+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13862 | |||||||||
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Title | Jumbo Phage phi-Kp24 empty capsid | |||||||||
Map data | Klebsiella phage phi-kp24 empty capsid | |||||||||
Sample |
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Keywords | Jumbo phage / Klebsiella pneumoniae / Capsid / VIRUS | |||||||||
Function / homology | Major head protein Function and homology information | |||||||||
Biological species | Klebsiella phage vB_KpM_FBKp24 (virus) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Ouyang R / Briegel A | |||||||||
Funding support | Netherlands, 1 items
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Citation | Journal: Nat Commun / Year: 2022 Title: High-resolution reconstruction of a Jumbo-bacteriophage infecting capsulated bacteria using hyperbranched tail fibers. Authors: Ruochen Ouyang / Ana Rita Costa / C Keith Cassidy / Aleksandra Otwinowska / Vera C J Williams / Agnieszka Latka / Phill J Stansfeld / Zuzanna Drulis-Kawa / Yves Briers / Daniël M Pelt / ...Authors: Ruochen Ouyang / Ana Rita Costa / C Keith Cassidy / Aleksandra Otwinowska / Vera C J Williams / Agnieszka Latka / Phill J Stansfeld / Zuzanna Drulis-Kawa / Yves Briers / Daniël M Pelt / Stan J J Brouns / Ariane Briegel / Abstract: The Klebsiella jumbo myophage ϕKp24 displays an unusually complex arrangement of tail fibers interacting with a host cell. In this study, we combine cryo-electron microscopy methods, protein ...The Klebsiella jumbo myophage ϕKp24 displays an unusually complex arrangement of tail fibers interacting with a host cell. In this study, we combine cryo-electron microscopy methods, protein structure prediction methods, molecular simulations, microbiological and machine learning approaches to explore the capsid, tail, and tail fibers of ϕKp24. We determine the structure of the capsid and tail at 4.1 Å and 3.0 Å resolution. We observe the tail fibers are branched and rearranged dramatically upon cell surface attachment. This complex configuration involves fourteen putative tail fibers with depolymerase activity that provide ϕKp24 with the ability to infect a broad panel of capsular polysaccharide (CPS) types of Klebsiella pneumoniae. Our study provides structural and functional insight into how ϕKp24 adapts to the variable surfaces of capsulated bacterial pathogens, which is useful for the development of phage therapy approaches against pan-drug resistant K. pneumoniae strains. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_13862.map.gz | 216.1 MB | EMDB map data format | |
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Header (meta data) | emd-13862-v30.xml emd-13862.xml | 12.3 KB 12.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13862_fsc.xml | 28 KB | Display | FSC data file |
Images | emd_13862.png | 251.7 KB | ||
Filedesc metadata | emd-13862.cif.gz | 3.8 KB | ||
Others | emd_13862_half_map_1.map.gz emd_13862_half_map_2.map.gz | 1.5 GB 1.5 GB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13862 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13862 | HTTPS FTP |
-Validation report
Summary document | emd_13862_validation.pdf.gz | 906.4 KB | Display | EMDB validaton report |
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Full document | emd_13862_full_validation.pdf.gz | 906 KB | Display | |
Data in XML | emd_13862_validation.xml.gz | 35 KB | Display | |
Data in CIF | emd_13862_validation.cif.gz | 47.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13862 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13862 | HTTPS FTP |
-Related structure data
Related structure data | 8bflMC 8bfpMC 8au1C 8bfkC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_13862.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Klebsiella phage phi-kp24 empty capsid | ||||||||||||||||||||
Voxel size | X=Y=Z: 2.055 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: phage phi-kp24 empty capsid half 1
File | emd_13862_half_map_1.map | ||||||||||||
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Annotation | phage phi-kp24 empty capsid half 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: phage phi-kp24 empty capsid half 2
File | emd_13862_half_map_2.map | ||||||||||||
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Annotation | phage phi-kp24 empty capsid half 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Phage capisd
Entire | Name: Phage capisd |
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Components |
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-Supramolecule #1: Phage capisd
Supramolecule | Name: Phage capisd / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Klebsiella phage vB_KpM_FBKp24 (virus) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7 |
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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 exposure time: 0.053 sec. / Average electron dose: 30.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 64000 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |