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

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Basic information

Entry
Database: PDB / ID: 6snv
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 (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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
DepositionAug 27, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author / database_2
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
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

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)117,3258
Polymers117,0634
Non-polymers2624
Water45025
1
A: DNA mismatch repair protein MLH1
B: DNA mismatch repair protein MLH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6624
Polymers58,5312
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-96 kcal/mol
Surface area26770 Å2
MethodPISA
2
D: DNA mismatch repair protein MLH1
E: DNA mismatch repair protein MLH3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,6624
Polymers58,5312
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2220 Å2
ΔGint-95 kcal/mol
Surface area26830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.893, 134.806, 102.569
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MLH1, PMS2, YMR167W, YM8520.16 / Production host: Escherichia coli (E. coli) / References: UniProt: P38920
#2: Protein DNA mismatch repair protein MLH3 / MutL protein homolog 3


Mass: 27767.180 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MLH3, YPL164C, P2550 / Production host: Escherichia coli (E. coli) / References: UniProt: Q12083
#3: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.81 Å3/Da / Density % sol: 56.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6 / Details: PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 2, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 30446 / % possible obs: 95 % / Redundancy: 6.8 % / Biso Wilson estimate: 96.73 Å2 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.02 / Rrim(I) all: 0.054 / Net I/σ(I): 18.56
Reflection shellResolution: 2.5→2.66 Å / Rmerge(I) obs: 0.779 / Mean I/σ(I) obs: 1.56 / Num. unique obs: 1559 / Rpim(I) all: 0.457 / Rrim(I) all: 0.908

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Processing

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

4e4w


Resolution: 2.5→44.66 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.901 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.382
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1496 4.98 %RANDOM
Rwork0.229 ---
obs0.231 30067 68.1 %-
Displacement parametersBiso max: 230.31 Å2 / Biso mean: 90.52 Å2 / Biso min: 22.67 Å2
Baniso -1Baniso -2Baniso -3
1--1.3517 Å20 Å20 Å2
2---2.5998 Å20 Å2
3---3.9515 Å2
Refine analyzeLuzzati coordinate error obs: 0.43 Å
Refinement stepCycle: final / Resolution: 2.5→44.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7842 0 4 25 7871
Biso mean--67.64 36.05 -
Num. residues----964
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2872SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1322HARMONIC5
X-RAY DIFFRACTIONt_it7986HARMONIC20
X-RAY DIFFRACTIONt_nbd4SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1040SEMIHARMONIC5
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_contact8568SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7986HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg10772HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion2.1
X-RAY DIFFRACTIONt_other_torsion19.27
LS refinement shellResolution: 2.5→2.57 Å / Rfactor Rfree error: 0 / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.2954 29 4.82 %
Rwork0.2278 573 -
all0.2308 602 -
obs--17.26 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.0921.6171-0.49457.7761-0.55351.4358-0.1928-0.1545-0.2290.24560.1273-0.45510.236-0.17560.0655-0.01350.05950.13530.06660.0616-0.043228.3328-20.157141.6571
21.7253-2.7619-0.74578.31550.6941.3558-0.30530.1235-0.44210.05550.06660.49290.3110.20330.2387-0.20820.00950.08360.049-0.03430.080262.3535-21.45449.6103
31.00520.13240.132800.15470.432-0.0092-0.0001-0.03040.02170.00410.0098-0.0550.00330.0051-0.0687-0.070.01210.05250.0035-0.068644.7565-1.922520.3627
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* B|* }A505 - 769
2X-RAY DIFFRACTION1{ A|* B|* }B477 - 712
3X-RAY DIFFRACTION2{ D|* E|* }D505 - 769
4X-RAY DIFFRACTION2{ D|* E|* }E477 - 712
5X-RAY DIFFRACTION3{ W|* }W1 - 25

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