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- PDB-7bdx: Armadillo domain of HSF2BP in complex with BRCA2 peptide -

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Basic information

Entry
Database: PDB / ID: 7bdx
TitleArmadillo domain of HSF2BP in complex with BRCA2 peptide
Components
  • Breast cancer type 2 susceptibility protein
  • Heat shock factor 2-binding protein
KeywordsNUCLEAR PROTEIN / HSF2BP / BRCA2
Function / homology
Function and homology information


BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / mitotic recombination-dependent replication fork processing / establishment of protein localization to telomere / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity ...BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / mitotic recombination-dependent replication fork processing / establishment of protein localization to telomere / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity / lateral element / telomere maintenance via recombination / regulation of DNA damage checkpoint / oocyte maturation / Impaired BRCA2 binding to PALB2 / HDR through MMEJ (alt-NHEJ) / gamma-tubulin binding / DNA repair complex / 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 / female meiosis I / Homologous DNA Pairing and Strand Exchange / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / response to UV-C / Resolution of D-loop Structures through Holliday Junction Intermediates / inner cell mass cell proliferation / DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / hematopoietic stem cell proliferation / Impaired BRCA2 binding to RAD51 / female gonad development / male meiosis I / Presynaptic phase of homologous DNA pairing and strand exchange / centrosome duplication / response to X-ray / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of mitotic cell cycle / regulation of cytokinesis / secretory granule / cellular response to ionizing radiation / nucleotide-excision repair / response to gamma radiation / double-strand break repair via homologous recombination / brain development / HDR through Homologous Recombination (HRR) / Meiotic recombination / double-strand break repair / cellular senescence / single-stranded DNA binding / chromosome / spermatogenesis / protease binding / transcription by RNA polymerase II / chromosome, telomeric region / centrosome / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein-containing complex / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Heat shock factor 2-binding protein / : / BRCA2, OB2 / BRCA2, OB3 / Tower domain / Breast cancer type 2 susceptibility protein, helical domain / BRCA2 helical domain superfamily / BRCA2, oligonucleotide/oligosaccharide-binding, domain 3 / Tower / BRCA2, helical ...Heat shock factor 2-binding protein / : / BRCA2, OB2 / BRCA2, OB3 / Tower domain / Breast cancer type 2 susceptibility protein, helical domain / BRCA2 helical domain superfamily / BRCA2, oligonucleotide/oligosaccharide-binding, domain 3 / Tower / BRCA2, helical / Tower / BRCA2 repeat / BRCA2, OB1 / Breast cancer type 2 susceptibility protein / BRCA2 repeat / BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 / BRCA2 repeat profile. / Armadillo-like helical / Armadillo-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Heat shock factor 2-binding protein / Breast cancer type 2 susceptibility protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLe Du, M.H. / Zinn-Justin, S. / Ghouil, R. / Miron, S. / Legrand, P.
CitationJournal: Nat Commun / Year: 2021
Title: BRCA2 binding through a cryptic repeated motif to HSF2BP oligomers does not impact meiotic recombination.
Authors: Ghouil, R. / Miron, S. / Koornneef, L. / Veerman, J. / Paul, M.W. / Le Du, M.H. / Sleddens-Linkels, E. / van Rossum-Fikkert, S.E. / van Loon, Y. / Felipe-Medina, N. / Pendas, A.M. / Maas, A. ...Authors: Ghouil, R. / Miron, S. / Koornneef, L. / Veerman, J. / Paul, M.W. / Le Du, M.H. / Sleddens-Linkels, E. / van Rossum-Fikkert, S.E. / van Loon, Y. / Felipe-Medina, N. / Pendas, A.M. / Maas, A. / Essers, J. / Legrand, P. / Baarends, W.M. / Kanaar, R. / Zinn-Justin, S. / Zelensky, A.N.
History
DepositionDec 22, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 28, 2021Group: Structure summary / Category: audit_author
Revision 1.2Jul 20, 2022Group: Advisory / Database references
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3May 1, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock factor 2-binding protein
B: Heat shock factor 2-binding protein
C: Heat shock factor 2-binding protein
D: Heat shock factor 2-binding protein
E: Breast cancer type 2 susceptibility protein
F: Breast cancer type 2 susceptibility protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,9238
Polymers108,8746
Non-polymers492
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16090 Å2
ΔGint-102 kcal/mol
Surface area39360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.887, 135.830, 75.794
Angle α, β, γ (deg.)90.000, 110.380, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Heat shock factor 2-binding protein


Mass: 23699.680 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HSF2BP, MEILB2 / Production host: Escherichia coli (E. coli) / References: UniProt: O75031
#2: Protein Breast cancer type 2 susceptibility protein / Fanconi anemia group D1 protein


Mass: 7037.761 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA2, FACD, FANCD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P51587
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.37 Å3/Da / Density % sol: 0.426 % / Description: Needle
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: PEG 3350 : 16% (w/v) Mes ph 6.0 100 mM MgCl2 100 mM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 20, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.6→49.6 Å / Num. obs: 30850 / % possible obs: 83.7 % / Redundancy: 7.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.158 / Rpim(I) all: 0.062 / Net I/σ(I): 9.4
Reflection shellResolution: 2.6→2.69 Å / Num. unique obs: 930 / CC1/2: 0.355

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (19-MAR-2020)refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: H3 domain from Robetta

Resolution: 2.6→49.58 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.911 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.342
RfactorNum. reflection% reflectionSelection details
Rfree0.2413 1226 4.74 %RANDOM
Rwork0.1976 ---
obs0.1997 25870 83.9 %-
Displacement parametersBiso max: 175.21 Å2 / Biso mean: 86.69 Å2 / Biso min: 34.16 Å2
Baniso -1Baniso -2Baniso -3
1-2.4176 Å20 Å2-0.3477 Å2
2--3.4747 Å20 Å2
3----5.8923 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: final / Resolution: 2.6→49.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7275 0 2 157 7434
Biso mean--63.4 62.93 -
Num. residues----943
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2608SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1218HARMONIC5
X-RAY DIFFRACTIONt_it7355HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion980SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6226SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7355HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg9950HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion19.84
LS refinement shellResolution: 2.6→2.65 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.267 31 5.98 %
Rwork0.2251 487 -
all0.2277 518 -
obs--27.5 %
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)
10.31780.1221-0.39771.31960.77582.627-0.0633-0.10330.0584-0.1582-0.01910.00310.0321-0.25580.0824-0.0270.0008-0.00510.0640.0124-0.092319.881159.724379.5258
20.27860.2110.8371.25050.83681.7055-0.00250.0855-0.04220.1893-0.01760.01560.0335-0.14740.0201-0.0278-0.0073-0.00790.12140.0014-0.071119.730759.868232.3183
32.94981.31952.00371.46291.20712.6326-0.13050.00020.0908-0.05340.15160.0228-0.46110.1837-0.02110.0863-0.1319-0.0032-0.1132-0.0215-0.100638.490985.497463.2348
43.3429-2.3649-1.19942.17351.76285.3040.05450.3331-0.09520.17580.10160.26620.68450.6094-0.15610.07810.1889-0.05050.0384-0.0721-0.236238.471834.176449.179
51.02160.96860.069100.09481.1111-0.0269-0.0406-0.1936-0.01380.2098-0.0471-0.03290.3665-0.18290.01340.0409-0.02880.1353-0.0412-0.010138.306867.900871.9315
60.2784-1.1145-0.22510-0.14750.3891-0.12970.05820.1911-0.03150.05090.00150.1750.60220.07870.02480.07240.01490.28860.0618-0.045238.10449.878240.7207
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 211
2X-RAY DIFFRACTION2{ B|* }B1 - 212
3X-RAY DIFFRACTION3{ C|* }C1 - 213
4X-RAY DIFFRACTION4{ D|* }D1 - 211
5X-RAY DIFFRACTION5{ E|* }E1 - 53
6X-RAY DIFFRACTION6{ F|* }F1 - 51

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