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Yorodumi- EMDB-39002: Composite cryo-EM map of PhiKZ capsid after applying the "block-b... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-39002 | |||||||||||||||
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Title | Composite cryo-EM map of PhiKZ capsid after applying the "block-based" reconstruction method | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | phiKZ / capsid protein / viral assembly / Pseudomonas aeruginosa / jumbo phage / VIRUS | |||||||||||||||
Biological species | Phikzvirus phiKZ | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||
Authors | Yang Y / Shao Q / Guo M / Han L / Zhao X / Wang A / Li X / Wang B / Pan J / Chen Z ...Yang Y / Shao Q / Guo M / Han L / Zhao X / Wang A / Li X / Wang B / Pan J / Chen Z / Fokine A / Sun L / Fang Q | |||||||||||||||
Funding support | China, 4 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Capsid structure of bacteriophage ΦKZ provides insights into assembly and stabilization of jumbo phages. Authors: Yashan Yang / Qianqian Shao / Mingcheng Guo / Lin Han / Xinyue Zhao / Aohan Wang / Xiangyun Li / Bo Wang / Ji-An Pan / Zhenguo Chen / Andrei Fokine / Lei Sun / Qianglin Fang / Abstract: Jumbo phages are a group of tailed bacteriophages with large genomes and capsids. As a prototype of jumbo phage, ΦKZ infects Pseudomonas aeruginosa, a multi-drug-resistant (MDR) opportunistic ...Jumbo phages are a group of tailed bacteriophages with large genomes and capsids. As a prototype of jumbo phage, ΦKZ infects Pseudomonas aeruginosa, a multi-drug-resistant (MDR) opportunistic pathogen leading to acute or chronic infection in immunocompromised individuals. It holds potential to be used as an antimicrobial agent and as a model for uncovering basic phage biology. Although previous low-resolution structural studies have indicated that jumbo phages may have more complicated capsid structures than smaller phages such as HK97, the detailed structures and the assembly mechanism of their capsids remain largely unknown. Here, we report a 3.5-Å-resolution cryo-EM structure of the ΦKZ capsid. The structure unveiled ten minor capsid proteins, with some decorating the outer surface of the capsid and the others forming a complex network attached to the capsid's inner surface. This network seems to play roles in driving capsid assembly and capsid stabilization. Similar mechanisms of capsid assembly and stabilization are probably employed by many other jumbo viruses. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_39002.map.gz | 2.1 GB | EMDB map data format | |
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Header (meta data) | emd-39002-v30.xml emd-39002.xml | 22.6 KB 22.6 KB | Display Display | EMDB header |
Images | emd_39002.png | 253.8 KB | ||
Masks | emd_39002_msk_1.map | 3.7 GB | Mask map | |
Filedesc metadata | emd-39002.cif.gz | 8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-39002 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-39002 | HTTPS FTP |
-Validation report
Summary document | emd_39002_validation.pdf.gz | 687.9 KB | Display | EMDB validaton report |
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Full document | emd_39002_full_validation.pdf.gz | 687.5 KB | Display | |
Data in XML | emd_39002_validation.xml.gz | 10 KB | Display | |
Data in CIF | emd_39002_validation.cif.gz | 11.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39002 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-39002 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_39002.map.gz / Format: CCP4 / Size: 3.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.6 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_39002_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Phikzvirus phiKZ
+Supramolecule #1: Phikzvirus phiKZ
+Macromolecule #1: gp28
+Macromolecule #2: gp35
+Macromolecule #3: gp85
+Macromolecule #4: gp86
+Macromolecule #5: gp91
+Macromolecule #6: gp93
+Macromolecule #7: gp119
+Macromolecule #8: gp120
+Macromolecule #9: gp162
+Macromolecule #10: gp184
+Macromolecule #11: gp244
-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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Grid | Model: EMS Lacey Carbon / Material: COPPER / Support film - Material: CARBON / Support film - topology: LACEY |
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: 30.0 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: 1.0 µm / Nominal magnification: 64000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 903900 |
Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |