+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13063 | |||||||||
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Title | The structure of MutS bound to two molecules of AMPPNP | |||||||||
Map data | ||||||||||
Sample |
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Keywords | DNA mismatch repair protein / DNA BINDING PROTEIN | |||||||||
Function / homology | Function and homology information adenine/cytosine mispair binding / MutS complex / mismatch repair complex / regulation of DNA recombination / mismatched DNA binding / DNA binding, bending / ATP-dependent DNA damage sensor activity / mismatch repair / ADP binding / damaged DNA binding ...adenine/cytosine mispair binding / MutS complex / mismatch repair complex / regulation of DNA recombination / mismatched DNA binding / DNA binding, bending / ATP-dependent DNA damage sensor activity / mismatch repair / ADP binding / damaged DNA binding / DNA damage response / ATP hydrolysis activity / ATP binding / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Lamers MH / Borsellini A | |||||||||
Funding support | European Union, 1 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2022 Title: Cryogenic electron microscopy structures reveal how ATP and DNA binding in MutS coordinates sequential steps of DNA mismatch repair. Authors: Alessandro Borsellini / Vladislav Kunetsky / Peter Friedhoff / Meindert H Lamers / Abstract: DNA mismatch repair detects and corrects mismatches introduced during DNA replication. The protein MutS scans for mismatches and coordinates the repair cascade. During this process, MutS undergoes ...DNA mismatch repair detects and corrects mismatches introduced during DNA replication. The protein MutS scans for mismatches and coordinates the repair cascade. During this process, MutS undergoes multiple conformational changes in response to ATP binding, hydrolysis and release, but how ATP induces the various MutS conformations is incompletely understood. Here we present four cryogenic electron microscopy structures of Escherichia coli MutS at sequential stages of the ATP hydrolysis cycle that reveal how ATP binding and hydrolysis induce closing and opening of the MutS dimer, respectively. Biophysical analysis demonstrates how DNA binding modulates the ATPase cycle by prevention of hydrolysis during scanning and mismatch binding, while preventing ADP release in the sliding clamp state. Nucleotide release is achieved when MutS encounters single-stranded DNA that is produced during removal of the daughter strand. The combination of ATP binding and hydrolysis and its modulation by DNA enables MutS to adopt the different conformations needed to coordinate the sequential steps of the mismatch repair cascade. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13063.map.gz | 2.9 MB | EMDB map data format | |
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Header (meta data) | emd-13063-v30.xml emd-13063.xml | 14.1 KB 14.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13063_fsc.xml | 9.1 KB | Display | FSC data file |
Images | emd_13063.png | 146.9 KB | ||
Filedesc metadata | emd-13063.cif.gz | 6.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13063 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13063 | HTTPS FTP |
-Validation report
Summary document | emd_13063_validation.pdf.gz | 460.5 KB | Display | EMDB validaton report |
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Full document | emd_13063_full_validation.pdf.gz | 460.1 KB | Display | |
Data in XML | emd_13063_validation.xml.gz | 8.9 KB | Display | |
Data in CIF | emd_13063_validation.cif.gz | 11.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13063 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13063 | HTTPS FTP |
-Related structure data
Related structure data | 7otoMC 7ou0C 7ou2C 7ou4C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13063.map.gz / Format: CCP4 / Size: 7.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : DNA mismatch repair protein MutS
Entire | Name: DNA mismatch repair protein MutS |
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Components |
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-Supramolecule #1: DNA mismatch repair protein MutS
Supramolecule | Name: DNA mismatch repair protein MutS / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: MutS bound to two molecules of AMPPNP |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 190 KDa |
-Macromolecule #1: DNA mismatch repair protein MutS
Macromolecule | Name: DNA mismatch repair protein MutS / type: protein_or_peptide / ID: 1 / Details: AMPPNP / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) / Strain: K12 |
Molecular weight | Theoretical: 90.433234 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: HHHHHHMSAI ENFDAHTPMM QQYLRLKAQH PEILLFYRMG DFYELFYDDA KRASQLLDIS LTKRGASAGE PIPMAGIPYH AVENYLAKL VNQGESVAIC EQIGDPATSK GPVERKVVRI VTPGTISDEA LLQERQDNLL AAIWQDSKGF GYATLDISSG R FRLSEPAD ...String: HHHHHHMSAI ENFDAHTPMM QQYLRLKAQH PEILLFYRMG DFYELFYDDA KRASQLLDIS LTKRGASAGE PIPMAGIPYH AVENYLAKL VNQGESVAIC EQIGDPATSK GPVERKVVRI VTPGTISDEA LLQERQDNLL AAIWQDSKGF GYATLDISSG R FRLSEPAD RETMAAELQR TNPAELLYAE DFAEMSLIEG RRGLRRRPLW EFEIDTARQQ LNLQFGTRDL VGFGVENAPR GL CAAGCLL QYAKDTQRTT LPHIRSITME REQDSIIMDA ATRRNLEITQ NLAGGAENTL ASVLDCTVTP MGSRMLKRWL HMP VRDTRV LLERQQTIGA LQDFTAGLQP VLRQVGDLER ILARLALRTA RPRDLARMRH AFQQLPELRA QLETVDSAPV QALR EKMGE FAELRDLLER AIIDTPPVLV RDGGVIASGY NEELDEWRAL ADGATDYLER LEVRERERTG LDTLKVGFNA VHGYY IQIS RGQSHLAPIN YMRRQTLKNA ERYIIPELKE YEDKVLTSKG KALALEKQLY EELFDLLLPH LEALQQSASA LAELDV LVN LAERAYTLNY TCPTFIDKPG IRITEGRHPV VEQVLNEPFI ANPLNLSPQR RMLIITGPNM GGKSTYMRQT ALIALMA YI GSYVPAQKVE IGPIDRIFTR VGAADDLASG RSTFMVEMTE TANILHNATE YSLVLMDEIG RGTSTYDGLS LAWACAEN L ANKIKALTLF ATHYFELTQL PEKMEGVANV HLDALEHGDT IAFMHSVQDG AASKSYGLAV AALAGVPKEV IKRARQKLR ELESIS UniProtKB: DNA mismatch repair protein MutS |
-Macromolecule #2: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 2 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #3: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / type: ligand / ID: 3 / Number of copies: 2 / Formula: ANP |
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Molecular weight | Theoretical: 506.196 Da |
Chemical component information | ChemComp-ANP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.95 mg/mL | ||||||||||||||||||
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Buffer | pH: 8.5 Component:
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Grid | Model: 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: 0.0004 kPa | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 57.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |