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- PDB-3eu7: Crystal Structure of a PALB2 / BRCA2 complex -

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Basic information

Entry
Database: PDB / ID: 3eu7
TitleCrystal Structure of a PALB2 / BRCA2 complex
Components
  • 19meric peptide from Breast cancer type 2 susceptibility protein
  • Partner and localizer of BRCA2
KeywordsTranscription/antitumor Protein / WD40 domain / Beta Propeller / Protein-Peptide Complex / Fanconi anemia / Nucleus / Phosphoprotein / WD repeat / Disease mutation / DNA damage / DNA repair / Transcription-antitumor Protein COMPLEX
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) / nuclear ubiquitin ligase complex / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity / lateral element ...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) / nuclear ubiquitin ligase complex / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity / lateral element / telomere maintenance via recombination / post-anal tail morphogenesis / 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 / 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 / mesoderm development / 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 / embryonic organ development / somitogenesis / positive regulation of mitotic cell cycle / regulation of cytokinesis / secretory granule / cellular response to ionizing radiation / nucleotide-excision repair / response to gamma radiation / animal organ morphogenesis / double-strand break repair via homologous recombination / brain development / multicellular organism growth / HDR through Homologous Recombination (HRR) / Meiotic recombination / KEAP1-NFE2L2 pathway / double-strand break repair / cellular senescence / single-stranded DNA binding / Neddylation / spermatogenesis / protease binding / chromosome, telomeric region / nuclear speck / centrosome / apoptotic process / regulation of DNA-templated transcription / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / protein-containing complex / DNA binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Partner and localiser of BRCA2, WD40 domain / Partner and localizer of BRCA2 / Partner and localizer of BRCA2 WD40 domain / : / BRCA2, OB2 / BRCA2, OB3 / Tower domain / Breast cancer type 2 susceptibility protein, helical domain / BRCA2 helical domain superfamily / BRCA2, oligonucleotide/oligosaccharide-binding, domain 3 ...Partner and localiser of BRCA2, WD40 domain / Partner and localizer of BRCA2 / Partner and localizer of BRCA2 WD40 domain / : / 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. / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Nucleic acid-binding, OB-fold / Mainly Beta
Similarity search - Domain/homology
Breast cancer type 2 susceptibility protein / Partner and localizer of BRCA2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsOliver, A.W. / Pearl, L.H.
CitationJournal: Embo Rep. / Year: 2009
Title: Structural basis for recruitment of BRCA2 by PALB2
Authors: Oliver, A.W. / Swift, S. / Lord, C.J. / Ashworth, A. / Pearl, L.H.
History
DepositionOct 9, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 5, 2014Group: Derived calculations
Revision 1.3Nov 12, 2014Group: Other
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Partner and localizer of BRCA2
X: 19meric peptide from Breast cancer type 2 susceptibility protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4874
Polymers41,3032
Non-polymers1842
Water1,76598
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-13 kcal/mol
Surface area14240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.815, 62.026, 77.975
Angle α, β, γ (deg.)90.00, 108.23, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Partner and localizer of BRCA2 / PALB2 / FANCONI ANEMIA GROUP N PROTEIN


Mass: 39195.793 Da / Num. of mol.: 1 / Fragment: C-terminal WD40 Domain, residues 835-1186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PALB2 / Plasmid: pTWO-B / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: Q86YC2
#2: Protein/peptide 19meric peptide from Breast cancer type 2 susceptibility protein / BRCA2 / Fanconi anemia group D1 protein


Mass: 2107.297 Da / Num. of mol.: 1 / Fragment: Interaction with PALB2, residues 21-39 / Source method: obtained synthetically
Details: chemically synthesized; This sequence occurs naturally in humans
References: UniProt: P51587
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O

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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: 2.3 Å3/Da / Density % sol: 46.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M Na-Cacodylate pH 6.5, 0.2M magnesium acetate, 10% (w/v) PEG 8000, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.943 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 8, 2007 / Details: Horizontally bended Ge(220)
RadiationMonochromator: Diamond (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.943 Å / Relative weight: 1
ReflectionResolution: 2.2→37.5 Å / Num. all: 19154 / Num. obs: 19026 / % possible obs: 99.9 % / Redundancy: 5.8 % / Biso Wilson estimate: 44.61 Å2 / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 16.5
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.602 / Mean I/σ(I) obs: 2.9 / Num. unique all: 2800 / Rsym value: 0.602 / % possible all: 99

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Processing

SoftwareName: PHENIX / Version: (phenix.refine) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2w18

2w18


Resolution: 2.2→37.495 Å / Occupancy max: 1 / Occupancy min: 0.47 / FOM free R set: 0.802 / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 0.91 / Phase error: 27.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2526 1691 5.13 %Random
Rwork0.1971 ---
all0.19991 ---
obs0.1999 19019 87.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.519 Å2 / ksol: 0.37 e/Å3
Displacement parametersBiso max: 105.85 Å2 / Biso mean: 47.989 Å2 / Biso min: 23.46 Å2
Baniso -1Baniso -2Baniso -3
1--5.1928 Å20 Å20.9654 Å2
2--2.0842 Å20 Å2
3---3.1086 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2469 0 12 98 2579
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142539
X-RAY DIFFRACTIONf_angle_d1.633457
X-RAY DIFFRACTIONf_chiral_restr0.097411
X-RAY DIFFRACTIONf_plane_restr0.009427
X-RAY DIFFRACTIONf_dihedral_angle_d19.007879
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
2.1995-2.26420.36831400.305225772202185
2.2642-2.33730.33541480.2605251786
2.3373-2.42080.29921320.2475257186
2.4208-2.51780.29381340.2262254386
2.5178-2.63230.2771390.2209256587
2.6323-2.77110.3231470.2188263988
2.7711-2.94460.30291160.2193261788
2.9446-3.17180.29841480.2028261189
3.1718-3.49080.24541530.1925263389
3.4908-3.99550.24361490.1694267290
3.9955-5.0320.17191390.1475266090
5.032-37.50050.21151460.1811264389

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