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- PDB-3fa2: Crystal Structure of the BRCA1 Associated Ring Domain (BARD1) Tan... -

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Basic information

Entry
Database: PDB / ID: 3fa2
TitleCrystal Structure of the BRCA1 Associated Ring Domain (BARD1) Tandem BRCT Domains
ComponentsBRCA1-associated RING domain protein 1
KeywordsPROTEIN BINDING / BARD1 / BRCA1 / BRCT / BRCA1 C-terminal Domain / Tandem / ANK repeat / Disease mutation / Metal-binding / Nucleus / Zinc-finger
Function / homology
Function and homology information


negative regulation of mRNA 3'-end processing / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / BRCA1-BARD1 complex / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / nuclear ubiquitin ligase complex / DNA strand resection involved in replication fork processing / homologous recombination ...negative regulation of mRNA 3'-end processing / Defective DNA double strand break response due to BRCA1 loss of function / Defective DNA double strand break response due to BARD1 loss of function / BRCA1-BARD1 complex / BRCA1-C complex / BRCA1-B complex / BRCA1-A complex / nuclear ubiquitin ligase complex / DNA strand resection involved in replication fork processing / homologous recombination / tissue homeostasis / protein K6-linked ubiquitination / regulation of DNA damage checkpoint / regulation of phosphorylation / Impaired BRCA2 binding to PALB2 / mitotic G2/M transition checkpoint / negative regulation of protein export from nucleus / 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 / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of cell cycle / regulation of DNA repair / ubiquitin ligase complex / cellular response to ionizing radiation / Nonhomologous End-Joining (NHEJ) / RING-type E3 ubiquitin transferase / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / Metalloprotease DUBs / kinase binding / cytoplasmic ribonucleoprotein granule / positive regulation of protein catabolic process / ubiquitin-protein transferase activity / UCH proteinases / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / regulation of cell cycle / protein ubiquitination / nuclear speck / positive regulation of apoptotic process / protein heterodimerization activity / DNA repair / DNA damage response / negative regulation of apoptotic process / protein homodimerization activity / RNA binding / nucleoplasm / nucleus / metal ion binding / cytoplasm
Similarity search - Function
BARD1, Zinc finger, RING-type / zf-RING of BARD1-type protein / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / BRCT domain profile. / BRCT domain / BRCT domain superfamily ...BARD1, Zinc finger, RING-type / zf-RING of BARD1-type protein / BRCT domain / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Zinc finger RING-type profile. / Zinc finger, RING-type / Ankyrin repeat-containing domain superfamily / Zinc finger, RING/FYVE/PHD-type / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHATE ION / BRCA1-associated RING domain protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsFox III, D. / Le Trong, I. / Stenkamp, R.E. / Klevit, R.E.
CitationJournal: TO BE PUBLISHED
Title: Crystal Structure of the BRCA1 Associated Ring Domain (BARD1) Tandem BRCT Domains
Authors: Fox III, D. / Le Trong, I. / Stenkamp, R.E. / Klevit, R.E.
History
DepositionNov 14, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.3Sep 6, 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_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_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

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Assembly

Deposited unit
A: BRCA1-associated RING domain protein 1
B: BRCA1-associated RING domain protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,4817
Polymers50,0122
Non-polymers4695
Water1,58588
1
A: BRCA1-associated RING domain protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1933
Polymers25,0061
Non-polymers1872
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: BRCA1-associated RING domain protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2884
Polymers25,0061
Non-polymers2823
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)44.979, 67.466, 86.783
Angle α, β, γ (deg.)90.00, 99.20, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BRCA1-associated RING domain protein 1 / BARD-1


Mass: 25005.881 Da / Num. of mol.: 2 / Fragment: Tandem BRCT Domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BARD1 / Plasmid: pET151D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q99728
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1M MES 15% w/v PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Feb 12, 2007 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.01→50 Å / Num. obs: 28268 / % possible obs: 82.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 39.37 Å2 / Rmerge(I) obs: 0.045 / Rsym value: 0.063 / Net I/σ(I): 16.77
Reflection shellResolution: 2.01→2.08 Å / Redundancy: 2.6 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 1.22 / Num. unique all: 1032 / Rsym value: 0.696 / % possible all: 30.4

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Processing

Software
NameVersionClassification
CrystalCleardata collection
PHASERphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2NTE CHAIN A

2nte


Resolution: 2.2→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.919 / SU B: 20.585 / SU ML: 0.254 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.299 / ESU R Free: 0.259 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29772 1255 5 %RANDOM
Rwork0.22237 ---
obs0.22605 23629 95.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.983 Å2
Baniso -1Baniso -2Baniso -3
1-3.48 Å20 Å2-1.85 Å2
2---2.37 Å20 Å2
3----1.7 Å2
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3295 0 27 88 3410
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0223424
X-RAY DIFFRACTIONr_bond_other_d0.0040.022421
X-RAY DIFFRACTIONr_angle_refined_deg1.2831.9694625
X-RAY DIFFRACTIONr_angle_other_deg0.8323.0015889
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8915409
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.26423.356149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.55315626
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9951523
X-RAY DIFFRACTIONr_chiral_restr0.0740.2504
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023668
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02693
X-RAY DIFFRACTIONr_nbd_refined0.1990.2747
X-RAY DIFFRACTIONr_nbd_other0.1870.22390
X-RAY DIFFRACTIONr_nbtor_refined0.180.21607
X-RAY DIFFRACTIONr_nbtor_other0.0830.21746
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2070.2137
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1810.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1670.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2550.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.24
X-RAY DIFFRACTIONr_mcbond_it0.6871.52643
X-RAY DIFFRACTIONr_mcbond_other0.1181.5825
X-RAY DIFFRACTIONr_mcangle_it0.83923305
X-RAY DIFFRACTIONr_scbond_it1.26731657
X-RAY DIFFRACTIONr_scangle_it1.7514.51316
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 79 -
Rwork0.289 1210 -
obs--65.87 %

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