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- PDB-7ypx: Cyanophage Pam3 fiber -

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Basic information

Entry
Database: PDB / ID: 7ypx
TitleCyanophage Pam3 fiber
Components
  • Pam3 tail fiber proreins
  • tail fiber chaperone
KeywordsVIRAL PROTEIN / fiber / VIRUS
Biological speciesuncultured cyanophage (environmental samples)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsWei, Z.L. / Jiang, Y.L. / Zhou, C.Z.
Funding support China, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFA0903100 China
CitationJournal: Viruses / Year: 2022
Title: Structural Insights into the Chaperone-Assisted Assembly of a Simplified Tail Fiber of the Myocyanophage Pam3.
Authors: Zi-Lu Wei / Feng Yang / Bo Li / Pu Hou / Wen-Wen Kong / Jie Wang / Yuxing Chen / Yong-Liang Jiang / Cong-Zhao Zhou /
Abstract: At the first step of phage infection, the receptor-binding proteins (RBPs) such as tail fibers are responsible for recognizing specific host surface receptors. The proper folding and assembly of tail ...At the first step of phage infection, the receptor-binding proteins (RBPs) such as tail fibers are responsible for recognizing specific host surface receptors. The proper folding and assembly of tail fibers usually requires a chaperone encoded by the phage genome. Despite extensive studies on phage structures, the molecular mechanism of phage tail fiber assembly remains largely unknown. Here, using a minimal myocyanophage, termed Pam3, isolated from Lake Chaohu, we demonstrate that the chaperone gp25 forms a stable complex with the tail fiber gp24 at a stoichiometry of 3:3. The 3.1-Å cryo-electron microscopy structure of this complex revealed an elongated structure with the gp25 trimer embracing the distal moieties of gp24 trimer at the center. Each gp24 subunit consists of three domains: the N-terminal α-helical domain required for docking to the baseplate, the tumor necrosis factor (TNF)-like and glycine-rich domains responsible for recognizing the host receptor. Each gp25 subunit consists of two domains: a non-conserved N-terminal β-sandwich domain that binds to the TNF-like and glycine-rich domains of the fiber, and a C-terminal α-helical domain that mediates trimerization/assembly of the fiber. Structural analysis enabled us to propose the assembly mechanism of phage tail fibers, in which the chaperone first protects the intertwined and repetitive distal moiety of each fiber subunit, further ensures the proper folding of these highly plastic structural elements, and eventually enables the formation of the trimeric fiber. These findings provide the structural basis for the design and engineering of phage fibers for biotechnological applications.
History
DepositionAug 4, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 9, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pam3 tail fiber proreins
B: Pam3 tail fiber proreins
C: Pam3 tail fiber proreins
a: tail fiber chaperone
b: tail fiber chaperone
c: tail fiber chaperone


Theoretical massNumber of molelcules
Total (without water)137,5256
Polymers137,5256
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Pam3 tail fiber proreins


Mass: 28383.873 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: The source organism is the myocyanophage Pam3 isolated from the Lake Chaohu, China.
Source: (gene. exp.) uncultured cyanophage (environmental samples)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#2: Protein tail fiber chaperone


Mass: 17457.660 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: The source organism is the myocyanophage Pam3 isolated from the Lake Chaohu, China.
Source: (gene. exp.) uncultured cyanophage (environmental samples)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)

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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: Pam3 tail fiber / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: uncultured cyanophage (environmental samples)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 300 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 243989 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049000
ELECTRON MICROSCOPYf_angle_d0.54812279
ELECTRON MICROSCOPYf_dihedral_angle_d4.1061299
ELECTRON MICROSCOPYf_chiral_restr0.0431347
ELECTRON MICROSCOPYf_plane_restr0.0041662

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