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- PDB-3thx: Human MutSbeta complexed with an IDL of 3 bases (Loop3) and ADP -

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Basic information

Entry
Database: PDB / ID: 3thx
TitleHuman MutSbeta complexed with an IDL of 3 bases (Loop3) and ADP
Components
  • (DNA mismatch repair protein ...) x 2
  • DNA Loop3 minus strand
  • DNA Loop3 plus strand
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 / MOLECULAR REPLACEMENT / Resolution: 2.7 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 1.2Jul 17, 2019Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: pdbx_unobs_or_zero_occ_atoms / software / struct_ref_seq
Item: _software.classification / _software.name ..._software.classification / _software.name / _software.version / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end
Revision 1.3Feb 28, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms / 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 Loop3 minus strand
E: DNA Loop3 plus strand
hetero molecules


Theoretical massNumber of molelcules
Total (without water)224,6306
Polymers224,1804
Non-polymers4502
Water48627
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14930 Å2
ΔGint-117 kcal/mol
Surface area78240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.120, 91.540, 95.580
Angle α, β, γ (deg.)67.88, 86.51, 72.86
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 / 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 219-1137
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

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DNA chain , 2 types, 2 molecules DE

#3: DNA chain DNA Loop3 minus strand


Mass: 7345.741 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized
#4: DNA chain DNA Loop3 plus strand


Mass: 7682.973 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: chemically synthesized

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Non-polymers , 3 types, 29 molecules

#5: 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
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / 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: 2.32 Å3/Da / Density % sol: 46.87 %
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: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Jun 18, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.7→27 Å / % possible obs: 91.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 1.9 % / Rmerge(I) obs: 0.047 / Net I/σ(I): 14.8
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.332 / Mean I/σ(I) obs: 1.44 / % possible all: 43.3

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.6.4_486)refinement
CNSrefinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→27 Å / SU ML: 0.41 / Isotropic thermal model: isotropic / σ(F): 1 / Phase error: 31.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.273 1315 2.77 %
Rwork0.21 --
obs0.212 49511 89.9 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.35 Å2 / ksol: 0.3 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-5.3597 Å2-0.0819 Å23.5102 Å2
2--1.114 Å21.6695 Å2
3----6.4737 Å2
Refinement stepCycle: LAST / Resolution: 2.7→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13522 937 28 27 14514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00214985
X-RAY DIFFRACTIONf_angle_d0.55820474
X-RAY DIFFRACTIONf_dihedral_angle_d15.5555669
X-RAY DIFFRACTIONf_chiral_restr0.0372359
X-RAY DIFFRACTIONf_plane_restr0.0022446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6995-2.80750.428660.35442915X-RAY DIFFRACTION48
2.8075-2.93510.38361170.3384345X-RAY DIFFRACTION73
2.9351-3.08970.39441520.30675039X-RAY DIFFRACTION84
3.0897-3.2830.32711470.27185363X-RAY DIFFRACTION90
3.283-3.53590.29411820.24945580X-RAY DIFFRACTION93
3.5359-3.89080.26651730.22015597X-RAY DIFFRACTION94
3.8908-4.45170.24991600.17535718X-RAY DIFFRACTION96
4.4517-5.60040.22641440.16635828X-RAY DIFFRACTION97
5.6004-27.02020.22811740.16665791X-RAY DIFFRACTION98
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)
10.8183-0.65210.19990.7440.34751.2859-0.0143-0.0710.20830.28170.0298-0.38440.1412-0.2013-0.02080.3203-0.0459-0.11280.1721-0.07950.32981.0727-3.328927.191
20.30010.2522-0.51220.9364-1.62412.7821-0.16360.0359-0.0354-0.4107-0.2174-0.31830.46450.32620.2660.4047-0.02080.05050.28340.0550.30613.6219-21.07265.1843
31.65470.6428-0.67990.6948-0.8181.3271-0.38380.3514-0.1092-0.1660.2715-0.02040.5927-0.50550.11970.487-0.20070.04420.3679-0.02040.147-2.8765-23.8206-1.4278
41.53920.0055-0.79941.05590.80261.0156-0.70330.30310.13170.34260.32870.36680.4844-0.1940.28270.5445-0.28440.09840.5889-0.02070.4383-27.3323-29.471517.154
50.6997-0.3494-0.54430.2964-0.00260.93240.5791-0.29910.06190.0634-0.1030.0198-0.54030.1628-0.37521.1977-0.11190.32431.0372-0.24350.9519-36.1115-16.375448.4112
60.5350.417-0.88780.6459-0.38551.4565-0.17970.55280.0767-0.36360.28410.08770.2974-0.8077-0.09260.3486-0.1232-0.03160.58110.10790.14441.9343-6.9536-22.1079
71.75880.1991-0.65350.77560.03410.3624-0.62670.0549-0.1089-0.17260.2558-0.01640.41370.22390.3220.5634-0.15480.0540.42990.01740.249225.569419.4576-52.9723
80.6847-0.8134-0.96481.1190.73381.86560.08090.4147-0.05550.0778-0.16870.1749-0.0362-0.63430.08350.14860.0311-0.04510.4099-0.07080.3616-23.774912.332923.3579
92.0473-0.6497-1.0081.03620.40370.5160.46991.01040.0389-0.474-0.33990.1049-0.264-0.5919-0.12540.45680.31380.02010.71460.10720.2718-12.052325.3828-0.1066
101.0327-0.1243-0.59160.46350.69951.060.3930.17930.0708-0.1513-0.0456-0.1642-0.5136-0.2171-0.30980.4170.12430.14040.22150.08570.29821.485229.75576.2233
111.63080.4652-1.34210.3165-0.31241.13570.2072-0.26290.13970.0866-0.0012-0.0017-0.25820.2037-0.07720.2112-0.01920.07160.1651-0.04210.2008-12.741426.530842.8282
120.8545-0.1997-1.14280.37610.70721.77180.43280.10230.3794-0.25270.0694-0.1954-0.5548-0.1169-0.41910.30460.0890.16220.10520.07860.254913.739826.1262-1.9586
130.07910.3809-0.16370.8849-0.75981.3143-0.00410.01070.0093-0.16980.26230.097-0.10360.0343-0.19180.4263-0.01370.14650.2864-0.00410.279327.331815.5792-27.779
140.51460.7864-0.58421.83090.21433.09180.012-0.2875-0.2974-0.29040.12710.3009-0.4770.3335-0.11931.14770.459-0.13180.97470.02040.9685-15.6469-3.185453.6857
154.03371.7028-0.49661.013-0.59250.9729-1.18060.7222-1.22140.02980.5941-0.66430.0759-0.45890.55150.303-0.06570.11110.7338-0.11280.7429-41.27565.409837.9549
163.0652.19141.371.61180.67215.5857-1.02330.38920.78850.0575-0.1876-0.32110.6031-1.66831.01040.559-0.20440.21570.9178-0.11290.7152-42.20135.956539.0474
170.25390.31981.20761.93440.5528.2199-0.7194-0.4255-0.09230.0725-1.03750.597-0.0597-0.08111.66450.1864-0.17440.05580.6046-0.34440.8216-17.77780.870531.1023
180.764-0.8244-0.43450.95930.31480.58120.23140.0759-0.5350.13850.5154-0.0516-0.0072-0.0969-0.65460.27230.448-0.0180.87630.09061.008-11.70893.514534.9226
192.481-0.0388-1.96057.0395-4.59234.7312-0.1265-0.7657-0.0411.20980.7310.37340.21430.8179-0.39470.87810.43730.06340.6472-0.12780.4984-13.4705-2.973653.1995
205.98751.18311.42561.1621.19861.3135-0.3032-0.68560.6138-0.06230.39020.40580.1245-0.4425-0.0460.6220.001-0.06181.26490.23330.8631-4.05692.1047-21.8621
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain a and resi 12:145
2X-RAY DIFFRACTION2chain a and resi 146:250
3X-RAY DIFFRACTION3chain a and resi 251:380
4X-RAY DIFFRACTION4chain a and resi 381:501
5X-RAY DIFFRACTION5chain a and resi 502:580
6X-RAY DIFFRACTION6chain a and resi 581:850
7X-RAY DIFFRACTION7chain a and resi 852:950
8X-RAY DIFFRACTION8chain b and resi 217:351
9X-RAY DIFFRACTION9chain b and resi 352:471
10X-RAY DIFFRACTION10chain b and resi 472:591
11X-RAY DIFFRACTION11chain b and resi 592:791
12X-RAY DIFFRACTION12chain b and resi 792:991
13X-RAY DIFFRACTION13chain b and resi 992:1120
14X-RAY DIFFRACTION14chain d and resi 3:14
15X-RAY DIFFRACTION15chain d and resi 15:23
16X-RAY DIFFRACTION16chain e and resi 26:35
17X-RAY DIFFRACTION17chain e and resi 36:38
18X-RAY DIFFRACTION18chain e and resi 39
19X-RAY DIFFRACTION19chain e and resi 40:50
20X-RAY DIFFRACTION20chain g

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