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- PDB-8rb0: The crystal structure of DNA-bound human MutSbeta (MSH2_E749A/MSH... -

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Basic information

Entry
Database: PDB / ID: 8rb0
TitleThe crystal structure of DNA-bound human MutSbeta (MSH2_E749A/MSH3) in the canonical mismatch bound conformation with ADP bound in MSH2
Components
  • (DNA mismatch repair protein ...) x 2
  • DNA (5'-D(*TP*CP*AP*TP*CP*GP*AP*TP*CP*GP*CP*AP*GP*CP*TP*TP*CP*AP*GP*AP*TP*AP*G)-3')
  • DNA (5'-D(P*AP*TP*CP*TP*GP*AP*AP*GP*CP*CP*GP*AP*TP*CP*GP*AP*TP*G)-3')
KeywordsDNA BINDING PROTEIN / DNA repair / DNA binding
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 / 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
DNA mismatch repair Msh2-type / DNA mismatch repair protein Msh2 / 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 ...DNA mismatch repair Msh2-type / DNA mismatch repair protein Msh2 / 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 / P-loop containing nucleoside triphosphate hydrolase
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsThomsen, M. / Costanzi, E.
Funding support United States, 1items
OrganizationGrant numberCountry
CHDI Foundation United States
CitationJournal: To Be Published
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
DepositionDec 1, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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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
C: DNA (5'-D(P*AP*TP*CP*TP*GP*AP*AP*GP*CP*CP*GP*AP*TP*CP*GP*AP*TP*G)-3')
D: DNA (5'-D(*TP*CP*AP*TP*CP*GP*AP*TP*CP*GP*CP*AP*GP*CP*TP*TP*CP*AP*GP*AP*TP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,4209
Polymers223,8094
Non-polymers6115
Water1,38777
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.426, 90.887, 96.293
Angle α, β, γ (deg.)67.59, 87.06, 74.56
Int Tables number1
Space group name H-MP1

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Components

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DNA mismatch repair protein ... , 2 types, 2 molecules AB

#1: Protein DNA mismatch repair protein Msh2


Mass: 104803.836 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSH2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43246
#2: Protein DNA mismatch repair protein Msh3


Mass: 104289.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSH3 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P20585

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DNA chain , 2 types, 2 molecules CD

#3: DNA chain DNA (5'-D(P*AP*TP*CP*TP*GP*AP*AP*GP*CP*CP*GP*AP*TP*CP*GP*AP*TP*G)-3')


Mass: 7345.741 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*TP*CP*AP*TP*CP*GP*AP*TP*CP*GP*CP*AP*GP*CP*TP*TP*CP*AP*GP*AP*TP*AP*G)-3')


Mass: 7369.766 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 82 molecules

#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.51 Å3/Da / Density % sol: 50.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 0.1 M MES pH 6.5 -7.5, 0.2 M Ammonium Acetate, 20 - 25 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.999965 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Mar 7, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999965 Å / Relative weight: 1
ReflectionResolution: 2.67→88.88 Å / Num. obs: 54597 / % possible obs: 96 % / Redundancy: 2.2 % / CC1/2: 0.997 / Net I/σ(I): 9.4
Reflection shellResolution: 2.67→2.716 Å / Num. unique obs: 2720 / CC1/2: 0.843

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→88.88 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.851 / SU B: 58.011 / SU ML: 0.528 / Cross valid method: THROUGHOUT / ESU R Free: 0.431 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.31247 813 1.5 %RANDOM
Rwork0.241 ---
obs0.24201 53781 95.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 111.106 Å2
Baniso -1Baniso -2Baniso -3
1--2.31 Å21.39 Å23.79 Å2
2---3.75 Å2-3.67 Å2
3---2.63 Å2
Refinement stepCycle: 1 / Resolution: 2.67→88.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13585 838 37 77 14537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01314044
X-RAY DIFFRACTIONr_bond_other_d0.0020.01712914
X-RAY DIFFRACTIONr_angle_refined_deg1.3261.619222
X-RAY DIFFRACTIONr_angle_other_deg1.1191.62229446
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20751696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.32222.655580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.318152096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0411562
X-RAY DIFFRACTIONr_chiral_restr0.0490.21965
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0215400
X-RAY DIFFRACTIONr_gen_planes_other0.0020.023154
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.7443.3396829
X-RAY DIFFRACTIONr_mcbond_other0.7443.3386828
X-RAY DIFFRACTIONr_mcangle_it1.3758510
X-RAY DIFFRACTIONr_mcangle_other1.3758511
X-RAY DIFFRACTIONr_scbond_it0.6023.3967215
X-RAY DIFFRACTIONr_scbond_other0.6023.3977216
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other0.8595.08510713
X-RAY DIFFRACTIONr_long_range_B_refined3.82138.95915055
X-RAY DIFFRACTIONr_long_range_B_other3.81738.93215051
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.67→2.739 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.391 74 -
Rwork0.372 3984 -
obs--96.97 %
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)
17.3148-3.0609-0.26468.52980.94754.0973-0.3107-0.64970.20550.57270.2648-0.51620.13260.08060.04590.58410.0593-0.05750.64890.12730.13970.392-3.17426.762
20.98320.6924-1.07492.1062-1.79264.906-0.3830.1274-0.1383-0.53790.2586-0.01091.1135-0.67810.12441.1832-0.07430.15750.95980.22860.10110.029-16.252-8.457
34.9441-1.976-5.37055.04825.08488.56340.22551.13160.57270.0361-0.40280.545-0.313-1.4970.17741.38720.13910.24171.46950.32270.4725-31.926-19.80247.185
411.73575.414-3.936513.414-2.37910.35280.0325-0.1577-0.18840.6212-0.0711-0.7668-0.13130.4660.03860.91220.0116-0.00890.76580.26370.172527.14720.634-54.997
52.55350.4844-1.58990.7980.07433.18280.33850.15580.0088-0.2542-0.0061-0.0513-0.8126-0.0887-0.33251.04740.16190.15630.81020.2130.1074-8.45725.40814.136
65.45530.0396-4.41151.1699-1.46498.92590.0475-0.5229-0.19730.40310.04420.1148-0.12120.3996-0.09170.81810.13510.10020.95260.15960.1433-25.51821.58252.539
72.9857-0.2949-0.26822.95782.38517.06150.3556-0.32080.1654-0.19090.2666-0.2414-0.56810.9127-0.62230.7871-0.11380.23330.80920.11560.168818.86123.069-11.803
80.9647-1.2961-0.331112.7651-9.626610.8939-0.2213-0.27370.42290.335-0.2791-0.9448-0.74130.6020.50040.96350.0324-0.02410.98890.12650.435726.6828.856-33.227
95.85031.1422-2.54555.47523.27556.2853-0.2231-1.237-0.9321.5035-0.00120.59181.1477-0.03820.22421.15230.1390.20681.06420.47250.4911-27.3981.88743.635
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A15 - 137
2X-RAY DIFFRACTION2A145 - 462
3X-RAY DIFFRACTION2A580 - 855
4X-RAY DIFFRACTION3A463 - 579
5X-RAY DIFFRACTION4A876 - 930
6X-RAY DIFFRACTION5B227 - 686
7X-RAY DIFFRACTION5B815 - 840
8X-RAY DIFFRACTION6B687 - 814
9X-RAY DIFFRACTION7B841 - 1064
10X-RAY DIFFRACTION8B1065 - 1119
11X-RAY DIFFRACTION9C6 - 23
12X-RAY DIFFRACTION9D26 - 48

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