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- EMDB-15417: human MutSalpha (MSH2/MSH6) binding to DNA with a GT mismatch -

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Basic information

Entry
Database: EMDB / ID: EMD-15417
Titlehuman MutSalpha (MSH2/MSH6) binding to DNA with a GT mismatch
Map data
Sample
  • Complex: MutSalpha on mismatched DNA
    • Complex: MSH2
      • Protein or peptide: DNA mismatch repair protein Msh2
    • Complex: MSH6
      • Protein or peptide: DNA mismatch repair protein Msh6
    • Complex: DNA containing a G/T mismatch
      • DNA: DNA (50-MER)
      • DNA: DNA (50-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsDNA mismatch repair / MMR / MutSa / Lynch Syndrome / DNA BINDING PROTEIN
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 / B cell mediated immunity / maintenance of DNA repeat elements ...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 / B cell mediated immunity / maintenance of DNA repeat elements / positive regulation of helicase activity / positive regulation of isotype switching to IgA isotypes / meiotic mismatch repair / centromeric DNA binding / mitotic recombination / positive regulation of isotype switching to IgG isotypes / mismatched DNA binding / negative regulation of DNA recombination / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / isotype switching / oxidative phosphorylation / response to UV-B / postreplication repair / 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 / mismatch repair / ATP-dependent activity, acting on DNA / 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 / 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 ...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 / domain with conserved PWWP motif / PWWP domain / PWWP domain profile. / PWWP domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA mismatch repair protein Msh2 / DNA mismatch repair protein Msh6
Similarity search - Component
Biological speciesHomo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsBruekner SR / Sixma TK
Funding support Netherlands, European Union, 2 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research (NWO)NOW-TOP 714.016.002 Netherlands
European CommissionH2020-MSCA-ITN-2016 722433 DNAREPAIRMANEuropean Union
CitationJournal: Nucleic Acids Res / Year: 2023
Title: Unexpected moves: a conformational change in MutSα enables high-affinity DNA mismatch binding.
Authors: Susanne R Bruekner / Wietske Pieters / Alexander Fish / A Manuel Liaci / Serge Scheffers / Emily Rayner / Daphne Kaldenbach / Lisa Drost / Marleen Dekker / Sandrine van Hees-Stuivenberg / ...Authors: Susanne R Bruekner / Wietske Pieters / Alexander Fish / A Manuel Liaci / Serge Scheffers / Emily Rayner / Daphne Kaldenbach / Lisa Drost / Marleen Dekker / Sandrine van Hees-Stuivenberg / Elly Delzenne-Goette / Charlotte de Konink / Hellen Houlleberghs / Hendrikus Jan Dubbink / Abeer AlSaegh / Niels de Wind / Friedrich Förster / Hein Te Riele / Titia K Sixma /
Abstract: The DNA mismatch repair protein MutSα recognizes wrongly incorporated DNA bases and initiates their correction during DNA replication. Dysfunctions in mismatch repair lead to a predisposition to ...The DNA mismatch repair protein MutSα recognizes wrongly incorporated DNA bases and initiates their correction during DNA replication. Dysfunctions in mismatch repair lead to a predisposition to cancer. Here, we study the homozygous mutation V63E in MSH2 that was found in the germline of a patient with suspected constitutional mismatch repair deficiency syndrome who developed colorectal cancer before the age of 30. Characterization of the mutant in mouse models, as well as slippage and repair assays, shows a mildly pathogenic phenotype. Using cryogenic electron microscopy and surface plasmon resonance, we explored the mechanistic effect of this mutation on MutSα function. We discovered that V63E disrupts a previously unappreciated interface between the mismatch binding domains (MBDs) of MSH2 and MSH6 and leads to reduced DNA binding. Our research identifies this interface as a 'safety lock' that ensures high-affinity DNA binding to increase replication fidelity. Our mechanistic model explains the hypomorphic phenotype of the V63E patient mutation and other variants in the MBD interface.
History
DepositionJul 19, 2022-
Header (metadata) releaseJan 25, 2023-
Map releaseJan 25, 2023-
UpdateJul 24, 2024-
Current statusJul 24, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_15417.png

Downloads & links

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Map

FileDownload / File: emd_15417.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 360 pix.
= 302.04 Å		0.84 Å/pix.
x 360 pix.
= 302.04 Å		0.84 Å/pix.
x 360 pix.
= 302.04 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.5
Minimum - Maximum0.0 - 20.713327
Average (Standard dev.)0.21388306 (±0.6674231)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 302.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_15417_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_15417_half_map_2.map
Projections & Slices
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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : MutSalpha on mismatched DNA

EntireName: MutSalpha on mismatched DNA
Components
  • Complex: MutSalpha on mismatched DNA
    • Complex: MSH2
      • Protein or peptide: DNA mismatch repair protein Msh2
    • Complex: MSH6
      • Protein or peptide: DNA mismatch repair protein Msh6
    • Complex: DNA containing a G/T mismatch
      • DNA: DNA (50-MER)
      • DNA: DNA (50-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: MutSalpha on mismatched DNA

SupramoleculeName: MutSalpha on mismatched DNA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 31 KDa

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Supramolecule #2: MSH2

SupramoleculeName: MSH2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 / Details: has ADP+Mg bound
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: MSH6

SupramoleculeName: MSH6 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Details: Contains N-terminal 10His-TwinStrep tag removable by 3C
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: DNA containing a G/T mismatch

SupramoleculeName: DNA containing a G/T mismatch / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: DNA mismatch repair protein Msh2

MacromoleculeName: DNA mismatch repair protein Msh2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 104.861875 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAVQPKETLQ LESAAEVGFV RFFQGMPEKP TTTVRLFDRG DFYTAHGEDA LLAAREVFKT QGVIKYMGPA GAKNLQSVVL SKMNFESFV KDLLLVRQYR VEVYKNRAGN KASKENDWYL AYKASPGNLS QFEDILFGNN DMSASIGVVG VKMSAVDGQR Q VGVGYVDS ...String:
MAVQPKETLQ LESAAEVGFV RFFQGMPEKP TTTVRLFDRG DFYTAHGEDA LLAAREVFKT QGVIKYMGPA GAKNLQSVVL SKMNFESFV KDLLLVRQYR VEVYKNRAGN KASKENDWYL AYKASPGNLS QFEDILFGNN DMSASIGVVG VKMSAVDGQR Q VGVGYVDS IQRKLGLCEF PDNDQFSNLE ALLIQIGPKE CVLPGGETAG DMGKLRQIIQ RGGILITERK KADFSTKDIY QD LNRLLKG KKGEQMNSAV LPEMENQVAV SSLSAVIKFL ELLSDDSNFG QFELTTFDFS QYMKLDIAAV RALNLFQGSV EDT TGSQSL AALLNKCKTP QGQRLVNQWI KQPLMDKNRI EERLNLVEAF VEDAELRQTL QEDLLRRFPD LNRLAKKFQR QAAN LQDCY RLYQGINQLP NVIQALEKHE GKHQKLLLAV FVTPLTDLRS DFSKFQEMIE TTLDMDQVEN HEFLVKPSFD PNLSE LREI MNDLEKKMQS TLISAARDLG LDPGKQIKLD SSAQFGYYFR VTCKEEKVLR NNKNFSTVDI QKNGVKFTNS KLTSLN EEY TKNKTEYEEA QDAIVKEIVN ISSGYVEPMQ TLNDVLAQLD AVVSFAHVSN GAPVPYVRPA ILEKGQGRII LKASRHA CV EVQDEIAFIP NDVYFEKDKQ MFHIITGPNM GGKSTYIRQT GVIVLMAQIG CFVPCESAEV SIVDCILARV GAGDSQLK G VSTFMAEMLE TASILRSATK DSLIIIDELG RGTSTYDGFG LAWAISEYIA TKIGAFCMFA THFHELTALA NQIPTVNNL HVTALTTEET LTMLYQVKKG VCDQSFGIHV AELANFPKHV IECAKQKALE LEEFQYIGES QGYDIMEPAA KKCYLEREQG EKIIQEFLS KVKQMPFTEM SEENITIKLK QLKAEVIAKN NSFVNEIISR IKVTT

UniProtKB: DNA mismatch repair protein Msh2

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Macromolecule #2: DNA mismatch repair protein Msh6

MacromoleculeName: DNA mismatch repair protein Msh6 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 158.767312 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MAHHHHHHHH HHGSAASWSH PQFEKGGGSG GGSGGGSWSH PQFEKGALEV LFQGPSRQST LYSFFPKSPA LSDANKASAR ASREGGRAA AAPEASPSPG GDAAWSEAGP GPRPLARSAS PPKAKNLNGG LRRSVAPAAP TSCDFSPGDL VWAKMEGYPW W PCLVYNHP ...String:
MAHHHHHHHH HHGSAASWSH PQFEKGGGSG GGSGGGSWSH PQFEKGALEV LFQGPSRQST LYSFFPKSPA LSDANKASAR ASREGGRAA AAPEASPSPG GDAAWSEAGP GPRPLARSAS PPKAKNLNGG LRRSVAPAAP TSCDFSPGDL VWAKMEGYPW W PCLVYNHP FDGTFIREKG KSVRVHVQFF DDSPTRGWVS KRLLKPYTGS KSKEAQKGGH FYSAKPEILR AMQRADEALN KD KIKRLEL AVCDEPSEPE EEEEMEVGTT YVTDKSEEDN EIESEEEVQP KTQGSRRSSR QIKKRRVISD SESDIGGSDV EFK PDTKEE GSSDEISSGV GDSESEGLNS PVKVARKRKR MVTGNGSLKR KSSRKETPSA TKQATSISSE TKNTLRAFSA PQNS ESQAH VSGGGDDSSR PTVWYHETLE WLKEEKRRDE HRRRPDHPDF DASTLYVPED FLNSCTPGMR KWWQIKSQNF DLVIC YKVG KFYELYHMDA LIGVSELGLV FMKGNWAHSG FPEIAFGRYS DSLVQKGYKV ARVEQTETPE MMEARCRKMA HISKYD RVV RREICRIITK GTQTYSVLEG DPSENYSKYL LSLKEKEEDS SGHTRAYGVC FVDTSLGKFF IGQFSDDRHC SRFRTLV AH YPPVQVLFEK GNLSKETKTI LKSSLSCSLQ EGLIPGSQFW DASKTLRTLL EEEYFREKLS DGIGVMLPQV LKGMTSES D SIGLTPGEKS ELALSALGGC VFYLKKCLID QELLSMANFE EYIPLDSDTV STTRSGAIFT KAYQRMVLDA VTLNNLEIF LNGTNGSTEG TLLERVDTCH TPFGKRLLKQ WLCAPLCNHY AINDRLDAIE DLMVVPDKIS EVVELLKKLP DLERLLSKIH NVGSPLKSQ NHPDSRAIMY EETTYSKKKI IDFLSALEGF KVMCKIIGIM EEVADGFKSK ILKQVISLQT KNPEGRFPDL T VELNRWDT AFDHEKARKT GLITPKAGFD SDYDQALADI RENEQSLLEY LEKQRNRIGC RTIVYWGIGR NRYQLEIPEN FT TRNLPEE YELKSTKKGC KRYWTKTIEK KLANLINAEE RRDVSLKDCM RRLFYNFDKN YKDWQSAVEC IAVLDVLLCL ANY SRGGDG PMCRPVILLP EDTPPFLELK GSRHPCITKT FFGDDFIPND ILIGCEEEEQ ENGKAYCVLV TGPNMGGKST LMRQ AGLLA VMAQMGCYVP AEVCRLTPID RVFTRLGASD RIMSGESTFF VELSETASIL MHATAHSLVL VDELGRGTAT FDGTA IANA VVKELAETIK CRTLFSTHYH SLVEDYSQNV AVRLGHMACM VENECEDPSQ ETITFLYKFI KGACPKSYGF NAARLA NLP EEVIQKGHRK AREFEKMNQS LRLFREVCLA SERSTVDAEA VHKLLTLIKE L

UniProtKB: DNA mismatch repair protein Msh6

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Macromolecule #3: DNA (50-MER)

MacromoleculeName: DNA (50-MER) / type: dna / ID: 3 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.418874 KDa
SequenceString:
(DC)(DT)(DT)(DA)(DG)(DC)(DT)(DT)(DA)(DG) (DG)(DA)(DT)(DC)(DA)(DT)(DC)(DG)(DA)(DG) (DG)(DA)(DT)(DC)(DG)(DA)(DG)(DC)(DT) (DC)(DG)(DG)(DT)(DG)(DC)(DA)(DA)(DT)(DT) (DC) (DA)(DG)(DC)(DG)(DG)(DT)(DA)(DC) (DC)(DC)

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Macromolecule #4: DNA (50-MER)

MacromoleculeName: DNA (50-MER) / type: dna / ID: 4 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 15.402874 KDa
SequenceString:
(DG)(DG)(DG)(DT)(DA)(DC)(DC)(DG)(DC)(DT) (DG)(DA)(DA)(DT)(DT)(DG)(DC)(DA)(DC)(DC) (DG)(DA)(DG)(DC)(DT)(DT)(DG)(DA)(DT) (DC)(DC)(DT)(DC)(DG)(DA)(DT)(DG)(DA)(DT) (DC) (DC)(DT)(DA)(DA)(DG)(DC)(DT)(DA) (DA)(DG)

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #6: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 6 / Number of copies: 1 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.53 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMHEPESHEPES
150.0 mMKClpotassium chloride
5.0 mMMgCl2magnesium chloride
1.0 mMTCEPTCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.01 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: 3 s blotting with blot force 10.
Details2 uM MutSa with 2-fold excess DNA oligo

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Detailscollected on Krios 1 at Netherlands Center for Electron Nanoscopy (NeCEN)
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4821 / Average exposure time: 1.9 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.000000001 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5412220
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0) / Number images used: 289289
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 4.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

2o8b


Chain - Source name: PDB / Chain - Initial model type: experimental model
DetailsPDB-REDO webserver: https://pdb-redo.eu/
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8ag6:
human MutSalpha (MSH2/MSH6) binding to DNA with a GT mismatch

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