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- PDB-8r7v: MutSbeta bound to compound CHDI-00898647 in the canonical DNA-mis... -

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Basic information

Entry
Database: PDB / ID: 8r7v
TitleMutSbeta bound to compound CHDI-00898647 in the canonical DNA-mismatch bound form
Components
  • (DNA mismatch repair protein ...) x 2
  • DNA_61bp_CAG2_loop_Fwd
  • DNA_61bp_Complement_Rev
KeywordsDNA BINDING PROTEIN / DNA REPAIR / MISMATCH RECOGNITION / ABC FAMILY ATPase / PROTEROS BIOSTRUCTURES GMBH
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsHaque, T. / Brace, G. / Felsenfeld, D. / Tilack, K. / Schaertl, S. / Ballantyne, G. / Maillard, M. / Iyer, R. / Prasad, B. / Thomsen, M. ...Haque, T. / Brace, G. / Felsenfeld, D. / Tilack, K. / Schaertl, S. / Ballantyne, G. / Maillard, M. / Iyer, R. / Prasad, B. / Thomsen, M. / Wilkionson, H. / Plotnikov, N. / Ritzefeld, M.
Funding support United States, 1items
OrganizationGrant numberCountry
CHDI Foundation United States
CitationJournal: To Be Published
Title: Identification of orthosteric inhibitors of MutSbeta ATPase function
Authors: Haque, T. / Brace, G.
History
DepositionNov 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 30, 2024Provider: 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_61bp_Complement_Rev
D: DNA_61bp_CAG2_loop_Fwd
hetero molecules


Theoretical massNumber of molelcules
Total (without water)272,3798
Polymers271,3434
Non-polymers1,0354
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area15180 Å2
ΔGint-144 kcal/mol
Surface area79500 Å2
MethodPISA

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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 / Fragment: MSH3 N-TERMINAL TRUNCATED
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 / hMSH3 / Divergent upstream protein / DUP / Mismatch repair protein 1 / MRP1


Mass: 127634.719 Da / Num. of mol.: 1 / Fragment: MSH3 N-TERMINAL TRUNCATED
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSH3, DUC1, DUG / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P20585

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DNA chain , 2 types, 2 molecules CD

#3: DNA chain DNA_61bp_Complement_Rev


Mass: 18491.850 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: DNA chain DNA_61bp_CAG2_loop_Fwd


Mass: 20355.037 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 4 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: Chemical ChemComp-YKQ / ~{N}-[3-[[2-[[3-fluoranyl-4-(4-methylpiperazin-1-yl)phenyl]amino]-7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl]oxy]phenyl]prop-2-enamide


Mass: 487.529 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H26FN7O2 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1MutSbeta in complex with the mismatched DNA and compoundCOMPLEX#1-#40MULTIPLE SOURCES
2MutSbetaCOMPLEX#1-#21RECOMBINANT
3Double stranded DNACOMPLEX#3-#41RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Spodoptera frugiperda (fall armyworm)7108
33synthetic construct (others)32630
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 49.77 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: NONE
3D reconstructionResolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 273352 / Symmetry type: POINT
RefinementResolution: 3.12→292.54 Å / Cor.coef. Fo:Fc: 0.839 / SU B: 7.562 / SU ML: 0.127 / ESU R: 0.11
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
RfactorNum. reflection% reflection
Rwork0.37688 --
obs0.37688 1726584 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 123.786 Å2
Baniso -1Baniso -2Baniso -3
1-3.09 Å21.18 Å2-0.54 Å2
2---0.72 Å20.21 Å2
3----2.38 Å2
Refinement stepCycle: 1 / Total: 14629
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0030.01214991
ELECTRON MICROSCOPYr_bond_other_d
ELECTRON MICROSCOPYr_angle_refined_deg0.9371.59620464
ELECTRON MICROSCOPYr_angle_other_deg
ELECTRON MICROSCOPYr_dihedral_angle_1_deg4.69651675
ELECTRON MICROSCOPYr_dihedral_angle_2_deg35.54223.052698
ELECTRON MICROSCOPYr_dihedral_angle_3_deg20.511152566
ELECTRON MICROSCOPYr_dihedral_angle_4_deg14.5681577
ELECTRON MICROSCOPYr_chiral_restr0.0760.21983
ELECTRON MICROSCOPYr_gen_planes_refined0.0030.0210668
ELECTRON MICROSCOPYr_gen_planes_other
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it5.33110.1186733
ELECTRON MICROSCOPYr_mcbond_other
ELECTRON MICROSCOPYr_mcangle_it9.51515.1438394
ELECTRON MICROSCOPYr_mcangle_other
ELECTRON MICROSCOPYr_scbond_it5.56214.2898258
ELECTRON MICROSCOPYr_scbond_other
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other
ELECTRON MICROSCOPYr_long_range_B_refined26.32862444
ELECTRON MICROSCOPYr_long_range_B_other
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.12→3.201 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.517 128195 -
obs--100 %

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