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Open data
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Basic information
Entry | ![]() | |||||||||||||||
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Title | Fiber I and fiber-tail-adaptor of phage GP4 | |||||||||||||||
![]() | portal-vertex of phage GP4 | |||||||||||||||
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![]() | Complex / VIRAL PROTEIN | |||||||||||||||
Function / homology | Virion-associated phage protein / Virion-associated phage protein![]() | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||||||||
![]() | Liu H / Chen W | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Asymmetric Structure of Podophage GP4 Reveals a Novel Architecture of Three Types of Tail Fibers. Authors: Jing Zheng / Wenyuan Chen / Hao Xiao / Fan Yang / Jingdong Song / Lingpeng Cheng / Hongrong Liu / ![]() Abstract: Bacteriophage tail fibers (or called tail spikes) play a critical role in the early stage of infection by binding to the bacterial surface. Podophages with known structures usually possess one or two ...Bacteriophage tail fibers (or called tail spikes) play a critical role in the early stage of infection by binding to the bacterial surface. Podophages with known structures usually possess one or two types of fibers. Here, we resolved an asymmetric structure of the podophage GP4 to near-atomic resolution by cryo-EM. Our structure revealed a symmetry-mismatch relationship between the components of the GP4 tail with previously unseen topologies. In detail, two dodecameric adaptors (adaptors I and II), a hexameric nozzle, and a tail needle form a conserved tail body connected to a dodecameric portal occupying a unique vertex of the icosahedral head. However, five chain-like extended fibers (fiber I) and five tulip-like short fibers (fiber II) are anchored to a 15-fold symmetric fiber-tail adaptor, encircling the adaptor I, and six bamboo-like trimeric fibers (fiber III) are connected to the nozzle. Five fibers I, each composed of five dimers of the protein gp80 linked by an elongated rope protein, are attached to the five edges of the tail vertex of the icosahedral head. In this study, we identified a new structure of the podophage with three types of tail fibers, and such phages with different types of fibers may have a broad host range and/or infect host cells with considerably high efficiency, providing evolutionary advantages in harsh environments. | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 580.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.2 KB 16.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 21.4 KB | Display | ![]() |
Images | ![]() | 174.6 KB | ||
Filedesc metadata | ![]() | 5.1 KB | ||
Others | ![]() ![]() | 582.1 MB 582.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jouMC ![]() 8jovC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Map
File | ![]() | ||||||||||||||||||||
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Annotation | portal-vertex of phage GP4 | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.27 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: half map2
File | emd_36462_half_map_1.map | ||||||||||||
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Annotation | half map2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map1
File | emd_36462_half_map_2.map | ||||||||||||
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Annotation | half map1 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Ralstonia phage GP4
Entire | Name: ![]() |
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Components |
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-Supramolecule #1: Ralstonia phage GP4
Supramolecule | Name: Ralstonia phage GP4 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 2282904 / Sci species name: Ralstonia phage GP4 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No |
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-Macromolecule #1: Virion-associated phage protein
Macromolecule | Name: Virion-associated phage protein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 14.360909 KDa |
Sequence | String: MAAASTYTEN NILNALLRGV AFPLPAKTYV SLHTGDPGVG AGANEVSLSN WPAYVRREAE QGGAIGSGWT PAASGQTSNV NQLTYPANN GVAAVTVTHY AVFDAPTGGN LLFKAPLTVA RTLQVGDVFV FDVGSLTAQA S UniProtKB: Virion-associated phage protein |
-Macromolecule #2: rope protein of phage GP4
Macromolecule | Name: rope protein of phage GP4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 10.230603 KDa |
Sequence | String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) |
-Macromolecule #3: Virion-associated phage protein
Macromolecule | Name: Virion-associated phage protein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 9.908155 KDa |
Sequence | String: MLGIVQKTAT EQLDYDIDFA RWMPDGDVLQ SAGVVITPDD GTLTSPAYEI DGTVVKVWLA GGTAGASYNV DVTVATAAGR IKETCFKTR VRSC UniProtKB: Virion-associated phage protein |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TECNAI ARCTICA |
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Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 35.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.8000000000000003 µm / Nominal defocus min: 0.1 µm |
Experimental equipment | ![]() Model: Talos Arctica / Image courtesy: FEI Company |