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Yorodumi- EMDB-48458: Structure of the bacteriophage T4 portal-neck-tail connector complex -
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Open data
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Basic information
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| Title | Structure of the bacteriophage T4 portal-neck-tail connector complex | |||||||||
Map data | Asymmetric cryo-EM reconstruction focused on the neck region of T4 virion | |||||||||
Sample |
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Keywords | bacteriophage T4 / portal vertex / phage neck / tail terminator protein / tube terminator protein / asymmetric phage reconstruction / DNA retention / neck stopper protein / head completion proteins / VIRAL PROTEIN | |||||||||
| Function / homology | Function and homology informationvirus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / viral capsid, decoration / T=13 icosahedral viral capsid / viral genome packaging / viral release from host cell / virion component / viral capsid / structural molecule activity Similarity search - Function | |||||||||
| Biological species | Escherichia phage T4 (virus) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Fokine A / Zhu J / Klose T / Vago F / Arnaud C / Wang Z / Khare B / Rossmann MG / Chen Z / Sun L ...Fokine A / Zhu J / Klose T / Vago F / Arnaud C / Wang Z / Khare B / Rossmann MG / Chen Z / Sun L / Fang Q / Kuhn R / Rao VB | |||||||||
| Funding support | United States, 1 items
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Citation | Journal: To Be PublishedTitle: In situ Atomic Structure of Phage T4 Head-Tail Connector Complex Shows Molecular Gates Open for Genome Ejection and DNA Pushed into the Tail Tube Authors: Fokine A / Zhu J / Klose T / Vago F / Arnaud C / Wang Z / Khare B / Rossmann MG / Chen Z / Sun L / Fang Q / Kuhn R / Rao VB | |||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_48458.map.gz | 229.2 MB | EMDB map data format | |
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| Header (meta data) | emd-48458-v30.xml emd-48458.xml | 29.5 KB 29.5 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_48458_fsc.xml | 14.9 KB | Display | FSC data file |
| Images | emd_48458.png | 305.5 KB | ||
| Masks | emd_48458_msk_1.map | 244.1 MB | Mask map | |
| Filedesc metadata | emd-48458.cif.gz | 8.9 KB | ||
| Others | emd_48458_half_map_1.map.gz emd_48458_half_map_2.map.gz | 193.9 MB 193.8 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-48458 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-48458 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9mofMC ![]() 9mkbC ![]() 9mogC ![]() 9mohC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_48458.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | Asymmetric cryo-EM reconstruction focused on the neck region of T4 virion | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.616 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Mask #1
| File | emd_48458_msk_1.map | ||||||||||||
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| Projections & Slices |
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| Density Histograms |
-Half map: Half map B
| File | emd_48458_half_map_1.map | ||||||||||||
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| Annotation | Half map B | ||||||||||||
| Projections & Slices |
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| Density Histograms |
-Half map: Half map A
| File | emd_48458_half_map_2.map | ||||||||||||
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| Annotation | Half map A | ||||||||||||
| Projections & Slices |
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| Density Histograms |
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Sample components
+Entire : Escherichia phage T4
+Supramolecule #1: Escherichia phage T4
+Macromolecule #1: gp14, neck protein
+Macromolecule #2: gp18, tail sheath protein
+Macromolecule #3: gp19, tail tube protein
+Macromolecule #4: gpwac, fibritin
+Macromolecule #5: gp20, portal protein
+Macromolecule #6: gp23, major capsid protein
+Macromolecule #7: gp13, neck protein
+Macromolecule #8: gp15, tail terminator protein
+Macromolecule #9: gp3, tube terminator protein
+Macromolecule #10: Hoc, highly immunogenic outer capsid protein
+Macromolecule #11: Soc, small outer capsid protein
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.5 |
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| Grid | Model: PELCO Ultrathin Carbon with Lacey Carbon / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. Details: The grids were glow-discharged using a PELCO easyGlow system for 60s at 25mA. |
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: Ted Pella lacey carbon 400 mesh grids (catalog No: 01824) were used.. |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 38.0 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: 2.0 µm / Nominal defocus min: 0.6 µm |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Escherichia phage T4 (virus)
Keywords
Authors
United States, 1 items
Citation












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Processing
FIELD EMISSION GUN

