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- PDB-6rmn: DNA mismatch repair proteins MLH1 and MLH3 -

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Basic information

Entry
Database: PDB / ID: 6rmn
TitleDNA mismatch repair proteins MLH1 and MLH3
Components
  • DNA mismatch repair protein MLH1
  • DNA mismatch repair protein MLH3
KeywordsRECOMBINATION / RESOLVASE / MMR / DNA REPAIR / MEIOSIS
Function / homology
Function and homology information


meiotic heteroduplex formation / MutLbeta complex / MutLgamma complex / MutLalpha complex / mismatch repair complex / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / mismatched DNA binding / reciprocal meiotic recombination / ATP-dependent DNA damage sensor activity ...meiotic heteroduplex formation / MutLbeta complex / MutLgamma complex / MutLalpha complex / mismatch repair complex / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / meiotic mismatch repair / mismatched DNA binding / reciprocal meiotic recombination / ATP-dependent DNA damage sensor activity / mismatch repair / ATP hydrolysis activity / mitochondrion / ATP binding / nucleus / cytoplasm
Similarity search - Function
DNA mismatch repair protein Mlh1, C-terminal / DNA mismatch repair protein Mlh1 C-terminus / MutL C terminal dimerisation domain / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like / DNA mismatch repair, conserved site ...DNA mismatch repair protein Mlh1, C-terminal / DNA mismatch repair protein Mlh1 C-terminus / MutL C terminal dimerisation domain / MutL, C-terminal, dimerisation / MutL, C-terminal domain superfamily / MutL, C-terminal domain, dimerisation subdomain / MutL C terminal dimerisation domain / DNA mismatch repair protein family, N-terminal / DNA mismatch repair protein, S5 domain 2-like / DNA mismatch repair, conserved site / DNA mismatch repair protein MutL/Mlh/Pms / DNA mismatch repair protein, C-terminal domain / DNA mismatch repair proteins mutL / hexB / PMS1 signature. / DNA mismatch repair protein, C-terminal domain / Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase / Histidine kinase/HSP90-like ATPase superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold
Similarity search - Domain/homology
DNA mismatch repair protein MLH1 / DNA mismatch repair protein MLH3
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsDai, J. / Chervy, P. / Legrand, P. / Ropars, V. / Charbonnier, J.B.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-Resolve France
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: Molecular basis of the dual role of the Mlh1-Mlh3 endonuclease in MMR and in meiotic crossover formation.
Authors: Dai, J. / Sanchez, A. / Adam, C. / Ranjha, L. / Reginato, G. / Chervy, P. / Tellier-Lebegue, C. / Andreani, J. / Guerois, R. / Ropars, V. / Le Du, M.H. / Maloisel, L. / Martini, E. / ...Authors: Dai, J. / Sanchez, A. / Adam, C. / Ranjha, L. / Reginato, G. / Chervy, P. / Tellier-Lebegue, C. / Andreani, J. / Guerois, R. / Ropars, V. / Le Du, M.H. / Maloisel, L. / Martini, E. / Legrand, P. / Thureau, A. / Cejka, P. / Borde, V. / Charbonnier, J.B.
History
DepositionMay 7, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Data collection / Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / database_2 / refine / reflns_shell
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id / _reflns_shell.pdbx_Rpim_I_all
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA mismatch repair protein MLH1
B: DNA mismatch repair protein MLH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,5334
Polymers58,4022
Non-polymers1312
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology, Complex coeluted by ion exchange chromatography this study Affinity Capture Western Copurification Reconstituted Complex
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-95 kcal/mol
Surface area26540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.260, 104.360, 135.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein DNA mismatch repair protein MLH1 / MutL protein homolog 1 / Post meiotic segregation protein 2


Mass: 30764.279 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae S288C / Gene: MLH1, PMS2, YMR167W, YM8520.16 / Variant: ATCC 204508 / S288c / Production host: Escherichia coli (E. coli) / References: UniProt: P38920
#2: Protein DNA mismatch repair protein MLH3 / MutL protein homolog 3


Mass: 27638.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The six X letters correspond to a proposed loop not assigned in sequence (unk in pdb for unknown)
Source: (gene. exp.) Saccharomyces cerevisiae S288C / Gene: MLH3, YPL164C, P2550 / Variant: ATCC 204508 / S288c / Production host: Escherichia coli (E. coli) / References: UniProt: Q12083
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 10% PEG4000, 200 mM imidazole-malate, pH6 and 10 mM MgCl2

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Data collection

DiffractionMean temperature: 163 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 13, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.2→48.4 Å / Num. obs: 33362 / % possible obs: 98.7 % / Redundancy: 13 % / Biso Wilson estimate: 51.47 Å2 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.029 / Rrim(I) all: 0.104 / Net I/σ(I): 12.8
Reflection shellResolution: 2.2→2.25 Å / Redundancy: 11.3 % / Num. unique obs: 2168 / Rpim(I) all: 0.42 / % possible all: 87.4

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
STARANISO1.10.9data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4E4W

4e4w


Resolution: 2.2→38.14 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.942 / SU R Cruickshank DPI: 0.381 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.382 / SU Rfree Blow DPI: 0.234 / SU Rfree Cruickshank DPI: 0.236
RfactorNum. reflection% reflectionSelection details
Rfree0.226 1180 5.14 %RANDOM
Rwork0.197 ---
obs0.199 22942 68.5 %-
Displacement parametersBiso mean: 69.09 Å2
Baniso -1Baniso -2Baniso -3
1-2.61 Å20 Å20 Å2
2---2.347 Å20 Å2
3----0.263 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.2→38.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3891 0 32 132 4055
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0093993HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.035386HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1436SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes661HARMONIC5
X-RAY DIFFRACTIONt_it3993HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.46
X-RAY DIFFRACTIONt_other_torsion17.71
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion520SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4269SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.33 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3599 -6.1 %
Rwork0.3133 431 -
all0.3161 459 -
obs--8.89 %
Refinement TLS params.Method: refined / Origin x: 28.7898 Å / Origin y: 16.2721 Å / Origin z: 20.6711 Å
111213212223313233
T-0.0614 Å20.019 Å2-0.0273 Å2--0.0072 Å2-0.009 Å2--0.0709 Å2
L0.6381 °2-0.2427 °2-1.5016 °2-0.743 °20.1671 °2--6.135 °2
S-0.07 Å °-0.1365 Å °0.1321 Å °0.042 Å °0.0591 Å °0.0443 Å °-0.0959 Å °0.4092 Å °0.0109 Å °
Refinement TLS groupSelection details: { *|* }

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