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- PDB-8c3n: Stapled peptide SP30 in complex with humanised RadA mutant HumRadA22 -

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Basic information

Entry
Database: PDB / ID: 8c3n
TitleStapled peptide SP30 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 / mitotic recombination-dependent replication fork processing / establishment of protein localization to telomere / nuclear ubiquitin ligase complex / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / lateral element / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity ...BRCA2-MAGE-D1 complex / negative regulation of mammary gland epithelial cell proliferation / mitotic recombination-dependent replication fork processing / establishment of protein localization to telomere / nuclear ubiquitin ligase complex / Impaired BRCA2 translocation to the nucleus / Impaired BRCA2 binding to SEM1 (DSS1) / lateral element / histone H4 acetyltransferase activity / histone H3 acetyltransferase activity / Impaired BRCA2 binding to PALB2 / telomere maintenance via recombination / regulation of DNA damage checkpoint / HDR through MMEJ (alt-NHEJ) / gamma-tubulin binding / DNA repair complex / oocyte maturation / 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) / : / Resolution of D-loop Structures through Holliday Junction Intermediates / inner cell mass cell proliferation / ATP-dependent DNA damage sensor activity / Impaired BRCA2 binding to RAD51 / hematopoietic stem cell proliferation / female gonad development / male meiosis I / Presynaptic phase of homologous DNA pairing and strand exchange / centrosome duplication / response to X-ray / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / positive regulation of mitotic cell cycle / regulation of cytokinesis / secretory granule / cellular response to ionizing radiation / response to gamma radiation / nucleotide-excision repair / 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
ADENOSINE-5'-DIPHOSPHATE / 4,6-diethylpyrimidin-2-amine / 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: 1.21 Å
AuthorsPantelejevs, T. / Hyvonen, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)DTP United Kingdom
Citation
Journal: 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.
#1: Journal: Biorxiv / 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. / Walsh, S.J. / Robertson, N.S. / Spring, D.R. / Downs, J. / Hyvonen, M.
History
DepositionDec 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2023Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Revision 1.2Oct 23, 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: Breast cancer type 2 susceptibility protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0545
Polymers28,4512
Non-polymers6033
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2520 Å2
ΔGint-30 kcal/mol
Surface area11660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.017, 37.961, 43.934
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AB

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


Mass: 25542.064 Da / Num. of mol.: 1
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: 2909.343 Da / Num. of mol.: 1
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

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Non-polymers , 4 types, 226 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-RF6 / 4,6-diethylpyrimidin-2-amine / 4,6-bis(ethenyl)pyrimidin-2-amine (precursor) / 4,6-Divinylpyrimidin-2-amine (precursor) / peptide staple


Mass: 151.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H13N3 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.32 Å3/Da / Density % sol: 46.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein: 0.5 mM SP30:HumRadA22 in 20 mM CHES pH 9.5, 100 mM NaCl, 20 mM ADP/MgCl 2 Condition: 14% w/v PEG 4000 (precipitant), 6% v/v MPD (precipitant), 0.1M Na K Phos pH 6.2 (buffer)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Mar 4, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.21→37.43 Å / Num. obs: 70100 / % possible obs: 94.9 % / Redundancy: 6.9 % / Biso Wilson estimate: 18.49 Å2 / CC1/2: 1 / Rrim(I) all: 0.053 / Net I/σ(I): 13.6
Reflection shellResolution: 1.21→1.23 Å / Mean I/σ(I) obs: 0.5 / Num. unique obs: 2237 / CC1/2: 0.4

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Processing

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

6hqu


Resolution: 1.21→37.43 Å / SU ML: 0.1559 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.5274
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2182 3419 4.89 %
Rwork0.2107 66437 -
obs0.211 69856 94.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 26.69 Å2
Refinement stepCycle: LAST / Resolution: 1.21→37.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1871 0 39 223 2133
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.03821997
X-RAY DIFFRACTIONf_angle_d2.0632702
X-RAY DIFFRACTIONf_chiral_restr0.1044300
X-RAY DIFFRACTIONf_plane_restr0.0317359
X-RAY DIFFRACTIONf_dihedral_angle_d16.0981758
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.230.354720.35891635X-RAY DIFFRACTION56.28
1.23-1.250.3745840.34011922X-RAY DIFFRACTION66.42
1.25-1.270.30191150.32882168X-RAY DIFFRACTION74.61
1.27-1.290.33161160.32142421X-RAY DIFFRACTION83.84
1.29-1.310.31421450.30942647X-RAY DIFFRACTION91.72
1.31-1.330.29621540.3022736X-RAY DIFFRACTION95.35
1.33-1.360.28651670.28672874X-RAY DIFFRACTION99.87
1.36-1.390.27821570.28342872X-RAY DIFFRACTION99.77
1.39-1.420.27471360.25652933X-RAY DIFFRACTION99.97
1.42-1.450.28741480.24352868X-RAY DIFFRACTION100
1.45-1.490.25361700.23262883X-RAY DIFFRACTION100
1.49-1.530.25081380.21382940X-RAY DIFFRACTION99.97
1.53-1.570.2111870.21342876X-RAY DIFFRACTION99.97
1.57-1.620.23011440.2142885X-RAY DIFFRACTION100
1.62-1.680.23121620.21152909X-RAY DIFFRACTION100
1.68-1.750.23531380.2212925X-RAY DIFFRACTION100
1.75-1.830.23941330.22312957X-RAY DIFFRACTION100
1.83-1.920.23381530.21312916X-RAY DIFFRACTION99.97
1.92-2.040.23111430.20262936X-RAY DIFFRACTION99.94
2.04-2.20.21941520.2052967X-RAY DIFFRACTION99.97
2.2-2.420.2381410.20052976X-RAY DIFFRACTION99.94
2.42-2.770.20841600.21082986X-RAY DIFFRACTION99.97
2.77-3.490.18631280.20663043X-RAY DIFFRACTION99.94
3.49-37.430.19531760.18913162X-RAY DIFFRACTION99.67
Refinement TLS params.Method: refined / Origin x: 19.7449916416 Å / Origin y: -27.0218585235 Å / Origin z: -42.139421308 Å
111213212223313233
T0.135388931741 Å20.00692751153226 Å2-0.0173922108316 Å2-0.149542500947 Å20.00137700026918 Å2--0.161624024474 Å2
L0.689710663716 °20.226927077994 °20.096988039862 °2-1.54077457741 °20.0276299197804 °2--1.76119128579 °2
S-0.0249490089242 Å °-0.0245753821329 Å °0.0167499716947 Å °0.0734405354279 Å °-0.0732581232282 Å °0.0470999161646 Å °-0.0928414910907 Å °0.0187664705927 Å °0.0769273272815 Å °
Refinement TLS groupSelection details: all

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