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- EMDB-34017: Cyanophage Pam3 fiber -

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Basic information

Entry
Database: EMDB / ID: EMD-34017
TitleCyanophage Pam3 fiber
Map data
Sample
  • Complex: Pam3 tail fiber
    • Protein or peptide: Pam3 tail fiber proreins
    • Protein or peptide: tail fiber chaperone
Keywordsfiber / VIRUS / VIRAL PROTEIN
Biological speciesuncultured cyanophage (environmental samples)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.12 Å
AuthorsWei ZL / Jiang YL / Zhou CZ
Funding support China, 1 items
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, 2022-
Header (metadata) releaseNov 9, 2022-
Map releaseNov 9, 2022-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34017.png

Downloads & links

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Map

FileDownload / File: emd_34017.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.39052615 - 1.2220985
Average (Standard dev.)0.0011998214 (±0.03308488)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_34017_half_map_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_34017_half_map_2.map
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Sample components

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Entire : Pam3 tail fiber

EntireName: Pam3 tail fiber
Components
  • Complex: Pam3 tail fiber
    • Protein or peptide: Pam3 tail fiber proreins
    • Protein or peptide: tail fiber chaperone

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Supramolecule #1: Pam3 tail fiber

SupramoleculeName: Pam3 tail fiber / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: uncultured cyanophage (environmental samples)

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Macromolecule #1: Pam3 tail fiber proreins

MacromoleculeName: Pam3 tail fiber proreins / type: protein_or_peptide / ID: 1
Details: The source organism is the myocyanophage Pam3 isolated from the Lake Chaohu, China.
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: uncultured cyanophage (environmental samples)
Molecular weightTheoretical: 28.383873 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: HHHHHHSSGM ASINLPFSLS GSKRIPTSEE LADGYQCGPL DVELDNWLMW WLTGQVDGVI EGAGLTTDDT DLARLYKAIQ SMTSGNLRT VVLTAASGNL PIPSDVSVLN WVRAVGGGGA GGNSNTGNSK ASGGGGGAGF DRFNVAVTPG SNVPYTVGAA G AVNGLGAG ...String:
HHHHHHSSGM ASINLPFSLS GSKRIPTSEE LADGYQCGPL DVELDNWLMW WLTGQVDGVI EGAGLTTDDT DLARLYKAIQ SMTSGNLRT VVLTAASGNL PIPSDVSVLN WVRAVGGGGA GGNSNTGNSK ASGGGGGAGF DRFNVAVTPG SNVPYTVGAA G AVNGLGAG YNGGAGGSTA ILGTTAGGGA GGLGVNNNAT AVQVNGGTTS GTTPEISYPG GLGTEGIVGT GGGSVLSQPT QR AFTNAGN NNPANSWGGG GPGGSDFGGA WQPGGVGKQG IIIVQYFSRF AP

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Macromolecule #2: tail fiber chaperone

MacromoleculeName: tail fiber chaperone / type: protein_or_peptide / ID: 2
Details: The source organism is the myocyanophage Pam3 isolated from the Lake Chaohu, China.
Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: uncultured cyanophage (environmental samples)
Molecular weightTheoretical: 17.45766 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MTDKHYARVV DGLVVETKTL PADFNLDDLF GPDHGWVEAP LEVEQGWRKV GAKFAPAPPP ERDPASILAG LKAEASRHIF ATISATAQS NLLLAVGLAS AKAPSARTPE ERDLLNVADE GRAWIDAVRA RVHALAEHDG VTPKGEDRWP APSEAVLEMA A KF

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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
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 300 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.12 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 243989
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT

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