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- PDB-2o8d: human MutSalpha (MSH2/MSH6) bound to ADP and a G dU mispair -

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Basic information

Entry
Database: PDB / ID: 2o8d
Titlehuman MutSalpha (MSH2/MSH6) bound to ADP and a G dU mispair
Components
  • (DNA mismatch repair protein ...) x 2
  • 5'-D(*CP*CP*TP*AP*GP*CP*GP*(DU)P*GP*CP*GP*GP*TP*TP*C)-3'
  • 5'-D(*GP*AP*AP*CP*CP*GP*CP*GP*CP*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 / 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 / meiotic mismatch repair / centromeric DNA binding / positive regulation of isotype switching to IgG isotypes / mismatched DNA binding / negative regulation of DNA recombination / mitotic recombination / isotype switching / 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 / response to UV / protein localization to chromatin / methylated histone binding / intrinsic apoptotic signaling pathway / B cell differentiation / determination of adult lifespan / TP53 Regulates Transcription of DNA Repair Genes / 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 / intracellular membrane-bounded organelle / DNA repair / chromatin binding / chromatin / Golgi apparatus / enzyme binding / protein homodimerization activity / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / membrane / nucleus / cytosol
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/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 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/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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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 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 / Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_special_symmetry / 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

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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*CP*GP*CP*TP*AP*GP*G)-3'
F: 5'-D(*CP*CP*TP*AP*GP*CP*GP*(DU)P*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)231,0048
Polymers230,1014
Non-polymers9034
Water82946
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)260.379, 260.379, 260.379
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

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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*CP*GP*CP*TP*AP*GP*G)-3'


Mass: 4620.000 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*CP*TP*AP*GP*CP*GP*(DU)P*GP*CP*GP*GP*TP*TP*C)-3'


Mass: 4562.932 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: 104861.875 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, 50 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 3.19 Å3/Da / Density % sol: 61.44 %
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: 0.9793 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: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. all: 60642 / Num. obs: 60518 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 77.191 Å2 / Rmerge(I) obs: 0.093 / Net I/σ(I): 12.22
Reflection shellResolution: 3→3.25 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 3.2 / Num. measured obs: 78322 / Num. unique all: 12729 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
XDSdata reduction
REFMAC5.2.005phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3→50 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.897 / SU B: 45.38 / SU ML: 0.385 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: TLS refinement by domain / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.43 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.278 3086 5.1 %
Rwork0.239 --
obs0.241 60505 99.8 %
all-60642 -
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 93.659 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13882 609 56 46 14593
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.02214913
X-RAY DIFFRACTIONr_angle_refined_deg1.3422.02720246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.3151747
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.14424.41644
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.85152602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8041588
X-RAY DIFFRACTIONr_chiral_restr0.0960.22278
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210855
X-RAY DIFFRACTIONr_nbd_refined0.1740.36368
X-RAY DIFFRACTIONr_nbtor_refined0.3090.510072
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.5671
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.354
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2280.56
X-RAY DIFFRACTIONr_mcbond_it0.2781.59098
X-RAY DIFFRACTIONr_mcangle_it0.486214126
X-RAY DIFFRACTIONr_scbond_it0.54236851
X-RAY DIFFRACTIONr_scangle_it0.9394.56120
LS refinement shellResolution: 3→3.078 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 240 -
Rwork0.317 4160 -
obs-4400 100 %
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)
17.4193-2.1291-1.13024.76432.73999.9138-0.03110.94040.228-0.6261-0.06130.1184-0.0040.00540.0924-0.2411-0.06150.0402-0.1254-0.048-0.4995-52.410429.760812.5088
26.36211.4450.28812.7565-0.77332.04070.17750.0208-0.60090.0954-0.2316-0.26170.62210.38730.05410.39950.4191-0.07120.0287-0.0022-0.1496-38.3951-9.083844.3064
32.12950.09121.09723.45580.37583.6944-0.2395-0.30620.40240.46150.2959-0.5690.04360.1894-0.0565-0.51420.0965-0.1489-0.4715-0.1348-0.4962-57.982244.134148.3658
45.2233-2.96672.56222.6833-0.51673.8430.33090.3682-1.1092-0.1064-0.09540.05551.23710.761-0.23540.52210.1639-0.0993-0.3038-0.16630.0672-65.1461-14.378628.2416
53.67560.49950.56466.732-0.59285.6874-0.0916-0.4478-0.43260.85310.09470.08910.6804-0.3241-0.0031-0.2228-0.0342-0.019-0.4828-0.0131-0.6599-78.070620.45846.818
62.17910.24740.63415.05571.56342.5045-0.03030.27250.0173-0.00130.07050.12930.1817-0.0291-0.0402-0.5476-0.08270.0158-0.390.0315-0.6528-83.265627.864623.0648
75.7607-0.2157-0.51495.0284-3.90915.1394-0.09430.40511.6038-0.57570.2368-1.1746-1.37311.2396-0.1425-0.2096-0.22270.0088-0.14680.00330.2366-52.392160.574132.9722
89.95584.474-4.04135.1243-0.99887.229-0.30641.18442.5153-0.97420.31631.0477-1.188-0.4296-0.00980.3907-0.202-0.1994-0.1550.44160.747-68.849374.069721.2407
96.7511-0.2076-0.84616.1165-4.06064.8603-0.30270.3834-0.0926-0.9752-0.0628-1.17760.63750.76950.36540.33810.38850.26090.5814-0.07690.0191-24.484213.40814.413
100.81711.8635-0.86098.38-1.59510.93990.27110.07640.33630.0942-0.2052-0.7641-0.3480.8143-0.06590.1598-0.02180.00320.7160.08710.3171-20.593429.488737.1807
1113.0995-4.19850.98258.91212.19443.35720.0750.4391.534-0.2843-0.1679-0.1922-0.20230.72110.09290.5307-0.4560.26240.42380.13890.4522-34.910271.916429.6259
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AC1 - 1241 - 124
22AC620 - 855620 - 855
32AE9351
42AG9361
53BD362 - 51824 - 180
64BD1075 - 1335737 - 997
74BF1021
84BH2021
95BD519 - 717181 - 379
106BD728 - 933390 - 595
116BD1009 - 1074671 - 736
127EA1 - 151 - 15
137FB16 - 301 - 15
148BD935 - 1008597 - 670
159AC125 - 297125 - 297
1610AC298 - 456298 - 456
1710AC554 - 619554 - 619
1811AC457 - 553457 - 553

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