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- PDB-3k0k: Crystal Structure of BRCA1 BRCT in complex with a minimal recogni... -

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Basic information

Entry
Database: PDB / ID: 3k0k
TitleCrystal Structure of BRCA1 BRCT in complex with a minimal recognition tetrapeptide with a free carboxy C-terminus.
Components
  • Breast cancer type 1 susceptibility protein
  • phospho peptide pSPTF-COOH
KeywordsPROTEIN BINDING / BRCA1 / BRCT domain / DNA damage response / phospho peptide interactions / Abraxas / Alternative initiation / Cell cycle / Disease mutation / DNA damage / DNA repair / DNA-binding / Fatty acid biosynthesis / Ligase / Lipid synthesis / Metal-binding / Nucleus / Phosphoprotein / Tumor suppressor / Ubl conjugation pathway / Zinc-finger
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 / negative regulation of centriole replication / sex-chromosome dosage compensation / random inactivation of X chromosome / negative regulation of intracellular estrogen receptor signaling pathway ...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 / negative regulation of centriole replication / sex-chromosome dosage compensation / random inactivation of X chromosome / negative regulation of intracellular estrogen receptor signaling pathway / gamma-tubulin ring complex / nuclear ubiquitin ligase complex / chordate embryonic development / negative regulation of fatty acid biosynthetic process / cellular response to indole-3-methanol / DNA strand resection involved in replication fork processing / homologous recombination / lateral element / protein K6-linked ubiquitination / regulation of DNA damage checkpoint / Impaired BRCA2 binding to PALB2 / XY body / mitotic G2/M transition checkpoint / DNA repair complex / postreplication repair / centrosome cycle / RNA polymerase binding / Homologous DNA Pairing and Strand Exchange / 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 / 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) / DNA-binding transcription activator activity / negative regulation of gene expression via chromosomal CpG island methylation / Impaired BRCA2 binding to RAD51 / intracellular membraneless organelle / 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 / protein autoubiquitination / regulation of DNA repair / 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 / 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 / G2/M DNA damage checkpoint / negative regulation of cell growth / HDR through Homologous Recombination (HRR) / Metalloprotease DUBs / Meiotic recombination / fatty acid biosynthetic process / intrinsic apoptotic signaling pathway in response to DNA damage / ubiquitin-protein transferase activity / positive regulation of angiogenesis / KEAP1-NFE2L2 pathway / p53 binding / double-strand break repair / cellular response to tumor necrosis factor / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Neddylation / chromosome / Processing of DNA double-strand break ends / Regulation of TP53 Activity through Phosphorylation / damaged DNA binding / transcription coactivator activity / nuclear body / regulation of cell cycle / transcription cis-regulatory region binding / protein ubiquitination / ribonucleoprotein complex / DNA repair / negative regulation of DNA-templated transcription / DNA damage response / ubiquitin protein ligase binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding
Similarity search - Function
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 ...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
NICKEL (II) ION / Breast cancer type 1 susceptibility protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsCampbell, S.J. / Edwards, R.A. / Glover, J.N.
CitationJournal: Structure / Year: 2010
Title: Comparison of the Structures and Peptide Binding Specificities of the BRCT Domains of MDC1 and BRCA1
Authors: Campbell, S.J. / Edwards, R.A. / Glover, J.N.
History
DepositionSep 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software

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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: phospho peptide pSPTF-COOH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2874
Polymers25,1932
Non-polymers942
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-25 kcal/mol
Surface area11100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.422, 114.422, 123.005
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Detailsbiological unit is the same as asym.

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Components

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


Mass: 24662.434 Da / Num. of mol.: 1 / Fragment: BRCT Domain (UNP residues 1646 to 1859)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA1, RNF53 / Plasmid: pLM1-CD6 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Gold / References: UniProt: P38398
#2: Protein/peptide phospho peptide pSPTF-COOH


Mass: 530.464 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: This sequence occurs naturally in humans in the protein Abraxas/CCDC98. The peptide is chemically synthesized.
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 4.64 Å3/Da / Density % sol: 73.48 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.3
Details: Li2SO4, Tris-HCl, NiCl2, pH 7.3, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97934 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 15, 2008
RadiationMonochromator: DCM / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 13551 / % possible obs: 99.3 % / Redundancy: 19.2 % / Rmerge(I) obs: 0.061 / Χ2: 0.87 / Net I/σ(I): 12.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.87.70.55712590.61194
2.8-2.9114.60.41613070.615199.7
2.91-3.0420.10.27113320.6481100
3.04-3.221.80.1813370.7141100
3.2-3.421.90.12613300.8111100
3.4-3.6621.70.08413550.9261100
3.66-4.0321.60.0713510.8921100
4.03-4.6221.20.06713711.0841100
4.62-5.81210.04914031.0531100
5.81-5019.30.03415061.057199.5

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 47.99 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.7 Å37.45 Å
Translation2.7 Å37.45 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→35.83 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.898 / WRfactor Rfree: 0.295 / WRfactor Rwork: 0.263 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.767 / SU B: 25.623 / SU ML: 0.262 / SU R Cruickshank DPI: 0.391 / SU Rfree: 0.305 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.391 / ESU R Free: 0.305 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.299 667 4.9 %RANDOM
Rwork0.259 ---
obs0.261 13512 99.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 81.4 Å2 / Biso mean: 48.285 Å2 / Biso min: 28.96 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.1 Å20 Å2
2---0.2 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.7→35.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1731 0 2 12 1745
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0221785
X-RAY DIFFRACTIONr_angle_refined_deg1.0351.9442424
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8675215
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46223.6984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.46815.049307
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6541512
X-RAY DIFFRACTIONr_chiral_restr0.0670.2268
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211349
X-RAY DIFFRACTIONr_mcbond_it0.3431.51076
X-RAY DIFFRACTIONr_mcangle_it0.64921756
X-RAY DIFFRACTIONr_scbond_it0.8443709
X-RAY DIFFRACTIONr_scangle_it1.4094.5668
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 48 -
Rwork0.33 850 -
all-898 -
obs--92.29 %
Refinement TLS params.Method: refined / Origin x: -18.7689 Å / Origin y: 48.8396 Å / Origin z: -3.8906 Å
111213212223313233
T0.0582 Å20.0062 Å20.0255 Å2-0.4727 Å20.1043 Å2--0.0415 Å2
L17.214 °23.5217 °2-1.9927 °2-2.855 °2-0.7288 °2--1.5473 °2
S-0.1937 Å °1.8444 Å °0.067 Å °-0.3247 Å °0.1786 Å °-0.1501 Å °0.2117 Å °-0.2722 Å °0.0151 Å °

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