+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36964 | |||||||||
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Title | the local map of DNA and dCTP binding site | |||||||||
Map data | ||||||||||
Sample |
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Keywords | MPXV / complex / RECOMBINATION / REPLICATION / VIRAL PROTEIN | |||||||||
Biological species | Monkeypox virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||
Authors | Shen YP / Li YN / Yan RH | |||||||||
Funding support | China, 1 items
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Citation | Journal: Structure / Year: 2024 Title: Structural basis for the inhibition mechanism of the DNA polymerase holoenzyme from mpox virus. Authors: Yaping Shen / Yaning Li / Renhong Yan / Abstract: There are three key components at the core of the mpox virus (MPXV) DNA polymerase holoenzyme: DNA polymerase F8, processivity factors A22, and the Uracil-DNA glycosylase E4. The holoenzyme is ...There are three key components at the core of the mpox virus (MPXV) DNA polymerase holoenzyme: DNA polymerase F8, processivity factors A22, and the Uracil-DNA glycosylase E4. The holoenzyme is recognized as a vital antiviral target because MPXV replicates in the cytoplasm of host cells. Nucleotide analogs such as cidofovir and cytarabine (Ara-C) have shown potential in curbing MPXV replication and they also display promise against other poxviruses. However, the mechanism behind their inhibitory effects remains unclear. Here, we present the cryo-EM structure of the DNA polymerase holoenzyme F8/A22/E4 bound with its competitive inhibitor Ara-C-derived cytarabine triphosphate (Ara-CTP) at an overall resolution of 3.0 Å and reveal its inhibition mechanism. Ara-CTP functions as a direct chain terminator in proximity to the deoxycytidine triphosphate (dCTP)-binding site. The extra hydrogen bond formed with Asn665 makes it more potent in binding than dCTP. Asn665 is conserved among eukaryotic B-family polymerases. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36964.map.gz | 59.7 MB | EMDB map data format | |
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Header (meta data) | emd-36964-v30.xml emd-36964.xml | 13.7 KB 13.7 KB | Display Display | EMDB header |
Images | emd_36964.png | 35.8 KB | ||
Filedesc metadata | emd-36964.cif.gz | 3.8 KB | ||
Others | emd_36964_half_map_1.map.gz emd_36964_half_map_2.map.gz | 59.4 MB 59.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36964 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36964 | HTTPS FTP |
-Validation report
Summary document | emd_36964_validation.pdf.gz | 821 KB | Display | EMDB validaton report |
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Full document | emd_36964_full_validation.pdf.gz | 820.6 KB | Display | |
Data in XML | emd_36964_validation.xml.gz | 12.3 KB | Display | |
Data in CIF | emd_36964_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36964 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36964 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_36964.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.087 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_36964_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36964_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : F8-A22-E4 complex of MPXV in complex with DNA and Ara-CTP
Entire | Name: F8-A22-E4 complex of MPXV in complex with DNA and Ara-CTP |
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Components |
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-Supramolecule #1: F8-A22-E4 complex of MPXV in complex with DNA and Ara-CTP
Supramolecule | Name: F8-A22-E4 complex of MPXV in complex with DNA and Ara-CTP type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#5 |
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Source (natural) | Organism: Monkeypox virus |
-Supramolecule #2: F8-A22-E4 complex of MPXV
Supramolecule | Name: F8-A22-E4 complex of MPXV / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#3 |
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-Supramolecule #3: DNA
Supramolecule | Name: DNA / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4-#5 |
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-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 (6k x 4k) / Average electron dose: 50.0 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: 1.8 µm / Nominal defocus min: 1.4000000000000001 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 392167 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |