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- PDB-3c5r: Crystal Structure of the BARD1 Ankyrin Repeat Domain and Its Func... -

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Basic information

Entry
Database: PDB / ID: 3c5r
TitleCrystal Structure of the BARD1 Ankyrin Repeat Domain and Its Functional Consequences
ComponentsBRCA1-associated RING domain protein 1
KeywordsPROTEIN BINDING / BARD1 / Ankyrin repeat / helix / extended loop / four repeat / protein / 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 / Ankyrin repeat-containing 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 / Ankyrin repeat-containing 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 repeat / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / Zinc finger, RING/FYVE/PHD-type / Mainly Alpha
Similarity search - Domain/homology
BRCA1-associated RING domain protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFox III, D. / Le Trong, I. / Stenkamp, R.E. / Klevit, R.E.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Crystal Structure of the BARD1 Ankyrin Repeat Domain and Its Functional Consequences.
Authors: Fox, D. / Le Trong, I. / Rajagopal, P. / Brzovic, P.S. / Stenkamp, R.E. / Klevit, R.E.
History
DepositionFeb 1, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 13, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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


Theoretical massNumber of molelcules
Total (without water)29,9532
Polymers29,9532
Non-polymers00
Water4,125229
1
A: BRCA1-associated RING domain protein 1


Theoretical massNumber of molelcules
Total (without water)14,9771
Polymers14,9771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BRCA1-associated RING domain protein 1


Theoretical massNumber of molelcules
Total (without water)14,9771
Polymers14,9771
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: BRCA1-associated RING domain protein 1

B: BRCA1-associated RING domain protein 1


Theoretical massNumber of molelcules
Total (without water)29,9532
Polymers29,9532
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area1370 Å2
ΔGint-12 kcal/mol
Surface area11700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.847, 74.112, 51.174
Angle α, β, γ (deg.)90.00, 105.23, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThere are 2 biological units in the asymmetric unit (chains A & B)

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Components

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


Mass: 14976.739 Da / Num. of mol.: 2
Fragment: BARD1 Ankyrin Repeat Domain (UNP residues 425-555)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BARD1 / Plasmid: pET151D / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99728
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.31 Å3/Da / Density % sol: 46.8 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 Mg Chloride, 0.1 M Tris Hydrochloride pH 8.5, 25% w/v PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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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: Apr 2, 2007 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. all: 19640 / Num. obs: 19640 / % possible obs: 81.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rsym value: 0.058 / Net I/σ(I): 17.83
Reflection shellResolution: 1.83→1.9 Å / Redundancy: 2 % / Mean I/σ(I) obs: 1.42 / Num. unique all: 649 / Rsym value: 0.527 / % possible all: 26.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
CrystalCleardata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SVX

1svx


Resolution: 2→49.39 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.923 / SU B: 10.04 / SU ML: 0.157 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.204 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26818 908 5.3 %RANDOM
Rwork0.19857 ---
all0.2022 16373 --
obs0.2022 16373 93.49 %-
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: 43.523 Å2
Baniso -1Baniso -2Baniso -3
1-3.65 Å20 Å20.15 Å2
2---1.27 Å20 Å2
3----2.3 Å2
Refinement stepCycle: LAST / Resolution: 2→49.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1928 0 0 229 2157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0211987
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.9532708
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4285251
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.38425.11190
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.00615322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.829156
X-RAY DIFFRACTIONr_chiral_restr0.0790.2310
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021506
X-RAY DIFFRACTIONr_nbd_refined0.2070.2948
X-RAY DIFFRACTIONr_nbtor_refined0.290.21355
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1620.2171
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.263
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1550.214
X-RAY DIFFRACTIONr_mcbond_it0.4441.51281
X-RAY DIFFRACTIONr_mcangle_it0.72822012
X-RAY DIFFRACTIONr_scbond_it1.2463782
X-RAY DIFFRACTIONr_scangle_it1.8564.5696
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 63 -
Rwork0.25 1098 -
obs--86.06 %
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)
12.7408-0.51-0.38183.7275-2.11836.0590.19520.03710.1789-0.1515-0.1732-0.4279-0.86410.3673-0.0220.0486-0.07150.0656-0.0355-0.0174-0.03573.011527.214612.8623
26.603-3.1484-2.104512.79841.70695.3649-0.0864-0.05570.01030.09410.01020.5155-0.194-0.31890.0762-0.01210.00060.0398-0.09920.0324-0.1064-4.586728.503222.4151
30.3651-0.44930.07362.0512-0.03974.44860.09660.04290.01320.08450.0095-0.04390.05540.1028-0.1061-0.0099-0.01380.00410.0111-0.0121-0.01740.043816.279717.048
411.42262.3735-0.9074.57470.01853.47110.12290.00430.01640.72030.1139-0.53930.25440.3248-0.23680.03140.0536-0.0841-0.0603-0.035-0.02694.205710.232824.4596
56.1312-2.97481.17042.81090.29583.62660.15440.1765-0.6382-0.2393-0.1218-0.08830.8560.2132-0.03260.24120.01760.0078-0.0228-0.03340.04334.32931.292214.7368
63.9493-0.2277-0.625812.3410.56517.9874-0.5198-0.4386-0.03210.56460.0481-0.49160.79270.62040.47170.07360.161-0.10410.0835-0.00330.050210.14430.840724.9446
72.0246-1.4222-2.42341.4333.14457.6936-0.17250.3864-0.2392-0.0002-0.04650.16150.7597-0.61480.21890.1813-0.03660.01420.02280.01540.007922.18651.285334.0846
86.58010.68960.530519.1107-4.31424.3173-0.1739-0.1216-0.07730.79530.006-0.1403-0.05690.07470.1680.11420.0229-0.0098-0.1043-0.0328-0.159123.90180.050646.3996
90.9768-0.3012-1.75814.1846-1.12873.8466-0.0263-0.02080.01850.00260.04420.08190.1115-0.0118-0.01790.0128-0.0209-0.0270.00870.0007-0.030322.670912.219139.3144
104.88621.265.20984.9392-3.228112.0928-0.0314-0.07370.0141-0.19290.38370.8594-0.2212-0.5943-0.35230.00160.0299-0.00220.02510.04320.115613.549418.068742.4243
113.1064-1.4513-1.26582.17980.868.0920.10920.22840.4172-0.0586-0.0154-0.0594-0.5833-0.0845-0.0938-0.0309-0.0497-0.0095-0.0326-0.01830.036320.579125.587637.4853
126.60870.7538-2.002411.47966.886422.9092-0.1073-0.20170.54720.4584-0.15421.3379-0.7811-1.51290.26160.09140.09450.03970.07980.04790.3429.839727.474940.0823
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA425 - 4387 - 20
2X-RAY DIFFRACTION2AA439 - 45421 - 36
3X-RAY DIFFRACTION3AA455 - 49937 - 81
4X-RAY DIFFRACTION4AA500 - 51882 - 100
5X-RAY DIFFRACTION5AA519 - 532101 - 114
6X-RAY DIFFRACTION6AA533 - 546115 - 128
7X-RAY DIFFRACTION7BB425 - 4387 - 20
8X-RAY DIFFRACTION8BB439 - 45421 - 36
9X-RAY DIFFRACTION9BB455 - 49937 - 81
10X-RAY DIFFRACTION10BB500 - 51482 - 96
11X-RAY DIFFRACTION11BB515 - 53297 - 114
12X-RAY DIFFRACTION12BB533 - 545115 - 127

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