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- PDB-8c3j: Stapled peptide SP2 in complex with humanised RadA mutant HumRadA22 -

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Basic information

Entry
Database: PDB / ID: 8c3j
TitleStapled peptide SP2 in complex with humanised RadA mutant HumRadA22
Components
  • Breast cancer type 2 susceptibility protein
  • DNA repair and recombination protein RadA
KeywordsRECOMBINATION / Stapled peptide / Rad51 / BRCA2 / BRC repeat
Function / homology
Function and homology information


BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / establishment of protein localization to telomere / mitotic recombination-dependent replication fork processing / nuclear ubiquitin ligase complex / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity / lateral element ...BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / establishment of protein localization to telomere / mitotic recombination-dependent replication fork processing / nuclear ubiquitin ligase complex / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity / lateral element / regulation of DNA damage checkpoint / Impaired BRCA2 binding to PALB2 / telomere maintenance via recombination / gamma-tubulin binding / HDR through MMEJ (alt-NHEJ) / oocyte maturation / DNA repair complex / response to UV-C / 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) / inner cell mass cell proliferation / Resolution of D-loop Structures through Holliday Junction Intermediates / ATP-dependent DNA damage sensor activity / female gonad development / Impaired BRCA2 binding to RAD51 / hematopoietic stem cell proliferation / male meiosis I / centrosome duplication / Presynaptic phase of homologous DNA pairing and strand exchange / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to X-ray / positive regulation of mitotic cell cycle / secretory granule / regulation of cytokinesis / response to gamma radiation / cellular response to ionizing radiation / nucleotide-excision repair / DNA damage response, signal transduction by p53 class mediator / double-strand break repair via homologous recombination / brain development / HDR through Homologous Recombination (HRR) / Meiotic recombination / cellular senescence / double-strand break repair / single-stranded DNA binding / protease binding / spermatogenesis / DNA recombination / damaged DNA binding / chromosome, telomeric region / DNA repair / centrosome / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / protein-containing complex / ATP hydrolysis activity / nucleoplasm / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
BRCA2, OB3 / Tower domain / Breast cancer type 2 susceptibility protein, helical domain / BRCA2 helical domain superfamily / : / : / BRCA2, oligonucleotide/oligosaccharide-binding, domain 3 / Tower / BRCA2, helical / BRCA2, OB2 ...BRCA2, OB3 / Tower domain / Breast cancer type 2 susceptibility protein, helical domain / BRCA2 helical domain superfamily / : / : / BRCA2, oligonucleotide/oligosaccharide-binding, domain 3 / Tower / BRCA2, helical / BRCA2, OB2 / BRCA2 TR2 domain / Tower / BRCA2 repeat / BRCA2, OB1 / Breast cancer type 2 susceptibility protein / BRCA2 repeat / BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 / BRCA2 repeat profile. / DNA recombination/repair protein RadA / DNA recombination and repair protein, RecA-like / DNA recombination and repair protein Rad51-like, C-terminal / Rad51 / DNA recombination and repair protein RecA, monomer-monomer interface / RecA family profile 2. / DNA recombination and repair protein RecA-like, ATP-binding domain / RecA family profile 1. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / Helix-hairpin-helix DNA-binding motif, class 1 / Helix-hairpin-helix DNA-binding motif class 1 / Nucleic acid-binding, OB-fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-TKI / DNA repair and recombination protein RadA / Breast cancer type 2 susceptibility protein
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.02 Å
AuthorsPantelejevs, T. / Hyvonen, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)DTP United Kingdom
CitationJournal: Chem Sci / Year: 2023
Title: A recombinant approach for stapled peptide discovery yields inhibitors of the RAD51 recombinase.
Authors: Pantelejevs, T. / Zuazua-Villar, P. / Koczy, O. / Counsell, A.J. / Walsh, S.J. / Robertson, N.S. / Spring, D.R. / Downs, J.A. / Hyvonen, M.
History
DepositionDec 26, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA repair and recombination protein RadA
B: DNA repair and recombination protein RadA
C: Breast cancer type 2 susceptibility protein
J: Breast cancer type 2 susceptibility protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6835
Polymers58,4584
Non-polymers2241
Water00
1
A: DNA repair and recombination protein RadA
C: Breast cancer type 2 susceptibility protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4533
Polymers29,2292
Non-polymers2241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-19 kcal/mol
Surface area11090 Å2
MethodPISA
2
B: DNA repair and recombination protein RadA
J: Breast cancer type 2 susceptibility protein


Theoretical massNumber of molelcules
Total (without water)29,2292
Polymers29,2292
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-20 kcal/mol
Surface area10920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.560, 112.560, 140.785
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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Components

#1: Protein DNA repair and recombination protein RadA / Humanised RadA mutant HumRadA22


Mass: 25542.064 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: radA, PF1926 / Production host: Escherichia coli (E. coli) / References: UniProt: O74036
#2: Protein/peptide Breast cancer type 2 susceptibility protein / Fanconi anemia group D1 protein


Mass: 3687.163 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BRCA2, FACD, FANCD1 / Production host: Escherichia coli (E. coli) / References: UniProt: P51587
#3: Chemical ChemComp-TKI / 2-[(4,6-diethyl-1,3,5-triazin-2-yl)-methyl-amino]ethanoic acid / 2-(N-methyl-N-(4,6-divinyl-1,3,5-triazin-2-yl)amino)acetic acid (precursor)


Mass: 224.260 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N4O2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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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: 4.23 Å3/Da / Density % sol: 70.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein in 20 mM CHES pH 9.5, 100 mM NaCl. Condition: 8 % w/v PEG 8000 (precipitant) 0.08 M Potassium phosphate pH 5.6 (buffer) 200:200 uL drop

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 3.02→87.92 Å / Num. obs: 18416 / % possible obs: 100 % / Redundancy: 12.8 % / Biso Wilson estimate: 89.08 Å2 / CC1/2: 1 / Rrim(I) all: 0.242 / Net I/σ(I): 10
Reflection shellResolution: 3.02→3.07 Å / Redundancy: 13.8 % / Mean I/σ(I) obs: 0.9 / Num. unique obs: 13512 / CC1/2: 0.3 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER1.19.2_4158refinement
PHENIX1.19.2_4158refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HQU

6hqu


Resolution: 3.02→87.92 Å / SU ML: 0.4747 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.7701
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2806 896 4.87 %
Rwork0.2487 17505 -
obs0.2503 18401 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 91.23 Å2
Refinement stepCycle: LAST / Resolution: 3.02→87.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3698 0 16 0 3714
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01123756
X-RAY DIFFRACTIONf_angle_d1.38865031
X-RAY DIFFRACTIONf_chiral_restr0.098567
X-RAY DIFFRACTIONf_plane_restr0.021656
X-RAY DIFFRACTIONf_dihedral_angle_d15.57931413
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.02-3.210.38341290.33862875X-RAY DIFFRACTION99.93
3.21-3.450.33441500.29692850X-RAY DIFFRACTION100
3.45-3.80.34721470.25342877X-RAY DIFFRACTION99.97
3.8-4.350.22871420.22772903X-RAY DIFFRACTION99.97
4.35-5.480.22691570.2162923X-RAY DIFFRACTION99.94
5.48-87.920.29631710.2533077X-RAY DIFFRACTION99.63

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