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- PDB-2o8e: human MutSalpha (MSH2/MSH6) bound to a G T mispair, with ADP boun... -

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Basic information

Entry
Database: PDB / ID: 2o8e
Titlehuman MutSalpha (MSH2/MSH6) bound to a G T mispair, with ADP bound to MSH2 only
Components
  • (DNA mismatch repair protein ...) x 2
  • 5'-D(*CP*CP*TP*AP*GP*CP*CP*TP*GP*CP*GP*GP*TP*TP*C)-3'
  • 5'-D(*GP*AP*AP*CP*CP*GP*CP*GP*GP*GP*CP*TP*AP*GP*G)-3'
KeywordsDNA BINDING PROTEIN/DNA / DNA mismatch repair / DNA damage response / somatic hypermutation / protein-DNA complex / DNA mispair / cancer / ABC transporter ATPase / DNA BINDING PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


somatic recombination of immunoglobulin genes involved in immune response / MutSbeta complex / histone H3K36me3 reader activity / 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 / B cell mediated immunity ...somatic recombination of immunoglobulin genes involved in immune response / MutSbeta complex / histone H3K36me3 reader activity / 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 / B cell mediated immunity / maintenance of DNA repeat elements / meiotic mismatch repair / positive regulation of isotype switching to IgA isotypes / centromeric DNA binding / positive regulation of isotype switching to IgG isotypes / mismatched DNA binding / mitotic recombination / negative regulation of DNA recombination / isotype switching / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / response to UV-B / oxidative phosphorylation / DNA damage tolerance / 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 / response to X-ray / ATP-dependent activity, acting on DNA / mismatch repair / somatic hypermutation of immunoglobulin genes / response to UV / intrinsic apoptotic signaling pathway / B cell differentiation / determination of adult lifespan / TP53 Regulates Transcription of DNA Repair Genes / enzyme activator activity / male gonad development / intrinsic apoptotic signaling pathway in response to DNA damage / double-strand break repair / spermatogenesis / in utero embryonic development / negative regulation of neuron apoptotic process / damaged DNA binding / chromosome, telomeric region / DNA repair / intracellular membrane-bounded organelle / chromatin binding / chromatin / enzyme binding / Golgi apparatus / protein homodimerization activity / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / membrane / cytosol
Similarity search - Function
MutS, DNA mismatch repair protein; Chain A, domain 3 / MutS, DNA mismatch repair protein; Chain A, domain 3 - #10 / MutS, connector domain / DNA repair protein MutS, domain I / DNA mismatch repair Msh2-type / DNA mismatch repair protein Msh2 / 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 ...MutS, DNA mismatch repair protein; Chain A, domain 3 / MutS, DNA mismatch repair protein; Chain A, domain 3 - #10 / MutS, connector domain / DNA repair protein MutS, domain I / DNA mismatch repair Msh2-type / DNA mismatch repair protein Msh2 / 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 / MutS, DNA mismatch repair protein, domain I / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / 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 Msh2 / DNA mismatch repair protein Msh6
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.3 Å
AuthorsWarren, J.J. / Pohlhaus, T.J. / Changela, A. / Modrich, P.L. / Beese, L.S.
CitationJournal: Mol.Cell / Year: 2007
Title: Structure of the Human MutSalpha DNA Lesion Recognition Complex.
Authors: Warren, J.J. / Pohlhaus, T.J. / Changela, A. / Iyer, R.R. / Modrich, P.L. / Beese, L.S.
History
DepositionDec 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 5, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / 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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
E: 5'-D(*GP*AP*AP*CP*CP*GP*CP*GP*GP*GP*CP*TP*AP*GP*G)-3'
F: 5'-D(*CP*CP*TP*AP*GP*CP*CP*TP*GP*CP*GP*GP*TP*TP*C)-3'
A: DNA mismatch repair protein Msh2
B: DNA mismatch repair protein MSH6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)230,4916
Polymers230,0394
Non-polymers4522
Water18010
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)257.510, 257.510, 257.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Components on special symmetry positions
IDModelComponents
11B-26-

HOH

Detailsthe crystallographic asymmetric unit contains one biological assembly (a heterodimeric protein complex bound to double stranded DNA and one ADP+Mg)

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Components

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DNA chain , 2 types, 2 molecules EF

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


Mass: 4660.023 Da / Num. of mol.: 1 / Mutation: F42A / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*CP*TP*AP*GP*CP*CP*TP*GP*CP*GP*GP*TP*TP*C)-3'


Mass: 4536.934 Da / Num. of mol.: 1 / Source method: obtained synthetically

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

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


Mass: 104785.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSH2 / Plasmid: pFasBacDual / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 / References: UniProt: P43246
#4: Protein DNA mismatch repair protein MSH6 / MutS-alpha 160 kDa subunit / G/T mismatch-binding protein / GTBP / GTMBP / p160


Mass: 116056.672 Da / Num. of mol.: 1 / Fragment: residues 341-1360
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSH6, GTBP / Plasmid: pFasBacDual / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9 / References: UniProt: P52701

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Non-polymers , 3 types, 12 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: 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
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 3.09 Å3/Da / Density % sol: 60.15 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 7
Details: 11% PEG 8000, 10 mM magnesium sulfate, 100 mM bis-tris-propane, pH 7, VAPOR DIFFUSION, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2magnesium sulfate11
3bis-tris-propane11
4HOH11
5PEG 800012
6magnesium sulfate12
7bis-tris-propane12
8HOH12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.005 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Details: mirrors
RadiationMonochromator: Si 220 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.005 Å / Relative weight: 1
ReflectionResolution: 3.3→91.044 Å / Num. all: 43653 / Num. obs: 43653 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Rmerge(I) obs: 0.096 / Rsym value: 0.096 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.3-3.397.70.4611.62476532110.46199.7
3.39-3.488.10.4171.82526031090.41799.5
3.48-3.588.50.36722568930310.36799.5
3.58-3.698.70.332.22560029490.3399.5
3.69-3.818.90.2742.72537528490.27499.5
3.81-3.949.10.2273.22535527720.22799.5
3.94-4.099.30.1913.92500526840.19199.2
4.09-4.269.50.1584.62424225620.15899.3
4.26-4.459.50.1365.42360024750.13699
4.45-4.679.60.1126.52278423650.11299.2
4.67-4.929.70.0977.52182622610.09798.9
4.92-5.229.70.0878.42052321230.08798.7
5.22-5.589.60.0858.61934520050.08598.5
5.58-6.029.60.0888.21802718700.08898.2
6.02-6.69.50.0838.41652017310.08398
6.6-7.389.60.0611.21509515710.0697.8
7.38-8.529.50.04613.91335514000.04697.8
8.52-10.449.50.03616.31135311920.03696.9
10.44-14.769.20.03217.686559410.03296.5
14.76-91.047.80.03614.943185520.03693.4

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
XDSdata reduction
REFMAC5.2.005phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2O8B

2o8b


Resolution: 3.3→20 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.858 / SU B: 62.226 / SU ML: 0.49 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS refinement by domains / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.584 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.291 2219 5.1 %
Rwork0.253 --
obs0.255 43392 98.47 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 103.516 Å2
Refinement stepCycle: LAST / Resolution: 3.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13939 610 28 10 14587
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02214903
X-RAY DIFFRACTIONr_angle_refined_deg1.3672.02520225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.37551742
X-RAY DIFFRACTIONr_dihedral_angle_2_deg23.02124.475657
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.969152614
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.6951589
X-RAY DIFFRACTIONr_chiral_restr0.0960.22269
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0210881
X-RAY DIFFRACTIONr_nbd_refined0.1840.36953
X-RAY DIFFRACTIONr_nbtor_refined0.3150.510067
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1820.5729
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1550.355
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.250.54
X-RAY DIFFRACTIONr_mcbond_it0.2971.59078
X-RAY DIFFRACTIONr_mcangle_it0.527214076
X-RAY DIFFRACTIONr_scbond_it0.61436867
X-RAY DIFFRACTIONr_scangle_it1.0794.56149
LS refinement shellResolution: 3.3→3.383 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 168 -
Rwork0.285 2939 -
obs-3107 99.58 %
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)
111.272-5.6964-5.003412.61.445712.75120.61811.9454-0.0791-2.06430.13550.63810.1969-1.1082-0.75360.0498-0.11090.00550.2955-0.0446-0.4551-52.42830.145411.903
29.46630.9338-0.44294.441-1.60062.37050.30090.0646-0.69270.0898-0.1469-0.50650.53280.391-0.1540.43420.6918-0.2378-0.0046-0.1943-0.0549-38.8794-9.132942.9611
32.5374-0.40651.40263.9647-0.27425.1614-0.1595-0.27060.41820.42510.2827-0.8988-0.12720.2158-0.1232-0.71040.0198-0.1304-0.6751-0.0884-0.6192-57.326543.740447.6953
47.6385-4.40963.17043.8916-0.94665.02560.58480.5438-1.7963-0.0651-0.16470.22331.41431.1594-0.42010.30310.3106-0.2844-0.4752-0.24430.2411-65.1963-14.490827.9295
54.2429-0.21180.32649.36080.28637.9724-0.0548-0.4869-0.48840.8320.11230.11880.7551-0.1887-0.0575-0.5506-0.0582-0.0805-0.72970.051-0.8773-77.237520.384646.0907
62.60890.19940.67575.84142.03332.6470.10.3401-0.0810.08750.02360.1580.14880.1246-0.1236-0.7186-0.0834-0.0044-0.62030.0542-0.9008-82.293727.741322.59
77.6458-0.0762-0.21486.6368-3.41051.76110.16790.61371.5511-0.7021-0.0514-1.8639-1.43650.8508-0.1166-0.264-0.25480.1811-0.36180.08760.1642-51.62260.056532.6648
821.51827.2851-9.33687.9907-6.012512.7358-0.02351.443.2344-0.9012-0.04040.6157-1.8019-0.22870.06380.4955-0.4245-0.0793-0.60260.62230.3373-68.153273.662321.2974
99.87410.719-1.28848.5487-5.87118.784-0.2180.455-0.0046-1.3452-0.0899-1.30891.55181.39550.30780.78790.48660.41880.8802-0.31260.3795-25.190813.929913.1709
101.32591.4395-0.907411.571-2.70630.9170.44650.36810.321-0.2053-0.3881-1.6807-0.25191.1805-0.05840.3330.09330.11540.9036-0.13370.643-20.413429.005435.4923
1112.7047-1.8875-1.065411.48893.24865.2996-0.34990.65390.95180.2568-0.18720.0802-0.71451.0970.53710.5163-0.72190.32650.37110.41820.603-34.723671.431329.0873
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 124
2X-RAY DIFFRACTION2A620 - 855
3X-RAY DIFFRACTION2A935
4X-RAY DIFFRACTION2A936
5X-RAY DIFFRACTION3B362 - 518
6X-RAY DIFFRACTION4B1075 - 1335
7X-RAY DIFFRACTION5B519 - 717
8X-RAY DIFFRACTION6B728 - 933
9X-RAY DIFFRACTION6B1009 - 1074
10X-RAY DIFFRACTION7E1 - 15
11X-RAY DIFFRACTION7F16 - 30
12X-RAY DIFFRACTION8B935 - 1008
13X-RAY DIFFRACTION9A125 - 297
14X-RAY DIFFRACTION10A298 - 456
15X-RAY DIFFRACTION10A554 - 619
16X-RAY DIFFRACTION11A457 - 553

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