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- PDB-2o8c: human MutSalpha (MSH2/MSH6) bound to ADP and an O6-methyl-guanine... -

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Basic information

Entry
Database: PDB / ID: 2o8c
Titlehuman MutSalpha (MSH2/MSH6) bound to ADP and an O6-methyl-guanine T mispair
Components
  • (DNA mismatch repair protein ...) x 2
  • 5'-D(*CP*CP*TP*AP*GP*CP*GP*TP*GP*CP*GP*GP*TP*TP*C)-3'
  • 5'-D(*GP*AP*AP*CP*CP*GP*CP*(6OG)P*CP*GP*CP*TP*AP*GP*G)-3'
KeywordsDNA BINDING PROTEIN/DNA / DNA mismatch repair / DNA damage response / protein-DNA complex / DNA mispair / cancer / O6-methyl-guanine / 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 / 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 / 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 / chromosome, telomeric region / damaged DNA binding / 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: 3.37 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 1.3Aug 30, 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_conn / struct_conn_type / 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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn_type.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*(6OG)P*CP*GP*CP*TP*AP*GP*G)-3'
F: 5'-D(*CP*CP*TP*AP*GP*CP*GP*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)231,0338
Polymers230,1304
Non-polymers9034
Water39622
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)259.810, 259.810, 259.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number212
Space group name H-MP4332
Detailsthe asymmetric unit contains one biological assembly

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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*(6OG)P*CP*GP*CP*TP*AP*GP*G)-3'


Mass: 4634.027 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*CP*TP*AP*GP*CP*GP*TP*GP*CP*GP*GP*TP*TP*C)-3'


Mass: 4576.958 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, 26 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


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


Mass: 18.015 Da / Num. of mol.: 22 / 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: 3.17 Å3/Da / Density % sol: 61.19 %
Crystal growTemperature: 290 K / Method: vapor diffusion / pH: 7
Details: 11% PEG 8000, 10mM 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 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 Å / Relative weight: 1
ReflectionResolution: 3.37→183.713 Å / Num. all: 42392 / Num. obs: 42392 / % possible obs: 99.3 % / Observed criterion σ(I): -3 / Redundancy: 10.9 % / Rmerge(I) obs: 0.201 / Rsym value: 0.201 / Net I/σ(I): 3.5
Reflection shell

Rmerge(I) obs: 0.012 / Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
3.37-3.5510.70.66467960311.17798.7
3.55-3.7711.20.96484458120.8299.9
3.77-4.0311.11.56104854760.5299.9
4.03-4.3511.12.55637150660.30399.8
4.35-4.7711.13.95238647210.19799.6
4.77-5.3311.14.84729742790.15899.5
5.33-6.15115.24142737780.14699.4
6.15-7.5410.86.53482632320.10799
7.54-10.6610.611.52678925290.05298.5
10.66-48.259.713.61430814680.04296.4

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
MAR345dtbdata collection
XDSdata reduction
REFMAC5.2.0005phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2O8B

2o8b


Resolution: 3.37→20 Å / Cor.coef. Fo:Fc: 0.892 / Cor.coef. Fo:Fc free: 0.849 / SU B: 74.922 / SU ML: 0.565 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: tls refinement by domains / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.602 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.29 2126 5 %
Rwork0.256 --
obs0.258 42153 99.11 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 73.394 Å2
Refinement stepCycle: LAST / Resolution: 3.37→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13882 611 56 22 14571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02214915
X-RAY DIFFRACTIONr_angle_refined_deg1.132.02820249
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.91751747
X-RAY DIFFRACTIONr_dihedral_angle_2_deg19.31124.41644
X-RAY DIFFRACTIONr_dihedral_angle_3_deg8.943152602
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.271588
X-RAY DIFFRACTIONr_chiral_restr0.0790.22278
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0210857
X-RAY DIFFRACTIONr_nbd_refined0.1580.36346
X-RAY DIFFRACTIONr_nbtor_refined0.3070.510120
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.5596
X-RAY DIFFRACTIONr_metal_ion_refined0.0170.51
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1220.351
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2730.56
X-RAY DIFFRACTIONr_mcbond_it0.1791.59146
X-RAY DIFFRACTIONr_mcangle_it0.318214126
X-RAY DIFFRACTIONr_scbond_it0.33936867
X-RAY DIFFRACTIONr_scangle_it0.6124.56123
LS refinement shellResolution: 3.37→3.455 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.325 141 -
Rwork0.312 2799 -
obs-2940 97.19 %
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)
110.9856-1.4822-1.00686.84733.344916.4320.04111.0730.3053-1.00870.02180.1829-0.1555-0.153-0.0629-0.393-0.04790.0972-0.2965-0.1249-0.6135-52.390729.706112.5398
210.12032.50170.0254.4514-0.46332.56840.0799-0.0241-0.8813-0.0771-0.153-0.27040.74190.45460.07320.38530.6282-0.0395-0.087-0.0123-0.3286-38.4453-9.092844.2707
33.39420.2091.44435.29870.2545.3254-0.366-0.43990.42750.72080.4236-0.8915-0.06870.2495-0.0577-0.7390.1432-0.2447-0.6634-0.2176-0.6371-57.872443.966548.3024
48.3369-4.62163.24753.9898-1.19586.41680.27560.4724-1.7926-0.1999-0.02610.04831.69121.1861-0.24950.55890.2735-0.0557-0.5665-0.2790.1002-64.9089-14.431328.2022
55.6308-0.10450.758410.2143-0.53068.9892-0.1958-0.5105-0.5881.05520.1980.16990.9079-0.3972-0.0023-0.39630.0052-0.0174-0.7753-0.003-0.9514-77.78420.348946.828
63.58470.18160.56457.3352.24813.1456-0.13920.45090.0244-0.01390.16920.16460.20410.0188-0.03-0.7289-0.1448-0.0004-0.56640.0276-0.9714-83.056727.723323.1172
78.45290.52320.99856.1771-4.01652.8248-0.0730.76222.0765-1.40560.4168-1.988-2.0181.1391-0.3439-0.1041-0.28760.1564-0.3573-0.02920.3704-52.501960.308532.7994
815.97769.2678-3.57578.8629-2.58157.1175-0.25291.54013.0032-0.982-0.10051.2485-1.6950.16110.35350.7577-0.2973-0.0422-0.07250.5321.2104-68.79973.658920.8537
98.29060.672-1.765711.8483-4.92848.2604-0.06630.4932-0.1389-1.3021-0.1518-1.76040.93741.50540.2180.3470.48330.37080.7099-0.1528-0.0143-24.568713.476714.3318
101.48072.2748-1.327812.7005-2.4391.2080.43510.05180.41060.0627-0.4805-1.1164-0.29381.13020.04540.09380.0768-0.01190.86390.05850.3322-20.807129.517937.0893
1117.7654-1.9163-1.23636.40792.23341.0908-0.47160.34411.7133-0.04380.17330.0911-0.18260.88570.29830.7743-0.51740.42030.62610.01280.7317-35.047171.805129.3927
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 124
2X-RAY DIFFRACTION2A620 - 855
3X-RAY DIFFRACTION2B1
4X-RAY DIFFRACTION2A936
5X-RAY DIFFRACTION3B362 - 518
6X-RAY DIFFRACTION4B1075 - 1335
7X-RAY DIFFRACTION4B2
8X-RAY DIFFRACTION4B202
9X-RAY DIFFRACTION5B519 - 717
10X-RAY DIFFRACTION6B728 - 933
11X-RAY DIFFRACTION6B1009 - 1074
12X-RAY DIFFRACTION7E1 - 15
13X-RAY DIFFRACTION7F16 - 30
14X-RAY DIFFRACTION8B935 - 1008
15X-RAY DIFFRACTION9A125 - 297
16X-RAY DIFFRACTION10A298 - 456
17X-RAY DIFFRACTION10A554 - 619
18X-RAY DIFFRACTION11A457 - 553

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