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- PDB-8a51: Crystal structure of HSF2BP-BRME1 complex -

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Basic information

Entry
Database: PDB / ID: 8a51
TitleCrystal structure of HSF2BP-BRME1 complex
Components
  • Break repair meiotic recombinase recruitment factor 1
  • Heat shock factor 2-binding protein
KeywordsRECOMBINATION / Complex
Function / homology
Function and homology information


double-strand break repair involved in meiotic recombination / female meiosis I / male meiosis I / chromosome / spermatogenesis / transcription by RNA polymerase II / nucleoplasm / cytosol
Similarity search - Function
Break repair meiotic recombinase recruitment factor 1 / Break repair meiotic recombinase recruitment factor 1 / Heat shock factor 2-binding protein / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / Heat shock factor 2-binding protein / Break repair meiotic recombinase recruitment factor 1
Similarity search - Component
Biological speciessynthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMiron, S. / Legrand, P. / Ropars, V. / Ghouil, R. / Zinn-Justin, S.
Funding support France, 1items
OrganizationGrant numberCountry
French Alternative Energies and Atomic Energy Commission (CEA) France
CitationJournal: Sci Adv / Year: 2023
Title: BRCA2-HSF2BP oligomeric ring disassembly by BRME1 promotes homologous recombination.
Authors: Rania Ghouil / Simona Miron / Koichi Sato / Dejan Ristic / Sari E van Rossum-Fikkert / Pierre Legrand / Malika Ouldali / Jean-Marie Winter / Virginie Ropars / Gabriel David / Ana-Andreea ...Authors: Rania Ghouil / Simona Miron / Koichi Sato / Dejan Ristic / Sari E van Rossum-Fikkert / Pierre Legrand / Malika Ouldali / Jean-Marie Winter / Virginie Ropars / Gabriel David / Ana-Andreea Arteni / Claire Wyman / Puck Knipscheer / Roland Kanaar / Alex N Zelensky / Sophie Zinn-Justin /
Abstract: In meiotic homologous recombination (HR), BRCA2 facilitates loading of the recombinases RAD51 and DMC1 at the sites of double-strand breaks (DSBs). The HSF2BP-BRME1 complex interacts with BRCA2. Its ...In meiotic homologous recombination (HR), BRCA2 facilitates loading of the recombinases RAD51 and DMC1 at the sites of double-strand breaks (DSBs). The HSF2BP-BRME1 complex interacts with BRCA2. Its absence causes a severe reduction in recombinase loading at meiotic DSB. We previously showed that, in somatic cancer cells ectopically producing HSF2BP, DNA damage can trigger HSF2BP-dependent degradation of BRCA2, which prevents HR. Here, we report that, upon binding to BRCA2, HSF2BP forms octameric rings that are able to interlock into a large ring-shaped 24-mer. Addition of BRME1 leads to dissociation of both of these ring structures and cancels the disruptive effect of HSF2BP on cancer cell resistance to DNA damage. It also prevents BRCA2 degradation during interstrand DNA crosslink repair in egg extracts. We propose that, during meiosis, the control of HSF2BPBRCA2 oligomerization by BRME1 ensures timely assembly of the ring complex that concentrates BRCA2 and controls its turnover, thus promoting HR.
History
DepositionJun 13, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _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.year
Revision 1.2May 1, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heat shock factor 2-binding protein
B: Break repair meiotic recombinase recruitment factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,17710
Polymers8,5752
Non-polymers6028
Water46826
1
A: Heat shock factor 2-binding protein
B: Break repair meiotic recombinase recruitment factor 1
hetero molecules

A: Heat shock factor 2-binding protein
B: Break repair meiotic recombinase recruitment factor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,35420
Polymers17,1504
Non-polymers1,20416
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_545x,-y-1/2,-z+1/41
Buried area8940 Å2
ΔGint-23 kcal/mol
Surface area9050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.866, 73.866, 92.801
Angle α, β, γ (deg.)90, 90, 90
Int Tables number98
Space group name H-MI4122

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Components

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Protein/peptide , 2 types, 2 molecules AB

#1: Protein/peptide Heat shock factor 2-binding protein


Mass: 3880.580 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: O75031
#2: Protein/peptide Break repair meiotic recombinase recruitment factor 1 / Pre-T/NK cell-associated protein 3B3


Mass: 4694.445 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) / References: UniProt: Q0VDD7

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Non-polymers , 4 types, 34 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 1.96 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES sodium salt, pH 7.5, 40% PEG200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.96546 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Feb 17, 2022 / Details: Be CRL
RadiationMonochromator: Diamond [110] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96546 Å / Relative weight: 1
ReflectionResolution: 1.9→36.93 Å / Num. obs: 6522 / % possible obs: 99.6 % / Redundancy: 6.9 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.019 / Net I/σ(I): 20.3
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 6.9 % / Rmerge(I) obs: 2.384 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 753 / CC1/2: 0.421 / Rpim(I) all: 0.976 / Rrim(I) all: 2.586 / % possible all: 99.6

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (3-FEB-2022)refinement
XDSJan 10, 2022 BUILT=20220110data reduction
STARANISO2.3.77data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AlfaFold2 model

Resolution: 1.9→36.93 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.923 / SU R Cruickshank DPI: 0.422 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.226 / SU Rfree Blow DPI: 0.175 / SU Rfree Cruickshank DPI: 0.173
RfactorNum. reflection% reflectionSelection details
Rfree0.243 345 -RANDOM
Rwork0.2346 ---
obs0.2351 6522 62.5 %-
Displacement parametersBiso mean: 56.62 Å2
Baniso -1Baniso -2Baniso -3
1-4.5619 Å20 Å20 Å2
2--4.5619 Å20 Å2
3----9.1237 Å2
Refine analyzeLuzzati coordinate error obs: 0.35 Å
Refinement stepCycle: LAST / Resolution: 1.9→36.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms570 0 38 26 634
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0071350HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.792438HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d438SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes201HARMONIC5
X-RAY DIFFRACTIONt_it1350HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion81SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies4HARMONIC1
X-RAY DIFFRACTIONt_ideal_dist_contact1085SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion2.46
X-RAY DIFFRACTIONt_other_torsion13.14
LS refinement shellResolution: 1.9→2.04 Å
RfactorNum. reflection% reflection
Rfree0.286 31 -
Rwork0.2207 --
obs--19.98 %
Refinement TLS params.Origin x: 27.8422 Å / Origin y: -22.7888 Å / Origin z: 6.9705 Å
111213212223313233
T0.1107 Å2-0.0619 Å20.0171 Å2--0.1556 Å2-0.0978 Å2---0.2082 Å2
L8.3155 °20.0859 °2-0.279 °2-3.7633 °21.4224 °2--5.3094 °2
S-0.1813 Å °-0.0512 Å °0.3251 Å °-0.0512 Å °0.309 Å °-0.0934 Å °0.3251 Å °-0.0934 Å °-0.1276 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ *|* }A1 - 30
2X-RAY DIFFRACTION1{ *|* }B9 - 47
3X-RAY DIFFRACTION1{ *|* }C1 - 7
4X-RAY DIFFRACTION1{ *|* }D1
5X-RAY DIFFRACTION1{ *|* }S1 - 26

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