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- EMDB-36462: Fiber I and fiber-tail-adaptor of phage GP4 -

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Basic information

Entry
Database: EMDB / ID: EMD-36462
TitleFiber I and fiber-tail-adaptor of phage GP4
Map dataportal-vertex of phage GP4
Sample
  • Virus: Ralstonia phage GP4 (virus)
    • Protein or peptide: Virion-associated phage protein
    • Protein or peptide: rope protein of phage GP4
    • Protein or peptide: Virion-associated phage protein
KeywordsComplex / VIRAL PROTEIN
Function / homologyVirion-associated phage protein / Virion-associated phage protein
Function and homology information
Biological speciesRalstonia phage GP4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsLiu H / Chen W
Funding support China, 4 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)12034006 China
National Natural Science Foundation of China (NSFC)32071209 China
National Natural Science Foundation of China (NSFC)31971122 China
National Natural Science Foundation of China (NSFC)32200994 China
CitationJournal: J Mol Biol / Year: 2023
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
DepositionJun 8, 2023-
Header (metadata) releaseJan 3, 2024-
Map releaseJan 3, 2024-
UpdateJan 3, 2024-
Current statusJan 3, 2024Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_36462.png

Downloads & links

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Map

FileDownload / File: emd_36462.map.gz / Format: CCP4 / Size: 641.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationportal-vertex of phage GP4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.27 Å/pix.
x 552 pix.
= 701.04 Å		1.27 Å/pix.
x 552 pix.
= 701.04 Å		1.27 Å/pix.
x 552 pix.
= 701.04 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.27 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-10.637188 - 19.740929000000001
Average (Standard dev.)0.10532702 (±2.6075187)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin444
Dimensions552552552
Spacing552552552
CellA=B=C: 701.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map2

Fileemd_36462_half_map_1.map
Annotationhalf map2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map1

Fileemd_36462_half_map_2.map
Annotationhalf map1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ralstonia phage GP4

EntireName: Ralstonia phage GP4 (virus)
Components
  • Virus: Ralstonia phage GP4 (virus)
    • Protein or peptide: Virion-associated phage protein
    • Protein or peptide: rope protein of phage GP4
    • Protein or peptide: Virion-associated phage protein

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Supramolecule #1: Ralstonia phage GP4

SupramoleculeName: 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

MacromoleculeName: Virion-associated phage protein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: Ralstonia phage GP4 (virus)
Molecular weightTheoretical: 14.360909 KDa
SequenceString:
MAAASTYTEN NILNALLRGV AFPLPAKTYV SLHTGDPGVG AGANEVSLSN WPAYVRREAE QGGAIGSGWT PAASGQTSNV NQLTYPANN GVAAVTVTHY AVFDAPTGGN LLFKAPLTVA RTLQVGDVFV FDVGSLTAQA S

UniProtKB: Virion-associated phage protein

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Macromolecule #2: rope protein of phage GP4

MacromoleculeName: rope protein of phage GP4 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Ralstonia phage GP4 (virus)
Molecular weightTheoretical: 10.230603 KDa
SequenceString: (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)

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Macromolecule #3: Virion-associated phage protein

MacromoleculeName: Virion-associated phage protein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Ralstonia phage GP4 (virus)
Molecular weightTheoretical: 9.908155 KDa
SequenceString:
MLGIVQKTAT EQLDYDIDFA RWMPDGDVLQ SAGVVITPDD GTLTSPAYEI DGTVVKVWLA GGTAGASYNV DVTVATAAGR IKETCFKTR VRSC

UniProtKB: Virion-associated phage protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 39883
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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