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- PDB-2w18: Crystal structure of the C-terminal WD40 domain of human PALB2 -

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Basic information

Entry
Database: PDB / ID: 2w18
TitleCrystal structure of the C-terminal WD40 domain of human PALB2
ComponentsPARTNER AND LOCALIZER OF BRCA2
KeywordsNUCLEAR PROTEIN / FANCONI ANEMIA / HOMOLOGOUS RECOMINATION / POLYMORPHISM / PHOSPHOPROTEIN / BETA-PROPELLER / WD40 / FANC-N / NUCLEUS / WD REPEAT / COILED COIL
Function / homology
Function and homology information


post-anal tail morphogenesis / Impaired BRCA2 binding to PALB2 / 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) / Resolution of D-loop Structures through Holliday Junction Intermediates / inner cell mass cell proliferation ...post-anal tail morphogenesis / Impaired BRCA2 binding to PALB2 / 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) / Resolution of D-loop Structures through Holliday Junction Intermediates / inner cell mass cell proliferation / mesoderm development / embryonic organ development / somitogenesis / animal organ morphogenesis / double-strand break repair via homologous recombination / multicellular organism growth / HDR through Homologous Recombination (HRR) / KEAP1-NFE2L2 pathway / Neddylation / nuclear speck / apoptotic process / negative regulation of apoptotic process / protein-containing complex / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Partner and localiser of BRCA2, WD40 domain / Partner and localizer of BRCA2 / Partner and localizer of BRCA2 WD40 domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Mainly Beta
Similarity search - Domain/homology
Partner and localizer of BRCA2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 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 15, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
A: PARTNER AND LOCALIZER OF BRCA2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,6246
Polymers39,1641
Non-polymers4605
Water3,369187
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)80.780, 64.650, 77.250
Angle α, β, γ (deg.)90.00, 109.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PARTNER AND LOCALIZER OF BRCA2 / PALB2 / FANCN


Mass: 39163.793 Da / Num. of mol.: 1 / Fragment: WD40 DOMAIN, RESIDUES 835-1186
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: Q86YC2
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 187 / 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: 2.41 Å3/Da / Density % sol: 48.9 % / Description: NONE
Crystal growpH: 6
Details: 100 MM MES PH 6.0, 50 MM KH2PO4, 12-20% (W/V) PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Apr 12, 2007 / Details: HORIZONTALLY BENDED GE(220)
RadiationMonochromator: DIAMOND (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.9→49.27 Å / Num. obs: 54291 / % possible obs: 94.1 % / Redundancy: 4 % / Biso Wilson estimate: 27.58 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.7 / % possible all: 75.4

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Processing

Software
NameClassification
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
SHARPphasing
PHENIXrefinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.9→49.265 Å / SU ML: 0.29 / σ(F): 0.95 / Phase error: 27.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2464 2742 5.05 %
Rwork0.2089 --
obs0.2109 29655 93.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.51 Å2 / ksol: 0.369 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.63 Å20 Å23.7163 Å2
2--6.7099 Å20 Å2
3----3.0799 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.265 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2320 0 30 187 2537
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012402
X-RAY DIFFRACTIONf_angle_d1.473268
X-RAY DIFFRACTIONf_dihedral_angle_d16.68826
X-RAY DIFFRACTIONf_chiral_restr0.1390
X-RAY DIFFRACTIONf_plane_restr0401
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.93280.30381130.32251799X-RAY DIFFRACTION65
1.9328-1.96790.35791370.31052002X-RAY DIFFRACTION74
1.9679-2.00580.34141300.30952335X-RAY DIFFRACTION86
2.0058-2.04670.30121300.30322594X-RAY DIFFRACTION96
2.0467-2.09120.36731400.29312728X-RAY DIFFRACTION96
2.0912-2.13990.28831390.27632692X-RAY DIFFRACTION97
2.1399-2.19340.30651350.24332646X-RAY DIFFRACTION97
2.1934-2.25270.31841500.23722687X-RAY DIFFRACTION97
2.2527-2.3190.26251190.23252646X-RAY DIFFRACTION97
2.319-2.39380.26611260.23442690X-RAY DIFFRACTION97
2.3938-2.47940.29951520.22582678X-RAY DIFFRACTION97
2.4794-2.57860.29151320.21772709X-RAY DIFFRACTION97
2.5786-2.6960.33791240.21652700X-RAY DIFFRACTION97
2.696-2.83810.2861300.21862657X-RAY DIFFRACTION97
2.8381-3.01590.24111860.19952650X-RAY DIFFRACTION98
3.0159-3.24870.23351530.1982706X-RAY DIFFRACTION98
3.2487-3.57560.23781370.17612655X-RAY DIFFRACTION98
3.5756-4.09270.22431400.17282706X-RAY DIFFRACTION98
4.0927-5.15550.16021570.15552678X-RAY DIFFRACTION97
5.1555-49.28110.20111120.20222591X-RAY DIFFRACTION93

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