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- PDB-3thw: Human MutSbeta complexed with an IDL of 4 bases (Loop4) and ADP -

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Basic information

Entry
Database: PDB / ID: 3thw
TitleHuman MutSbeta complexed with an IDL of 4 bases (Loop4) and ADP
Components
  • DNA Loop4 hairpin
  • DNA mismatch repair protein Msh2
  • DNA mismatch repair protein Msh3
KeywordsDNA BINDING PROTEIN/DNA / ABC family ATPase / mismatch recognition / mismatched unpaired IDL DNA / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


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 / guanine/thymine mispair binding / somatic recombination of immunoglobulin gene segments / maintenance of DNA repeat elements / 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 / guanine/thymine mispair binding / somatic recombination of immunoglobulin gene segments / maintenance of DNA repeat elements / B cell mediated immunity / positive regulation of helicase activity / positive regulation of isotype switching to IgA isotypes / centromeric DNA binding / positive regulation of isotype switching to IgG isotypes / mismatched DNA binding / negative regulation of DNA recombination / isotype switching / mitotic recombination / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / oxidative phosphorylation / postreplication repair / response to UV-B / mitotic intra-S DNA damage checkpoint signaling / ATP-dependent DNA damage sensor activity / germ cell development / response to X-ray / intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / somatic hypermutation of immunoglobulin genes / ATP-dependent activity, acting on DNA / mismatch repair / protein localization to chromatin / 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 / in utero embryonic development / negative regulation of neuron apoptotic process / chromosome, telomeric region / damaged DNA binding / DNA repair / chromatin binding / enzyme binding / protein homodimerization activity / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / membrane / nucleus
Similarity search - Function
DNA mismatch repair Msh2-type / DNA mismatch repair protein Msh2 / MutS, connector domain / DNA repair protein MutS, domain I / MutS, DNA mismatch repair protein; Chain A, domain 3 / MutS, DNA mismatch repair protein; Chain A, domain 3 - #10 / 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 ...DNA mismatch repair Msh2-type / DNA mismatch repair protein Msh2 / MutS, connector domain / DNA repair protein MutS, domain I / MutS, DNA mismatch repair protein; Chain A, domain 3 / MutS, DNA mismatch repair protein; Chain A, domain 3 - #10 / 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 / MutS, DNA mismatch repair protein, domain I / Nucleotidyltransferase; domain 5 / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / : / DNA / DNA (> 10) / DNA mismatch repair protein Msh3 / DNA mismatch repair protein Msh2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.09 Å
AuthorsYang, W.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2012
Title: Mechanism of mismatch recognition revealed by human MutSbeta bound to unpaired DNA loops
Authors: Gupta, S. / Gellert, M. / Yang, W.
History
DepositionAug 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA mismatch repair protein Msh2
B: DNA mismatch repair protein Msh3
D: DNA Loop4 hairpin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)225,9064
Polymers225,4793
Non-polymers4271
Water724
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12460 Å2
ΔGint-98 kcal/mol
Surface area84340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.840, 116.130, 180.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DNA mismatch repair protein Msh2 / hMSH2 / MutS protein homolog 2


Mass: 104861.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSH2 / Cell line (production host): Hi5 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43246
#2: Protein DNA mismatch repair protein Msh3 / hMSH3 / Divergent upstream protein / DUP / Mismatch repair protein 1 / MRP1


Mass: 104289.664 Da / Num. of mol.: 1 / Fragment: UNP residues 219- 1134
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DUC1, DUG, MSH3 / Cell line (production host): Hi5 / Production host: Spodoptera frugiperda (fall armyworm) / References: GenBank: 119616268, UniProt: P20585*PLUS
#3: DNA chain DNA Loop4 hairpin


Mass: 16327.484 Da / Num. of mol.: 1 / Source method: obtained synthetically
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.2M Ammonium Acetate, 20-25% PEG3350 (w/v) and 0.1M MES pH 6.5-7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 19, 2008 / Details: mirror
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.09→33.2 Å / Num. obs: 41282 / % possible obs: 99 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Rmerge(I) obs: 0.0996 / Net I/σ(I): 7.5
Reflection shellResolution: 3.09→3.14 Å / Redundancy: 2.4 % / Rmerge(I) obs: 0.554 / Mean I/σ(I) obs: 1.1 / Num. unique all: 1966 / % possible all: 98.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
X-GENdata reduction
X-GENdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O8B

2o8b


Resolution: 3.09→32.53 Å / SU ML: 0.44 / σ(F): 0 / Phase error: 29.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2872 1919 4.98 %
Rwork0.2261 --
obs0.2291 38509 92.75 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.878 Å2 / ksol: 0.279 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.3742 Å2-0 Å20 Å2
2---14.1928 Å2-0 Å2
3---19.567 Å2
Refinement stepCycle: LAST / Resolution: 3.09→32.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13755 1084 27 4 14870
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00315294
X-RAY DIFFRACTIONf_angle_d0.56320903
X-RAY DIFFRACTIONf_dihedral_angle_d16.5875784
X-RAY DIFFRACTIONf_chiral_restr0.0382404
X-RAY DIFFRACTIONf_plane_restr0.0022480
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.0859-3.19610.41541700.37593207X-RAY DIFFRACTION82
3.1961-3.32390.42431670.33393357X-RAY DIFFRACTION86
3.3239-3.4750.39111830.32183450X-RAY DIFFRACTION89
3.475-3.6580.3461530.26253614X-RAY DIFFRACTION92
3.658-3.88680.30271960.24043642X-RAY DIFFRACTION94
3.8868-4.18640.27292240.2123754X-RAY DIFFRACTION96
4.1864-4.60660.24171990.17563847X-RAY DIFFRACTION98
4.6066-5.27070.25112080.1723878X-RAY DIFFRACTION98
5.2707-6.63130.32010.22283892X-RAY DIFFRACTION97
6.6313-32.53170.20632180.17483949X-RAY DIFFRACTION95

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