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- PDB-7z8z: Crystal structure of the MEILB2-BRME1 2:2 core complex -

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Basic information

Entry
Database: PDB / ID: 7z8z
TitleCrystal structure of the MEILB2-BRME1 2:2 core complex
Components
  • Break repair meiotic recombinase recruitment factor 1
  • Heat shock factor 2-binding protein
KeywordsRECOMBINATION / Meiosis / DNA repair / DNA clamp / double-strand break
Function / homology
Function and homology information


double-strand break repair involved in meiotic recombination / protein localization to site of double-strand break / reciprocal meiotic recombination / female meiosis I / male meiosis I / chromosome / site of double-strand break / spermatogenesis / damaged DNA binding / 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
Break repair meiotic recombinase recruitment factor 1 / Heat shock factor 2-binding protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 1.5 Å
AuthorsGurusaran, M. / Davies, O.R.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust219413/Z/19/Z United Kingdom
CitationJournal: Nat Commun / Year: 2024
Title: MEILB2-BRME1 forms a V-shaped DNA clamp upon BRCA2-binding in meiotic recombination.
Authors: Gurusaran, M. / Zhang, J. / Zhang, K. / Shibuya, H. / Davies, O.R.
History
DepositionMar 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 14, 2024Group: Database references / Category: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)23,8964
Polymers23,8964
Non-polymers00
Water5,621312
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering, SEC-MALS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9670 Å2
ΔGint-95 kcal/mol
Surface area11650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.054, 43.992, 178.712
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Heat shock factor 2-binding protein


Mass: 7635.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Hsf2bp, Meilb2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9D4G2
#2: Protein/peptide Break repair meiotic recombinase recruitment factor 1


Mass: 4311.989 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Brme1, Meiok21 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6DIA7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 312 / 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: 2.23 Å3/Da / Density % sol: 44.73 %
Crystal growTemperature: 277 K / Method: batch mode / pH: 7.5 / Details: 20mM HEPES pH 7.5, 150mM KCl

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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 XE 16M / Detector: PIXEL / Date: Dec 10, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.5→89.36 Å / Num. obs: 34897 / % possible obs: 99.1 % / Redundancy: 35.2 % / Biso Wilson estimate: 21.17 Å2 / Rpim(I) all: 0.02 / Net I/σ(I): 16.7
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1603 / Rpim(I) all: 0.309 / % possible all: 94.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PHENIX1.19.2_4158model building
autoPROCdata processing
Aimlessdata scaling
Arcimboldophasing
XDSdata reduction
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 1.5→44.68 Å / SU ML: 0.1782 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.1043
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2347 1685 4.84 %
Rwork0.1965 33148 -
obs0.1983 34833 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.94 Å2
Refinement stepCycle: LAST / Resolution: 1.5→44.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1575 0 0 312 1887
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00451595
X-RAY DIFFRACTIONf_angle_d0.62342127
X-RAY DIFFRACTIONf_chiral_restr0.0384248
X-RAY DIFFRACTIONf_plane_restr0.0077273
X-RAY DIFFRACTIONf_dihedral_angle_d12.0273658
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.550.2781440.23722562X-RAY DIFFRACTION95.55
1.55-1.60.27091380.21462679X-RAY DIFFRACTION96.37
1.6-1.650.29411340.21012640X-RAY DIFFRACTION97.85
1.65-1.720.27631400.20432731X-RAY DIFFRACTION98.36
1.72-1.80.27121400.19572760X-RAY DIFFRACTION99.79
1.8-1.890.2491470.19312717X-RAY DIFFRACTION99.86
1.89-2.010.23191590.18642756X-RAY DIFFRACTION99.79
2.01-2.170.24591340.1752777X-RAY DIFFRACTION99.83
2.17-2.380.2191350.16672798X-RAY DIFFRACTION99.86
2.38-2.730.2471410.18612848X-RAY DIFFRACTION99.77
2.73-3.440.20711300.19392865X-RAY DIFFRACTION99.7
3.44-44.680.22791430.2133015X-RAY DIFFRACTION99.68

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