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- PDB-8raw: The crystal structure of DNA-bound human MutSbeta (MSH2/MSH3_G901... -
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Basic information
Entry | Database: PDB / ID: 8raw | ||||||
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Title | The crystal structure of DNA-bound human MutSbeta (MSH2/MSH3_G901D) in the canonical mismatch bound conformation with ADP bound in MSH2 | ||||||
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![]() | DNA BINDING PROTEIN / DNA repair / DNA binding | ||||||
Function / homology | ![]() somatic recombination of immunoglobulin genes involved in immune response / MutSbeta complex / Defective Mismatch Repair Associated With MSH3 / MutSalpha complex / Defective Mismatch Repair Associated With MSH2 / Defective Mismatch Repair Associated With MSH6 / positive regulation of helicase activity / guanine/thymine mispair binding / somatic recombination of immunoglobulin gene segments / B cell mediated immunity ...somatic recombination of immunoglobulin genes involved in immune response / MutSbeta complex / Defective Mismatch Repair Associated With MSH3 / MutSalpha complex / Defective Mismatch Repair Associated With MSH2 / Defective Mismatch Repair Associated With MSH6 / positive regulation of helicase activity / guanine/thymine mispair binding / somatic recombination of immunoglobulin gene segments / B cell mediated immunity / maintenance of DNA repeat elements / positive regulation of isotype switching to IgA isotypes / centromeric DNA binding / positive regulation of isotype switching to IgG isotypes / mitotic recombination / mismatched DNA binding / negative regulation of DNA recombination / isotype switching / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / oxidative phosphorylation / response to UV-B / postreplication repair / mitotic intra-S DNA damage checkpoint signaling / ATP-dependent DNA damage sensor activity / germ cell development / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / ATP-dependent activity, acting on DNA / response to X-ray / somatic hypermutation of immunoglobulin genes / mismatch repair / B cell differentiation / determination of adult lifespan / TP53 Regulates Transcription of DNA Repair Genes / male gonad development / double-strand break repair / double-stranded DNA binding / negative regulation of neuron apoptotic process / in utero embryonic development / damaged DNA binding / chromosome, telomeric region / DNA repair / chromatin binding / enzyme binding / protein homodimerization activity / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / membrane Similarity search - Function | ||||||
Biological species | ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Thomsen, M. / Costanzi, E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: The crystal structure of DNA-bound human MutSbeta (MSH2/MSH3) in the canonical mismatch bound conformation with ADP bound in MSH2 and MSH3 Authors: Thomsen, M. / Neudegger, T. / Thieulin-Pardo, G. / Blaesse, M. / Costanzi, E. / Steinbacher, S. / Plotnikov, N.V. / Dominguez, C. / Iyer, R.R. / Wilkinson, H.A. / Monteagudo, E. / Haque, T.S. ...Authors: Thomsen, M. / Neudegger, T. / Thieulin-Pardo, G. / Blaesse, M. / Costanzi, E. / Steinbacher, S. / Plotnikov, N.V. / Dominguez, C. / Iyer, R.R. / Wilkinson, H.A. / Monteagudo, E. / Haque, T.S. / Prasad, B.C. / Finley, M. / Boudet, J. / Vogt, T.F. / Felsenfeld, D.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 759.5 KB | Display | ![]() |
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PDB format | ![]() | 614.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8rauC ![]() 8ravC ![]() 8raxC ![]() 8razC ![]() 8rb0C ![]() 8rb1C ![]() 8rb2C C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
-DNA mismatch repair protein ... , 2 types, 2 molecules AB
#1: Protein | Mass: 104861.875 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 104347.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-DNA chain , 2 types, 2 molecules CD
#3: DNA chain | Mass: 7345.741 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
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#4: DNA chain | Mass: 7369.766 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 57 molecules 




#5: Chemical | ChemComp-ADP / |
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#6: Chemical | ChemComp-EDO / |
#7: Water | ChemComp-HOH / |
-Details
Has ligand of interest | Y |
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Has protein modification | N |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46.59 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion Details: 0.1 M MES pH 6.5 -7.5, 0.2 M Ammonium Acetate, 20 - 25 % PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 27, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 2.69→47.3 Å / Num. obs: 53080 / % possible obs: 95.5 % / Redundancy: 1.8 % / Rsym value: 0.037 / Net I/σ(I): 13.16 |
Reflection shell | Resolution: 2.69→2.94 Å / Num. unique obs: 12483 / Rsym value: 0.437 |
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 88.414 Å2
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Refinement step | Cycle: 1 / Resolution: 2.69→47.3 Å
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Refine LS restraints |
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