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- PDB-7ldg: Crystal structure of the MEILB2-BRCA2 complex -

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Basic information

Entry
Database: PDB / ID: 7ldg
TitleCrystal structure of the MEILB2-BRCA2 complex
Components
  • Breast cancer type 2 susceptibility protein
  • Heat shock factor 2-binding protein
KeywordsRECOMBINATION / Complex / Recruiter / Protein-protein interaction / Armadillo-repeat
Function / homology
Function and homology information


BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / establishment of protein localization to telomere / mitotic recombination-dependent replication fork processing / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity ...BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / establishment of protein localization to telomere / mitotic recombination-dependent replication fork processing / double-strand break repair involved in meiotic recombination / nuclear ubiquitin ligase complex / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity / lateral element / regulation of DNA damage checkpoint / Impaired BRCA2 binding to PALB2 / telomere maintenance via recombination / gamma-tubulin binding / HDR through MMEJ (alt-NHEJ) / oocyte maturation / DNA repair complex / response to UV-C / female meiosis I / 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 / inner cell mass cell proliferation / Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA) / Resolution of D-loop Structures through Holliday Junction Intermediates / female gonad development / hematopoietic stem cell proliferation / Impaired BRCA2 binding to RAD51 / male meiosis I / centrosome duplication / Presynaptic phase of homologous DNA pairing and strand exchange / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to X-ray / positive regulation of mitotic cell cycle / secretory granule / regulation of cytokinesis / response to gamma radiation / cellular response to ionizing radiation / nucleotide-excision repair / DNA damage response, signal transduction by p53 class mediator / double-strand break repair via homologous recombination / brain development / HDR through Homologous Recombination (HRR) / Meiotic recombination / cellular senescence / double-strand break repair / single-stranded DNA binding / chromosome / protease binding / spermatogenesis / 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, 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, OB3 / Tower domain / Breast cancer type 2 susceptibility protein, helical domain / BRCA2 helical domain superfamily / : / : / BRCA2, oligonucleotide/oligosaccharide-binding, domain 3 / Tower / BRCA2, helical / BRCA2, OB2 / BRCA2 TR2 domain / Tower / BRCA2 repeat / BRCA2, OB1 / Breast cancer type 2 susceptibility protein / BRCA2 repeat / BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 / BRCA2 repeat profile. / Leucine-rich Repeat Variant / Leucine-rich Repeat Variant / Armadillo-like helical / Alpha Horseshoe / Armadillo-type fold / Nucleic acid-binding, OB-fold / Mainly Alpha
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 / SAD / Resolution: 2.56 Å
AuthorsNandakumar, J. / Pendlebury, D.F.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM120094 United States
National Institutes of Health/National Institute on Aging (NIH/NIA)R01-AG050509 United States
American Cancer SocietyRSG-17-037-01-DMC United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2021
Title: Structure of a meiosis-specific complex central to BRCA2 localization at recombination sites.
Authors: Pendlebury, D.F. / Zhang, J. / Agrawal, R. / Shibuya, H. / Nandakumar, J.
History
DepositionJan 13, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)72,0874
Polymers72,0874
Non-polymers00
Water1086
1
A: Heat shock factor 2-binding protein
B: Breast cancer type 2 susceptibility protein
C: Heat shock factor 2-binding protein
D: Breast cancer type 2 susceptibility protein

A: Heat shock factor 2-binding protein
B: Breast cancer type 2 susceptibility protein
C: Heat shock factor 2-binding protein
D: Breast cancer type 2 susceptibility protein


Theoretical massNumber of molelcules
Total (without water)144,1758
Polymers144,1758
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area18610 Å2
ΔGint-129 kcal/mol
Surface area44080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)179.889, 179.889, 179.186
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3

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Components

#1: Protein Heat shock factor 2-binding protein / MEILB2


Mass: 28304.908 Da / Num. of mol.: 2 / Fragment: aa83-334
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: 7738.730 Da / Num. of mol.: 2 / Fragment: MEILB2-binding domain (aa2271-2335)
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 3.87 Å3/Da / Density % sol: 68.22 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1 M sodium acetate (pH 4.6), 2 M lithium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97895 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Mar 10, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97895 Å / Relative weight: 1
ReflectionResolution: 2.56→89.94 Å / Num. obs: 35987 / % possible obs: 100 % / Redundancy: 21 % / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Net I/σ(I): 18.9
Reflection shellResolution: 2.56→2.7 Å / Redundancy: 21.7 % / Rmerge(I) obs: 1.467 / Mean I/σ(I) obs: 2 / Num. unique obs: 5188 / CC1/2: 0.833 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.17.1-3600refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.56→31.1 Å / Cross valid method: FREE R-VALUE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2307 1711 -
Rwork0.2106 --
obs-35955 99.97 %
Displacement parametersBiso mean: 96.72 Å2
Refinement stepCycle: LAST / Resolution: 2.56→31.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3806 0 0 6 3812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00373859
X-RAY DIFFRACTIONf_angle_d0.61145212
X-RAY DIFFRACTIONf_chiral_restr0.0363630
X-RAY DIFFRACTIONf_plane_restr0.0037652
X-RAY DIFFRACTIONf_dihedral_angle_d15.70111443
LS refinement shellResolution: 2.56→2.63 Å
RfactorNum. reflection% reflection
Rfree0.3496 --
Rwork0.3027 --
obs-2968 100 %

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