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- PDB-2gfu: NMR solution structure of the PWWP domain of Mismatch repair prot... -

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Basic information

Entry
Database: PDB / ID: 2gfu
TitleNMR solution structure of the PWWP domain of Mismatch repair protein hMSH6
ComponentsDNA mismatch repair protein MSH6
KeywordsDNA BINDING PROTEIN / PWWP domain / Tudor domain / DNA binding / mismatch repair
Function / homology
Function and homology information


MutSalpha complex / Defective Mismatch Repair Associated With MSH2 / Defective Mismatch Repair Associated With MSH6 / guanine/thymine mispair binding / somatic recombination of immunoglobulin gene segments / positive regulation of helicase activity / meiotic mismatch repair / mismatched DNA binding / negative regulation of DNA recombination / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) ...MutSalpha complex / Defective Mismatch Repair Associated With MSH2 / Defective Mismatch Repair Associated With MSH6 / guanine/thymine mispair binding / somatic recombination of immunoglobulin gene segments / positive regulation of helicase activity / meiotic mismatch repair / mismatched DNA binding / negative regulation of DNA recombination / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / isotype switching / ATP-dependent DNA damage sensor activity / mismatch repair / somatic hypermutation of immunoglobulin genes / ATP-dependent activity, acting on DNA / response to UV / methylated histone binding / intrinsic apoptotic signaling pathway / determination of adult lifespan / intrinsic apoptotic signaling pathway in response to DNA damage / spermatogenesis / damaged DNA binding / DNA repair / intracellular membrane-bounded organelle / chromatin binding / chromatin / Golgi apparatus / enzyme binding / nucleoplasm / ATP binding / nucleus / cytosol
Similarity search - Function
DNA mismatch repair protein MutS/MSH / DNA mismatch repair protein MutS-like, N-terminal / DNA mismatch repair protein MutS, connector domain / DNA mismatch repair protein MutS, clamp / DNA mismatch repair protein MutS, N-terminal / MutS, connector domain superfamily / MutS domain I / MutS domain II / MutS family domain IV / MutS domain III ...DNA mismatch repair protein MutS/MSH / DNA mismatch repair protein MutS-like, N-terminal / DNA mismatch repair protein MutS, connector domain / DNA mismatch repair protein MutS, clamp / DNA mismatch repair protein MutS, N-terminal / MutS, connector domain superfamily / MutS domain I / MutS domain II / MutS family domain IV / MutS domain III / DNA mismatch repair MutS family / DNA mismatch repair protein MutS, C-terminal / DNA mismatch repair protein MutS, core / DNA mismatch repair protein MutS, core domain superfamily / MutS domain V / DNA mismatch repair proteins mutS family signature. / DNA-binding domain of DNA mismatch repair MUTS family / ATPase domain of DNA mismatch repair MUTS family / SH3 type barrels. - #140 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / SH3 type barrels. / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
DNA mismatch repair protein Msh6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR
AuthorsLaguri, C. / Friedrich, N. / Axt, M. / Gilquin, B. / Zinn-Justin, S. / Couprie, J.
CitationJournal: To be Published
Title: The PWWP domain of Mismatch Repair protein hMSH6 is involved in double stranded and single stranded DNA binding
Authors: Laguri, C. / Duband-Goulet, I. / Friedrich, N. / Axt, M. / Belin, P. / Gilquin, B. / Zinn-Justin, S. / Couprie, J.
History
DepositionMar 23, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 10, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA mismatch repair protein MSH6


Theoretical massNumber of molelcules
Total (without water)15,1171
Polymers15,1171
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein DNA mismatch repair protein MSH6 / / MutS-alpha 160 kDa subunit / G/T mismatch binding protein / GTBP / GTMBP / p160


Mass: 15117.146 Da / Num. of mol.: 1 / Fragment: PWWP Domain / Mutation: C88S, C108S, C196S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET M30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 star / References: UniProt: P52701

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY

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Sample preparation

DetailsContents: 1mM protein concentration, 225mM NaCl, 50mM NaPhosphate pH 6.9, 1mM TSP 10% D2O, Protease inhibitors (sigma)
Solvent system: 10% D2O
Sample conditionsIonic strength: 225mM NaCl / pH: 6.9 / Pressure: 1 atm / Temperature: 300 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX5001
Bruker DRXBrukerDRX6002
Varian INOVAVarianINOVA8003

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Processing

NMR software
NameVersionDeveloperClassification
Felix2000accelrysdata analysis
NMRPipe1Delaglioprocessing
INCA1P. Savarin, B. Gilquinstructure solution
INCA1P. Savarin, B. Gilquinrefinement
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / Conformers submitted total number: 20

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