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Yorodumi- EMDB-16925: Focused refinement of HSV-1 DNA polymerase processivity factor in... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16925 | |||||||||
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Title | Focused refinement of HSV-1 DNA polymerase processivity factor in halted elongation state | |||||||||
Map data | ||||||||||
Sample |
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Keywords | DNA / Polymerase / Complex / TRANSFERASE | |||||||||
Biological species | Human alphaherpesvirus 1 strain KOS | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.97 Å | |||||||||
Authors | Gustavsson E / Grunewald K / Elias P / Hallberg M | |||||||||
Funding support | Sweden, Germany, 2 items
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Citation | Journal: To Be Published Title: Trapped functional states of HSV-1 DNA Polymerase-processivity factor complex by cryo-EM Authors: Gustavsson E / Grunewald K / Elias P / Hallberg M | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16925.map.gz | 154.4 MB | EMDB map data format | |
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Header (meta data) | emd-16925-v30.xml emd-16925.xml | 15.6 KB 15.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16925_fsc.xml | 14.3 KB | Display | FSC data file |
Images | emd_16925.png | 111.2 KB | ||
Masks | emd_16925_msk_1.map | 307.5 MB | Mask map | |
Filedesc metadata | emd-16925.cif.gz | 4.4 KB | ||
Others | emd_16925_half_map_1.map.gz emd_16925_half_map_2.map.gz | 285 MB 285 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16925 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16925 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16925.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16925_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_16925_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_16925_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : HSV-1 DNA polymerase-processivity factor complex in halted elonga...
Entire | Name: HSV-1 DNA polymerase-processivity factor complex in halted elongation state |
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Components |
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-Supramolecule #1: HSV-1 DNA polymerase-processivity factor complex in halted elonga...
Supramolecule | Name: HSV-1 DNA polymerase-processivity factor complex in halted elongation state type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 |
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Source (natural) | Organism: Human alphaherpesvirus 1 strain KOS |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.4 mg/mL | |||||||||||||||
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Buffer | pH: 7.8 Component:
Details: 20mM HEPES pH7.8, 150mM NaCl, 5mM MgCl2, 2mM DTT | |||||||||||||||
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY | |||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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