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- PDB-4ofb: Crystal structure of human BRCA1 BRCT in complex with nonphosphop... -

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Basic information

Entry
Database: PDB / ID: 4ofb
TitleCrystal structure of human BRCA1 BRCT in complex with nonphosphopeptide inhibitor
Components
  • Breast cancer type 1 susceptibility protein
  • nonphosphopeptide inhibitor
KeywordsPROTEIN BINDING / BRCT domain / DSB DNA damage repair / non-phosphorylated peptide
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 / 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 / random inactivation of X chromosome / negative regulation of centriole replication / 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 / 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 / Neddylation / cellular response to tumor necrosis factor / Processing of DNA double-strand break ends / 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 / 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
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
Breast cancer type 1 susceptibility protein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.05 Å
AuthorsSun, L. / Edwards, R.A. / Glover, J.N.M.
CitationJournal: Acs Chem.Biol. / Year: 2015
Title: Peptide Library Approach to Uncover Phosphomimetic Inhibitors of the BRCA1 C-Terminal Domain.
Authors: White, E.R. / Sun, L. / Ma, Z. / Beckta, J.M. / Danzig, B.A. / Hacker, D.E. / Huie, M. / Williams, D.C. / Edwards, R.A. / Valerie, K. / Glover, J.N. / Hartman, M.C.
History
DepositionJan 14, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1May 27, 2015Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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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: nonphosphopeptide inhibitor


Theoretical massNumber of molelcules
Total (without water)26,1852
Polymers26,1852
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-1 kcal/mol
Surface area11400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.811, 37.811, 175.993
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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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 1 domain (UNP residues 1646-1859)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA1, RNF53 / Plasmid: pLM1 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: P38398
#2: Protein/peptide nonphosphopeptide inhibitor


Mass: 1653.786 Da / Num. of mol.: 1 / Source method: obtained synthetically

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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: 2.4 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.1M Sodium Cacodylate, 0.1M Magnesium Acetate,24% PEG6000, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08B1-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Mar 13, 2013
RadiationMonochromator: KOHZU double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.05→37.811 Å / Num. all: 4741 / Num. obs: 4741 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 52.9 Å2 / Rmerge(I) obs: 0.135 / Χ2: 1.022 / Net I/σ(I): 7.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
3.05-3.160.6394920.9991100
3.16-3.294.20.4894330.9991100
3.29-3.444.40.3415001.0421100
3.44-3.624.20.2374581.0331100
3.62-3.844.40.2084881.0371100
3.84-4.144.20.1314591.0341100
4.14-4.564.30.0874591.0271100
4.56-5.224.30.0754811.0121100
5.22-6.574.20.0644811.0071100
6.57-10004.30.0354901.028199.2

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.05 Å37.81 Å
Translation3.05 Å37.81 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.2phasing
PHENIX1.8.3_1479refinement
PDB_EXTRACT3.14data extraction
MxDCdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→37.811 Å / FOM work R set: 0.8173 / SU ML: 0.4 / σ(F): 1.37 / Phase error: 25.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2375 216 4.6 %Random
Rwork0.2105 ---
obs0.2118 4692 99.81 %-
all-4692 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 159.23 Å2 / Biso mean: 60.89 Å2 / Biso min: 19.23 Å2
Refinement stepCycle: LAST / Resolution: 3.05→37.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1791 0 0 0 1791
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041833
X-RAY DIFFRACTIONf_angle_d1.0552485
X-RAY DIFFRACTIONf_chiral_restr0.043275
X-RAY DIFFRACTIONf_plane_restr0.006315
X-RAY DIFFRACTIONf_dihedral_angle_d13.694666
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
3.05-3.84540.29151190.26822372356
3.8454-37.81390.2028970.178822392336
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)
13.0062-0.651-0.4172.73521.07373.4418-0.38590.4237-0.42110.2511-0.30870.22041.0264-0.53170.34260.4919-0.12980.11640.3683-0.16760.3941-9.128412.2086-2.8499
21.5889-0.8584-0.70531.5870.21471.8315-0.43060.4011-0.63980.2399-0.28820.78050.9004-1.46960.5060.5891-0.29180.15531.0149-0.33110.624-26.795218.73459.35
37.94783.18240.29023.9933-0.9760.4612-0.887-1.8233-0.2321-0.0669-0.04160.29761.1576-0.87890.63810.7846-0.17130.2120.8542-0.08060.4946-36.100820.407118.2146
43.0031-0.8242-0.59143.00820.7533.317-0.6388-0.3143-0.25570.49260.08010.60911.0907-1.01890.45690.6121-0.23240.16860.5782-0.14690.4485-24.028223.886721.48
51.5456-0.36160.24030.64520.01965.02470.09110.00990.61760.341-0.2904-0.6932-2.26681.46520.050.4434-0.1353-0.06030.2734-0.04480.6034-9.396526.10854.6442
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESID 1649:1747)A0
2X-RAY DIFFRACTION2CHAIN A AND (RESID 1748:1797)A0
3X-RAY DIFFRACTION3CHAIN A AND (RESID 1798:1810)A0
4X-RAY DIFFRACTION4CHAIN A AND (RESID 1811:1859)A0
5X-RAY DIFFRACTION5CHAIN B AND (RESID 2:13)B0

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