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- PDB-2r1z: Crystal Structure of the BARD1 BRCT Repeat -

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Basic information

Entry
Database: PDB / ID: 2r1z
TitleCrystal Structure of the BARD1 BRCT Repeat
ComponentsBRCA1-associated RING domain protein 1
KeywordsANTITUMOR PROTEIN / BRCT Repeat / 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
BRCA1-associated RING domain protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å
AuthorsLee, M.S. / Edwards, R.A. / Williams, R.S. / Glover, M.J.N.
CitationJournal: To be Published
Title: Crystal Structure of the BARD1 BRCT Repeat
Authors: Lee, M.S. / Edwards, R.A. / Tsutakawa, S.E. / Williams, R.S. / Glover, M.J.N.
History
DepositionAug 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_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)48,2764
Polymers48,0922
Non-polymers1842
Water2,072115
1
A: BRCA1-associated RING domain protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,1382
Polymers24,0461
Non-polymers921
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)24,1382
Polymers24,0461
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)56.821, 75.550, 117.967
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13A
23B
14A
24B
15A
25B
16A
26B

NCS domain segments:

Component-ID: 1 / Refine code: 3

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LEULEUSERSERAA570 - 5792 - 11
21LEULEUSERSERBB570 - 5792 - 11
12LYSLYSCYSCYSAA596 - 63928 - 71
22LYSLYSCYSCYSBB596 - 63928 - 71
13VALVALARGARGAA644 - 66476 - 96
23VALVALARGARGBB644 - 66476 - 96
14LYSLYSLEULEUAA670 - 679102 - 111
24LYSLYSLEULEUBB670 - 679102 - 111
15PROPROLYSLYSAA687 - 706119 - 138
25PROPROLYSLYSBB687 - 706119 - 138
16VALVALLEULEUAA755 - 775187 - 207
26VALVALLEULEUBB755 - 775187 - 207

NCS ensembles :
ID
1
2
3
4
5
6
DetailsThe biological unit is a monomer. There are two biological units in the asymmetric unit.

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Components

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


Mass: 24045.855 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BARD1 / Plasmid: pDEST15 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q99728
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 115 / 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: 2.63 Å3/Da / Density % sol: 53.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: pSDDE peptide, 20% PEG 3350, 0.2 M ammonium chloride, 100 mM NaCl, 5 mM tris-HCl, 1 mM DTT, pH 7.5, temperature 298K, VAPOR DIFFUSION, HANGING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 22, 2007
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionRedundancy: 3.5 % / Av σ(I) over netI: 15 / Number: 87562 / Rmerge(I) obs: 0.052 / Χ2: 1.06 / D res high: 2.6 Å / D res low: 50 Å / Num. obs: 13944 / % possible obs: 95.3
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.65099.910.0281.1493.8
4.455.610010.0311.0454
3.884.4510010.0380.9324.1
3.533.8810010.0551.0624
3.283.5310010.0851.1194
3.083.2899.910.141.0833.9
2.933.0899.910.1981.0673.6
2.82.939810.2551.0493
2.692.885.810.2761.0342.4
2.62.6968.210.2821.0152
ReflectionResolution: 2.1→30 Å / Num. obs: 28825 / % possible obs: 94.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.032 / Χ2: 1.281 / Net I/σ(I): 27.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.1-2.1820.43720491.209170
2.18-2.262.40.31626111.281186.9
2.26-2.3730.2228491.299194.8
2.37-2.493.60.15829611.321199.1
2.49-2.653.90.10429891.335199.5
2.65-2.8540.0730211.252199.6
2.85-3.1440.04730061.327199.5
3.14-3.594.10.03130511.284199.7
3.59-4.5240.02330791.31199.7
4.52-303.80.02132091.147198.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4 Å45.05 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→29.49 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.926 / SU B: 12.273 / SU ML: 0.161 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.243 / ESU R Free: 0.202 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1445 5 %RANDOM
Rwork0.222 ---
obs0.224 28782 94.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.941 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20 Å20 Å2
2---0.39 Å20 Å2
3----0.91 Å2
Refinement stepCycle: LAST / Resolution: 2.1→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3311 0 12 115 3438
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0223402
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.9694597
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9255407
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.99723.649148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.14315618
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.1121522
X-RAY DIFFRACTIONr_chiral_restr0.0890.2503
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022516
X-RAY DIFFRACTIONr_nbd_refined0.1970.21476
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22264
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2134
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.180.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1620.212
X-RAY DIFFRACTIONr_mcbond_it0.5731.52108
X-RAY DIFFRACTIONr_mcangle_it1.02523325
X-RAY DIFFRACTIONr_scbond_it1.32431487
X-RAY DIFFRACTIONr_scangle_it2.0934.51272
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
140TIGHT POSITIONAL0.030.05
125LOOSE POSITIONAL0.215
140TIGHT THERMAL0.060.5
125LOOSE THERMAL0.4410
2176TIGHT POSITIONAL0.050.05
2167LOOSE POSITIONAL0.385
2176TIGHT THERMAL0.080.5
2167LOOSE THERMAL0.7610
384TIGHT POSITIONAL0.050.05
396LOOSE POSITIONAL1.015
384TIGHT THERMAL0.080.5
396LOOSE THERMAL1.1810
440TIGHT POSITIONAL0.030.05
449LOOSE POSITIONAL0.195
440TIGHT THERMAL0.10.5
449LOOSE THERMAL1.0210
580TIGHT POSITIONAL0.040.05
567LOOSE POSITIONAL0.545
580TIGHT THERMAL0.090.5
567LOOSE THERMAL1.4110
684TIGHT POSITIONAL0.050.05
689LOOSE POSITIONAL0.345
684TIGHT THERMAL0.10.5
689LOOSE THERMAL0.810
LS refinement shellResolution: 2.1→2.154 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 82 -
Rwork0.283 1429 -
all-1511 -
obs--69.79 %
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)
15.4129-1.3884-3.79257.05264.16611.3504-0.114-0.96890.92350.20620.684-0.54840.04440.6626-0.57-0.17110.0214-0.05470.0551-0.3092-0.047717.90510.14137.809
23.88390.9636-0.76085.41571.56456.26620.14230.12140.2284-0.0841-0.16450.17760.1265-0.32180.0221-0.1313-0.0393-0.034-0.1915-0.042-0.275518.185-4.88713.745
32.98771.48951.535811.79766.1517.01220.15910.1079-0.29640.19260.3472-0.517-0.64420.5099-0.50640.0998-0.12250.0989-0.1116-0.0208-0.135442.56213.05911.493
44.68410.10410.85966.95011.47974.34350.11780.27860.0807-0.67020.1281-0.4091-0.395-0.0663-0.2459-0.03170.07250.1298-0.1647-0.0034-0.212635.074-6.753-8.204
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA569 - 6681 - 100
2X-RAY DIFFRACTION2AA669 - 776101 - 208
3X-RAY DIFFRACTION3BB569 - 6681 - 100
4X-RAY DIFFRACTION4BB669 - 776101 - 208

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