+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41700 | |||||||||
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Title | Head map of E. coli ExoVII (H238A) | |||||||||
Map data | Focused refinement of head | |||||||||
Sample |
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Keywords | Exonuclease / Endonuclease / DNA repair / DNA BINDING PROTEIN | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Liu C / Berger JM | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2024 Title: Structure of exonuclease VII. Authors: Chuan Liu / Glenn Hauk / Qianyun Yan / James M Berger / Abstract: Exonuclease VII (ExoVII) is a ubiquitous bacterial nuclease. Encoded by the and genes, ExoVII participates in multiple nucleic acid-dependent pathways including the processing of multicopy single- ...Exonuclease VII (ExoVII) is a ubiquitous bacterial nuclease. Encoded by the and genes, ExoVII participates in multiple nucleic acid-dependent pathways including the processing of multicopy single-stranded DNA and the repair of covalent DNA-protein crosslinks (DPCs). Although many biochemical properties of ExoVII have been defined, little is known about its structure/function relationships. Here, we use cryoelectron microscopy (cryoEM) to determine that ExoVII comprises a highly elongated XseA·XseB holo-complex. Each XseA subunit dimerizes through a central extended α-helical segment decorated by six XseB subunits and a C-terminal, domain-swapped β-barrel element; two XseA·XseB subcomplexes further associate using N-terminal OB (oligonucleotide/oligosaccharide-binding) folds and catalytic domains to form a spindle-shaped, catenated octaicosamer. The catalytic domains of XseA, which adopt a nuclease fold related to 3-dehydroquinate dehydratases, are sequestered in the center of the complex and accessible only through large pores formed between XseA tetramers. The architectural organization of ExoVII, combined with biochemical studies, indicate that substrate selectivity is controlled by steric access to its nuclease elements and that tetramer dissociation results from substrate DNA binding. Despite a lack of sequence and fold homology, the physical organization of ExoVII is reminiscent of Mre11·Rad50/SbcCD ATP (adenosine triphosphate)-dependent nucleases used in the repair of double-stranded DNA breaks, including those formed by DPCs through aberrant topoisomerase activity, suggesting that there may have been convergent evolutionary pressure to contend with such damage events. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41700.map.gz | 49.8 MB | EMDB map data format | |
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Header (meta data) | emd-41700-v30.xml emd-41700.xml | 13.6 KB 13.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41700_fsc.xml | 7.9 KB | Display | FSC data file |
Images | emd_41700.png | 53.2 KB | ||
Filedesc metadata | emd-41700.cif.gz | 3.9 KB | ||
Others | emd_41700_additional_1.map.gz emd_41700_half_map_1.map.gz emd_41700_half_map_2.map.gz | 146.8 MB 48.9 MB 48.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41700 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41700 | HTTPS FTP |
-Validation report
Summary document | emd_41700_validation.pdf.gz | 861.5 KB | Display | EMDB validaton report |
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Full document | emd_41700_full_validation.pdf.gz | 861.1 KB | Display | |
Data in XML | emd_41700_validation.xml.gz | 15.4 KB | Display | |
Data in CIF | emd_41700_validation.cif.gz | 19.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41700 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-41700 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41700.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Focused refinement of head | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4933 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: EMReady processed map
File | emd_41700_additional_1.map | ||||||||||||
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Annotation | EMReady processed map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_41700_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_41700_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : XseA4-XseB24 complex of ExoVII
Entire | Name: XseA4-XseB24 complex of ExoVII |
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Components |
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-Supramolecule #1: XseA4-XseB24 complex of ExoVII
Supramolecule | Name: XseA4-XseB24 complex of ExoVII / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 420 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.3 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.75 µm / Nominal defocus min: 0.75 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |