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- PDB-4igk: Structure of human BRCA1 BRCT in complex with ATRIP peptide -

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Basic information

Entry
Database: PDB / ID: 4igk
TitleStructure of human BRCA1 BRCT in complex with ATRIP peptide
Components
  • ATRIP 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


ATR-ATRIP complex / 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 / sex-chromosome dosage compensation ...ATR-ATRIP complex / 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 / sex-chromosome dosage compensation / 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 / cellular response to indole-3-methanol / negative regulation of fatty acid biosynthetic process / homologous recombination / lateral element / regulation of double-strand break repair / protein K6-linked ubiquitination / regulation of DNA damage checkpoint / Impaired BRCA2 binding to PALB2 / XY body / mitotic G2/M transition checkpoint / postreplication repair / nucleobase-containing compound metabolic process / 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 / K63-linked polyubiquitin modification-dependent protein binding / negative regulation of gene expression via chromosomal CpG island methylation / intracellular non-membrane-bounded organelle / HDR through Single Strand Annealing (SSA) / Impaired BRCA2 binding to RAD51 / DNA-binding transcription activator activity / response to ionizing radiation / 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 / protein autoubiquitination / regulation of DNA repair / Activation of ATR in response to replication stress / SUMOylation of DNA damage response and repair proteins / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / ubiquitin ligase complex / Meiotic synapsis / positive regulation of DNA repair / tubulin binding / DNA damage checkpoint signaling / male germ cell nucleus / chromosome segregation / cellular response to ionizing radiation / Fanconi Anemia Pathway / TP53 Regulates Transcription of DNA Repair Genes / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / RING-type E3 ubiquitin transferase / G2/M DNA damage checkpoint / HDR through Homologous Recombination (HRR) / Metalloprotease DUBs / negative regulation of cell growth / Meiotic recombination / fatty acid biosynthetic process / ubiquitin-protein transferase activity / positive regulation of angiogenesis / intrinsic apoptotic signaling pathway in response to DNA damage / KEAP1-NFE2L2 pathway / double-strand break repair / p53 binding / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromosome / cellular response to tumor necrosis factor / Neddylation / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / transcription coactivator activity / nuclear body / transcription cis-regulatory region binding / regulation of cell cycle / protein ubiquitination / ribonucleoprotein complex / DNA repair / negative regulation of DNA-templated transcription / ubiquitin protein ligase binding / DNA damage response / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription
Similarity search - Function
ATR-interacting protein / Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / BRCT domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / BRCA1 C Terminus (BRCT) domain / breast cancer carboxy-terminal domain ...ATR-interacting protein / Breast cancer type 1 susceptibility protein (BRCA1) / BRCA1, serine-rich domain / BRCA1-associated / Serine-rich domain associated with BRCT / BRCT domain / 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 / Zinc finger, RING/FYVE/PHD-type / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Breast cancer type 1 susceptibility protein / ATR-interacting protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 17, 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

Downloads & links

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Assembly

Deposited unit
A: Breast cancer type 1 susceptibility protein
B: Breast cancer type 1 susceptibility protein
C: ATRIP peptide
D: ATRIP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,0088
Polymers50,6404
Non-polymers3684
Water7,728429
1
A: Breast cancer type 1 susceptibility protein
C: ATRIP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5044
Polymers25,3202
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-9 kcal/mol
Surface area11280 Å2
MethodPISA
2
B: Breast cancer type 1 susceptibility protein
D: ATRIP peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,5044
Polymers25,3202
Non-polymers1842
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-7 kcal/mol
Surface area11240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.666, 50.309, 73.977
Angle α, β, γ (deg.)90.00, 116.03, 90.00
Int Tables number3
Space group name H-MP121
Components on special symmetry positions
IDModelComponents
11A-2118-

HOH

21A-2184-

HOH

31B-2194-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.998429, -0.002344, -0.055991), (-0.002478, 0.999994, 0.002324), (0.055986, 0.002459, -0.998429)47.18395, 0.33283, -34.21409

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Components

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


Mass: 24531.234 Da / Num. of mol.: 2 / Fragment: BRCT domain, UNP residues 1646-1859
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 ATRIP peptide / ATM and Rad3-related-interacting protein


Mass: 788.762 Da / Num. of mol.: 2 / Fragment: UNP residues 237-243 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans. / Source: (synth.) Homo sapiens (human) / References: UniProt: Q8WXE1
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 429 / 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: 2.17 Å3/Da / Density % sol: 43.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG3350, 0.2 M ammonium acetate, 8% glycerol, 0.1 M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 9, 2011 / Details: mirrors
RadiationMonochromator: Fast monochromatic rotary beam shutters / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 43950 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Biso Wilson estimate: 24.4 Å2 / Rsym value: 0.059 / Net I/σ(I): 18.22
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 7.5 / Num. unique all: 4350 / Rsym value: 0.178 / % possible all: 100

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Processing

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

1y98


Resolution: 1.75→27.51 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.631 / SU ML: 0.07 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.5 / σ(I): 7.5 / ESU R: 0.11 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20414 2204 5 %RANDOM
Rwork0.15918 ---
all0.223 43821 --
obs0.16147 41617 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.039 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å21.49 Å2
2---0.82 Å2-0 Å2
3----0.53 Å2
Refine analyzeLuzzati coordinate error obs: 0.225 Å
Refinement stepCycle: LAST / Resolution: 1.75→27.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3442 0 24 429 3895
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0193573
X-RAY DIFFRACTIONr_bond_other_d0.0010.023392
X-RAY DIFFRACTIONr_angle_refined_deg1.9821.9464843
X-RAY DIFFRACTIONr_angle_other_deg0.97437790
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4655435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40823.481158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.80515590
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.731522
X-RAY DIFFRACTIONr_chiral_restr0.1270.2535
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0213985
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02849
LS refinement shellResolution: 1.751→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 159 -
Rwork0.178 3060 -
obs-4350 98.92 %
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)
11.24020.0285-0.2292.60070.20040.6988-0.0551-0.14960.16490.17850.04190.1793-0.03260.06270.01320.07870.0002-0.00490.0582-0.00860.041119.9218-1.29067.4321
21.34660.41290.12243.8259-0.30350.8796-0.08770.124-0.1582-0.43520.15950.61250.0204-0.0431-0.07180.1102-0.0057-0.06610.04340.0120.145313.8314-20.1968-7.6079
30.76111.37180.30996.6831-0.20210.7723-0.04830.0237-0.179-0.22860.18060.4560.06020.0027-0.13230.0952-0.0054-0.00180.05430.03330.211816.6091-29.7327-3.6346
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1649 - 1749
2X-RAY DIFFRACTION2A1750 - 1815
3X-RAY DIFFRACTION3A1819 - 1859

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