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1429X-RAY DIFFRACTIONPOSITIONAL0.03
12B1429X-RAY DIFFRACTIONPOSITIONAL0.03
21C1429X-RAY DIFFRACTIONPOSITIONAL0.026
22D1429X-RAY DIFFRACTIONPOSITIONAL0.026
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.70430.3171490.2632838298795
2.7043-2.82730.33251490.26812822297196
2.8273-2.97630.25811470.23952789293695
2.9763-3.16260.30351480.23122820296896
3.1626-3.40660.30061480.20962817296596
3.4066-3.74910.22911480.18392841298996
3.7491-4.29070.1951470.15822783293095
4.2907-5.40250.17941470.13982788293594
5.4025-34.56950.19921470.1822809295696
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)
12.31630.3559-0.38281.5830.23071.0307-0.00010.21970.0968-0.11980.01660.00320.0094-0.03560.01570.0761-0.04450.07790.0988-0.00090.18073.14536.40225.1576
21.26690.2149-0.20651.6790.42260.9906-0.0065-0.15810.24030.13790.033-0.15630.0009-0.0053-0.05580.04-0.04740.04920.1026-0.08660.2051-10.166514.963931.1855
32.00430.05210.00052.046-0.10922.12590.03620.61630.1172-0.60450.023-0.2342-0.0490.2009-0.00050.1868-0.03130.10540.2433-0.0010.221820.243834.3842-1.9138
42.05440.0470.24591.8328-0.15711.437-0.0133-0.5450.22260.58030.0165-0.0036-0.224-0.09590.0160.1724-0.04640.04430.1341-0.07740.12738.025842.290738.1505
52.32850.1767-0.82663.03080.34651.05060.0085-0.0806-0.10610.4882-0.16530.12750.0057-0.2501-0.02690.238-0.0374-0.06270.1838-0.00610.6317-5.820133.060229.5867
61.61160.84280.1752.43611.1090.8604-0.14110.1524-0.1553-0.00840.1084-0.41480.12850.1249-0.17930.1481-0.01230.00210.1547-0.05930.547719.161317.21248.625
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN AA0
2X-RAY DIFFRACTION2CHAIN BB0
3X-RAY DIFFRACTION3CHAIN CC0
4X-RAY DIFFRACTION4CHAIN DD0
5X-RAY DIFFRACTION5CHAIN EE0
6X-RAY DIFFRACTION6CHAIN FF0

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