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- PDB-8jou: Fiber I and fiber-tail-adaptor of phage GP4 -

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Basic information

Entry
Database: PDB / ID: 8jou
TitleFiber I and fiber-tail-adaptor of phage GP4
Components
  • (Virion-associated phage protein) x 2
  • rope protein of phage GP4
KeywordsVIRAL PROTEIN / Complex
Function / homologyVirion-associated phage protein / Virion-associated phage protein
Function and homology information
Biological speciesRalstonia phage GP4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsLiu, H. / Chen, W.
Funding support China, 4items
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, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 3, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
a: Virion-associated phage protein
b: Virion-associated phage protein
c: Virion-associated phage protein
d: Virion-associated phage protein
e: Virion-associated phage protein
f: Virion-associated phage protein
g: Virion-associated phage protein
h: Virion-associated phage protein
i: Virion-associated phage protein
j: Virion-associated phage protein
A: rope protein of phage GP4
D: Virion-associated phage protein
B: Virion-associated phage protein
C: Virion-associated phage protein


Theoretical massNumber of molelcules
Total (without water)183,56414
Polymers183,56414
Non-polymers00
Water00
1
a: Virion-associated phage protein
b: Virion-associated phage protein
c: Virion-associated phage protein
d: Virion-associated phage protein
e: Virion-associated phage protein
f: Virion-associated phage protein
g: Virion-associated phage protein
h: Virion-associated phage protein
i: Virion-associated phage protein
j: Virion-associated phage protein
A: rope protein of phage GP4
D: Virion-associated phage protein
B: Virion-associated phage protein
C: Virion-associated phage protein
x 5


Theoretical massNumber of molelcules
Total (without water)917,82170
Polymers917,82170
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
SymmetryPoint symmetry: (Schoenflies symbol: C5 (5 fold cyclic))

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Components

#1: Protein
Virion-associated phage protein / gp80


Mass: 14360.909 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Ralstonia phage GP4 (virus) / References: UniProt: A0A345GU11
#2: Protein rope protein of phage GP4


Mass: 10230.603 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ralstonia phage GP4 (virus)
#3: Protein Virion-associated phage protein / gp77


Mass: 9908.155 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Ralstonia phage GP4 (virus) / References: UniProt: A0A345GU08

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ralstonia phage GP4 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Ralstonia phage GP4 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3800 nm / Nominal defocus min: 100 nm
Image recordingElectron dose: 35 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 39883 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00312720
ELECTRON MICROSCOPYf_angle_d0.66817469
ELECTRON MICROSCOPYf_dihedral_angle_d4.8891839
ELECTRON MICROSCOPYf_chiral_restr0.0462068
ELECTRON MICROSCOPYf_plane_restr0.0072308

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