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- PDB-3al3: Crystal Structure of TopBP1 BRCT7/8-BACH1 peptide complex -

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Basic information

Entry
Database: PDB / ID: 3al3
TitleCrystal Structure of TopBP1 BRCT7/8-BACH1 peptide complex
Components
  • DNA topoisomerase 2-binding protein 1
  • Peptide of Fanconi anemia group J protein
KeywordsDNA BINDING PROTEIN/PROTEIN BINDING / BRCT domain-phosphopeptide complex / DNA BINDING PROTEIN-PROTEIN BINDING complex
Function / homology
Function and homology information


meiotic DNA double-strand break processing involved in reciprocal meiotic recombination / chiasma assembly / broken chromosome clustering / catalytic activity, acting on a nucleic acid / BRCA1-B complex / spermatogonial cell division / Cytosolic iron-sulfur cluster assembly / double-strand break repair involved in meiotic recombination / phosphorylation-dependent protein binding / homologous recombination ...meiotic DNA double-strand break processing involved in reciprocal meiotic recombination / chiasma assembly / broken chromosome clustering / catalytic activity, acting on a nucleic acid / BRCA1-B complex / spermatogonial cell division / Cytosolic iron-sulfur cluster assembly / double-strand break repair involved in meiotic recombination / phosphorylation-dependent protein binding / homologous recombination / seminiferous tubule development / DNA replication checkpoint signaling / Impaired BRCA2 binding to PALB2 / double-strand break repair via alternative nonhomologous end joining / DNA 5'-3' helicase / chromatin-protein adaptor activity / protein-DNA covalent cross-linking repair / double-strand break repair via classical nonhomologous end joining / protein localization to site of double-strand break / mitotic DNA replication checkpoint signaling / Homologous DNA Pairing and Strand Exchange / Defective homologous recombination repair (HRR) due to BRCA1 loss of function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA1 binding function / Defective HDR through Homologous Recombination Repair (HRR) due to PALB2 loss of BRCA2/RAD51/RAD51C binding function / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / 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 / spermatid development / DNA replication initiation / chromosome organization / DNA helicase activity / DNA damage checkpoint signaling / protein serine/threonine kinase activator activity / condensed nuclear chromosome / replication fork / double-strand break repair via homologous recombination / male germ cell nucleus / nucleotide-excision repair / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / PML body / spindle pole / site of double-strand break / double-strand break repair / actin cytoskeleton / Processing of DNA double-strand break ends / chromosome / 4 iron, 4 sulfur cluster binding / 5'-3' DNA helicase activity / Regulation of TP53 Activity through Phosphorylation / nuclear membrane / RNA helicase activity / nuclear body / DNA repair / centrosome / DNA damage response / regulation of transcription by RNA polymerase II / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / metal ion binding / 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 / ATP-dependent helicase Rad3/Chl1-like / Helicase-like, DEXD box c2 type ...: / TopBP1, BRCT0 domain / TopBP1, first BRCT domain / : / TopBP1/SLF1, BRCT domain / Secretoglobin superfamily / twin BRCT domain / BRCT domain / ATP-dependent helicase Rad3/Chl1-like / Helicase-like, DEXD box c2 type / DEAD2 / DEAD_2 / DEXDc2 / Helicase superfamily 1/2, DinG/Rad3-like / HELICc2 / ATP-dependent helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain, DinG/Rad3-type / Helicase C-terminal domain / Superfamilies 1 and 2 helicase ATP-binding type-2 domain profile. / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / BRCT domain profile. / BRCT domain / BRCT domain superfamily / DEAD-like helicases superfamily / Helicase superfamily 1/2, ATP-binding domain / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
FORMIC ACID / DNA topoisomerase 2-binding protein 1 / Fanconi anemia group J protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.15 Å
AuthorsLeung, C.C. / Glover, J.N.
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Molecular basis of BACH1/FANCJ recognition by TopBP1 in DNA replication checkpoint control
Authors: Leung, C.C. / Gong, Z. / Chen, J. / Glover, J.N.
History
DepositionJul 22, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 30, 2011Group: Database references
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ref_seq_dif / struct_site
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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED
Remark 700SHEET DETERMINATION METHOD: AUTHOR DETERMINED

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA topoisomerase 2-binding protein 1
B: Peptide of Fanconi anemia group J protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8453
Polymers27,7992
Non-polymers461
Water1,72996
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1350 Å2
ΔGint-10 kcal/mol
Surface area11400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.069, 78.069, 136.766
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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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: 26471.287 Da / Num. of mol.: 1 / Fragment: BRCT7 and BRCT8, UNP residues 1264-1493
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 Peptide of Fanconi anemia group J protein / Protein FANCJ / ATP-dependent RNA helicase BRIP1 / BRCA1-interacting protein C-terminal helicase 1 ...Protein FANCJ / ATP-dependent RNA helicase BRIP1 / BRCA1-interacting protein C-terminal helicase 1 / BRCA1-interacting protein 1 / BRCA1-associated C-terminal helicase 1


Mass: 1327.330 Da / Num. of mol.: 1 / Fragment: UNP residues 1129-1138 / Source method: obtained synthetically / Details: synthetic / References: UniProt: Q9BX63
#3: Chemical ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 96 / 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: 2.16 Å3/Da / Density % sol: 43.16 % / Mosaicity: 0.507 °
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Sodium formate, pH 8, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 14063 / % possible obs: 99.9 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.06 / Χ2: 0.797 / Net I/σ(I): 28.987
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.15-2.236.20.52613650.6621100
2.23-2.326.80.46313700.6711100
2.32-2.427.10.37413620.7031100
2.42-2.557.10.2913720.711100
2.55-2.717.10.18813840.7151100
2.71-2.927.10.13213840.771100
2.92-3.217.10.08114000.8491100
3.21-3.686.90.05714100.9391100
3.68-4.636.80.04214491.051100
4.63-506.30.02615670.875199.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 46.59 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å33.9 Å
Translation2.5 Å33.9 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3AL2

3al2


Resolution: 2.15→33.9 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.939 / WRfactor Rfree: 0.2364 / WRfactor Rwork: 0.1956 / Occupancy max: 1 / Occupancy min: 0.3 / FOM work R set: 0.8292 / SU B: 12.379 / SU ML: 0.146 / SU R Cruickshank DPI: 0.2561 / SU Rfree: 0.1986 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2364 699 5 %RANDOM
Rwork0.1955 ---
obs0.1975 14021 99.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 98.78 Å2 / Biso mean: 47.2525 Å2 / Biso min: 27.54 Å2
Baniso -1Baniso -2Baniso -3
1-0.27 Å20.14 Å20 Å2
2--0.27 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.15→33.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1823 0 3 96 1922
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221915
X-RAY DIFFRACTIONr_angle_refined_deg1.2581.9522607
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8225243
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.49924.04394
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.27515325
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.8741512
X-RAY DIFFRACTIONr_chiral_restr0.080.2283
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211470
X-RAY DIFFRACTIONr_mcbond_it0.5721.51160
X-RAY DIFFRACTIONr_mcangle_it1.05321869
X-RAY DIFFRACTIONr_scbond_it1.5013755
X-RAY DIFFRACTIONr_scangle_it2.4594.5729
LS refinement shellResolution: 2.151→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 63 -
Rwork0.225 932 -
all-995 -
obs--99.3 %
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)
12.8124-0.92452.41411.202-1.48284.0167-0.05530.0767-0.1425-0.0386-0.0483-0.02540.324-0.03930.10360.1398-0.02180.1020.0594-0.03240.0951-20.3815-17.1593-0.4357
21.793-2.37721.86736.5409-5.81628.4023-0.22760.1230.25030.3582-0.2176-0.5114-0.08470.63830.44520.1123-0.0316-0.01240.1641-0.0010.1846-15.6655-4.1494-2.1742
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1266 - 1491
2X-RAY DIFFRACTION2B1129 - 1138

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