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- PDB-4ifi: Structure of human BRCA1 BRCT in complex with BAAT peptide -

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Basic information

Entry
Database: PDB / ID: 4ifi
TitleStructure of human BRCA1 BRCT in complex with BAAT peptide
Components
  • BAAT peptide
  • Breast cancer type 1 susceptibility protein
KeywordsTRANSCRIPTION / Cell cycle / Disease mutation / DNA damage / DNA repair / Fatty acid biosynthesis / Ligase / Lipid synthesis / Metal-binding / Nucleus / Phosphoprotein / Tumor suppressor / Ubl conjugation pathway / Zinc-finger / BRCT domain / DNA damage response / phospho peptide interactions / DNA-binding / phospho peptide binding
Function / homology
Function and homology information


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 / random inactivation of X chromosome / negative regulation of centriole replication / mitochondrion localization ...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 / random inactivation of X chromosome / negative regulation of centriole replication / mitochondrion localization / negative regulation of intracellular estrogen receptor signaling pathway / gamma-tubulin ring complex / nuclear ubiquitin ligase complex / DNA strand resection involved in replication fork processing / chordate embryonic development / negative regulation of fatty acid biosynthetic process / cellular response to indole-3-methanol / homologous recombination / lateral element / XY body / protein K6-linked ubiquitination / regulation of DNA damage checkpoint / dosage compensation by inactivation of X chromosome / negative regulation of gene expression via chromosomal CpG island methylation / Impaired BRCA2 binding to PALB2 / : / mitotic G2/M transition checkpoint / postreplication repair / DNA repair complex / RNA polymerase binding / centrosome cycle / 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 / response to ionizing radiation / DNA-binding transcription activator activity / intracellular non-membrane-bounded organelle / Transcriptional Regulation by E2F6 / mitotic G2 DNA damage checkpoint signaling / Presynaptic phase of homologous DNA pairing and strand exchange / negative regulation of cell cycle / positive regulation of vascular endothelial growth factor production / negative regulation of reactive oxygen species metabolic process / localization / regulation of DNA repair / protein autoubiquitination / ubiquitin ligase complex / SUMOylation of DNA damage response and repair proteins / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of DNA repair / Meiotic synapsis / tubulin binding / male germ cell nucleus / chromosome segregation / cellular response to ionizing radiation / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / HDR through Homologous Recombination (HRR) / G2/M DNA damage checkpoint / negative regulation of cell growth / Metalloprotease DUBs / Meiotic recombination / ubiquitin-protein transferase activity / fatty acid biosynthetic process / glucose metabolic process / positive regulation of angiogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / KEAP1-NFE2L2 pathway / double-strand break repair / cell migration / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / Neddylation / cellular response to tumor necrosis factor / Processing of DNA double-strand break ends / positive regulation of cell growth / cell population proliferation / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / transcription coactivator activity / protein ubiquitination / nuclear body / transcription cis-regulatory region binding / regulation of cell cycle / positive regulation of protein phosphorylation / ribonucleoprotein complex / DNA repair / negative regulation of DNA-templated transcription / apoptotic process / DNA damage response / ubiquitin protein ligase binding / positive regulation of gene expression
Similarity search - Function
BRCA1-associated ATM activator 1 / Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / BRCT domain / HEAT repeat / HEAT repeat / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) ...BRCA1-associated ATM activator 1 / Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / BRCT domain / HEAT repeat / HEAT repeat / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / 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 / Ring finger / Zinc finger RING-type profile. / Zinc finger, RING-type / Armadillo-like helical / Armadillo-type fold / Zinc finger, RING/FYVE/PHD-type / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Breast cancer type 1 susceptibility protein / BRCA1-associated ATM activator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsLiu, X. / Ladias, J.A.A.
CitationJournal: Biochemistry / Year: 2013
Title: Structural Basis for the BRCA1 BRCT Interaction with the Proteins ATRIP and BAAT1.
Authors: Liu, X. / Ladias, J.A.
History
DepositionDec 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 30, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Sep 20, 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_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_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: Breast cancer type 1 susceptibility protein
B: BAAT peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,3633
Polymers25,3042
Non-polymers591
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-8 kcal/mol
Surface area11050 Å2
MethodPISA
2
A: Breast cancer type 1 susceptibility protein
B: BAAT peptide
hetero molecules

A: Breast cancer type 1 susceptibility protein
B: BAAT peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,7266
Polymers50,6084
Non-polymers1182
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_554x-y,-y,-z-2/31
Buried area3620 Å2
ΔGint-25 kcal/mol
Surface area20220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.220, 65.220, 91.356
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Breast cancer type 1 susceptibility protein / RING finger protein 53


Mass: 24531.234 Da / Num. of mol.: 1 / Fragment: BRCT domain, UNP residues 1650-1859
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA1, RNF53 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P38398, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: Protein/peptide BAAT peptide


Mass: 772.763 Da / Num. of mol.: 1 / Fragment: UNP residues 268-273 / Source method: obtained synthetically / Details: The sequence occurs naturally in humans / Source: (synth.) Homo sapiens (human) / References: UniProt: Q6PJG6
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.25 Å3/Da / Density % sol: 45.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.8
Details: 30% PEG 6000, 1M LiCl. 0.1M Sodium Acetate , pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 28, 2012 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 11813 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 3.3 / Redundancy: 9.2 % / Biso Wilson estimate: 40.8 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 3.3
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 1144 / Rsym value: 0.533 / % possible all: 99

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Processing

Software
NameVersionClassification
CBASSdata collection
PHASERphasing
REFMAC5.7.0029refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1Y98

1y98


Resolution: 2.2→35.54 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.936 / SU B: 14.96 / SU ML: 0.193 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 3.3 / σ(I): 11.6 / ESU R: 0.29 / ESU R Free: 0.232 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26063 562 4.8 %RANDOM
Rwork0.19719 ---
all0.20021 11873 --
obs0.20021 11236 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.697 Å2
Baniso -1Baniso -2Baniso -3
1-1.7 Å21.7 Å2-0 Å2
2--1.7 Å2-0 Å2
3----5.51 Å2
Refine analyzeLuzzati coordinate error obs: 0.296 Å
Refinement stepCycle: LAST / Resolution: 2.2→35.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1708 0 4 66 1778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0191753
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7011.9422385
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1135215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.31723.63677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.13615281
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9231510
X-RAY DIFFRACTIONr_chiral_restr0.1140.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211327
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.201→2.258 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 41 -
Rwork0.238 803 -
obs--99.18 %
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)
10.88320.0305-0.08252.42210.74441.380.0404-0.1425-0.00820.00580.0501-0.33580.01550.0637-0.09050.0067-0.0016-0.01110.0331-0.03360.1524-19.69683.4078-16.8302
20.7128-0.4563-0.54391.5098-0.22251.04570.07030.0050.0323-0.06960.0347-0.0489-0.0801-0.0332-0.1050.0602-0.00030.02480.0532-0.03570.1224-35.167622.4266-20.6842
32.0925-0.96820.24463.2663-0.42691.6346-0.047-0.04940.26580.1420.0066-0.2212-0.3025-0.07580.04040.07880.0020.00720.0427-0.08020.1845-30.963831.6404-16.8481
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1649 - 1749
2X-RAY DIFFRACTION2A1750 - 1815
3X-RAY DIFFRACTION3A1816 - 1859

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