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- EMDB-42163: ssRNA phage PhiCb5 virion -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-42163
TitlessRNA phage PhiCb5 virion
Map datamap
Sample
  • Complex: A complex of phiCb5 maturation protein and phiCb5 shell
    • Protein or peptide: Coat protein
    • Protein or peptide: Maturation protein
  • Ligand: CALCIUM ION
KeywordsssRNA phage / VIRUS
Function / homologyPhage phiCb5, coat protein / Assembly protein / Phage maturation protein / virion attachment to host cell pilus / virion component / viral capsid / Maturation protein / Coat protein
Function and homology information
Biological speciesCaulobacter vibrioides (bacteria) / Caulobacter phage phiCb5 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsWang Y / Zhang J
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1R01GM141659 United States
CitationJournal: Sci Adv / Year: 2024
Title: Structural mechanisms of Tad pilus assembly and its interaction with an RNA virus.
Authors: Yuhang Wang / Matthew Theodore / Zhongliang Xing / Utkarsh Narsaria / Zihao Yu / Lanying Zeng / Junjie Zhang /
Abstract: Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle regulation. Unlike other type IV ... Tad (tight adherence) pili, part of the type IV pili family, are crucial for mechanosensing, surface adherence, bacteriophage (phage) adsorption, and cell-cycle regulation. Unlike other type IV pilins, Tad pilins lack the typical globular β sheet domain responsible for pilus assembly and phage binding. The mechanisms of Tad pilus assembly and its interaction with phage ΦCb5 have been elusive. Using cryo-electron microscopy, we unveiled the Tad pilus assembly mechanism, featuring a unique network of hydrogen bonds at its core. We then identified the Tad pilus binding to the ΦCb5 maturation protein (Mat) through its β region. Notably, the amino terminus of ΦCb5 Mat is exposed outside the capsid and phage/pilus interface, enabling the attachment of fluorescent and affinity tags. These engineered ΦCb5 virions can be efficiently assembled and purified in , maintaining infectivity against , which presents promising applications, including RNA delivery and phage display.
History
DepositionOct 1, 2023-
Header (metadata) releaseMay 15, 2024-
Map releaseMay 15, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42163.png

Downloads & links

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Map

FileDownload / File: emd_42163.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 512 pix.
= 440.32 Å		0.86 Å/pix.
x 512 pix.
= 440.32 Å		0.86 Å/pix.
x 512 pix.
= 440.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0334
Minimum - Maximum-0.0049704043 - 1.7943912
Average (Standard dev.)0.006223467 (±0.056497477)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 440.32 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half

Fileemd_42163_half_map_1.map
Annotationhalf
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half

Fileemd_42163_half_map_2.map
Annotationhalf
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A complex of phiCb5 maturation protein and phiCb5 shell

EntireName: A complex of phiCb5 maturation protein and phiCb5 shell
Components
  • Complex: A complex of phiCb5 maturation protein and phiCb5 shell
    • Protein or peptide: Coat protein
    • Protein or peptide: Maturation protein
  • Ligand: CALCIUM ION

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Supramolecule #1: A complex of phiCb5 maturation protein and phiCb5 shell

SupramoleculeName: A complex of phiCb5 maturation protein and phiCb5 shell
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: A complex of phiCb5 maturation protein and phiCb5 shell
Source (natural)Organism: Caulobacter vibrioides (bacteria)
Molecular weightTheoretical: 2.1 MDa

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Macromolecule #1: Coat protein

MacromoleculeName: Coat protein / type: protein_or_peptide / ID: 1 / Number of copies: 178 / Enantiomer: LEVO
Source (natural)Organism: Caulobacter phage phiCb5 (virus)
Molecular weightTheoretical: 13.498981 KDa
SequenceString:
ALGDTLTITL GGSGGTAKVL RKINQDGYTS EYYLPETSSS FRAKVRHTKE SVKPNQVQYE RHNVEFTETV YASGSTPEFV RQAYVVIRH KVGDVSATVS DLGEALSFYL NEALYGKLIG WES

UniProtKB: Coat protein

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Macromolecule #2: Maturation protein

MacromoleculeName: Maturation protein / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Caulobacter phage phiCb5 (virus)
Molecular weightTheoretical: 40.725336 KDa
SequenceString: MARIRNRSSI ASSGMSTFYL FGTPIVNEEI IVRNTEWCSD VIGNPGDNPL DIHKQEWTIK PLSGQIIFGS GTYRSLQCPP EYCRGASLS HLSLPSQSGL GTTALARTNP SRPAFNLPAF IGELRDLPRM FKIAGDTMLR KGANAFLSYQ FGWKPLISDI S KALDFSAT ...String:
MARIRNRSSI ASSGMSTFYL FGTPIVNEEI IVRNTEWCSD VIGNPGDNPL DIHKQEWTIK PLSGQIIFGS GTYRSLQCPP EYCRGASLS HLSLPSQSGL GTTALARTNP SRPAFNLPAF IGELRDLPRM FKIAGDTMLR KGANAFLSYQ FGWKPLISDI S KALDFSAT VRTRSDEWHR LYSNGGLKRR INLGVDIEQK KENDVVLHSS NGFVVASHTV ITVRKTWATV RWRPDAGSLP PI TKSSSEK HARALLGLGV GGLIEGAWQL MPWSWMVDWF GNVGTFLQAS NNTIGASPGL VNIMTTTTTN HQFSVKRDLS DGW IKGGDC SATVTSKARS QSSGPTITAS IPNLSGRQLS ILGALGIQRV PRHLLR

UniProtKB: Maturation protein

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 236 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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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
Component:
ConcentrationFormulaName
2.0 mMMgCl2Magnesium chloride
20.0 mMC4H11NO3Tris
3.0 mMCaCl2Calcium chloride

Details: 20mM tris, 2mM MgCl2, 3mM CaCl2
GridModel: C-flat-2/1
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 25.0 µm / Nominal defocus min: 5.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 272204
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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