[English] 日本語
Yorodumi
- PDB-6snv: DNA mismatch repair proteins MLH1 and MLH3 -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more