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- EMDB-14491: Assymetric reconstruction of bacteriophage SU10 genome release in... -

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Basic information

Entry
Database: EMDB / ID: EMD-14491
TitleAssymetric reconstruction of bacteriophage SU10 genome release intermediate capsid cap
Map data
Sample
  • Virus: Escherichia phage vB_EcoP_SU10 (virus)
    • Protein or peptide: major capsid protein
Keywordsbacteriophage / capsid / assymetric / VIRUS
Biological speciesEscherichia phage vB_EcoP_SU10 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.3 Å
AuthorsSiborova M / Fuzik T / Prochazkova M / Novacek J / Plevka P
Funding support Czech Republic, 1 items
OrganizationGrant numberCountry
Ministry of Education, Youth and Sports of the Czech RepublicLL1906 Czech Republic
CitationJournal: Nat Commun / Year: 2022
Title: Tail proteins of phage SU10 reorganize into the nozzle for genome delivery.
Authors: Marta Šiborová / Tibor Füzik / Michaela Procházková / Jiří Nováček / Martin Benešík / Anders S Nilsson / Pavel Plevka /
Abstract: Escherichia coli phage SU10 belongs to the genus Kuravirus from the class Caudoviricetes of phages with short non-contractile tails. In contrast to other short-tailed phages, the tails of Kuraviruses ...Escherichia coli phage SU10 belongs to the genus Kuravirus from the class Caudoviricetes of phages with short non-contractile tails. In contrast to other short-tailed phages, the tails of Kuraviruses elongate upon cell attachment. Here we show that the virion of SU10 has a prolate head, containing genome and ejection proteins, and a tail, which is formed of portal, adaptor, nozzle, and tail needle proteins and decorated with long and short fibers. The binding of the long tail fibers to the receptors in the outer bacterial membrane induces the straightening of nozzle proteins and rotation of short tail fibers. After the re-arrangement, the nozzle proteins and short tail fibers alternate to form a nozzle that extends the tail by 28 nm. Subsequently, the tail needle detaches from the nozzle proteins and five types of ejection proteins are released from the SU10 head. The nozzle with the putative extension formed by the ejection proteins enables the delivery of the SU10 genome into the bacterial cytoplasm. It is likely that this mechanism of genome delivery, involving the formation of the tail nozzle, is employed by all Kuraviruses.
History
DepositionMar 3, 2022-
Header (metadata) releaseAug 10, 2022-
Map releaseAug 10, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14491.png

Downloads & links

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Map

FileDownload / File: emd_14491.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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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 256 pix.
= 343.04 Å		1.34 Å/pix.
x 256 pix.
= 343.04 Å		1.34 Å/pix.
x 256 pix.
= 343.04 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.011347943 - 0.025712011
Average (Standard dev.)0.00059967255 (±0.0023190475)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 343.04 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_14491_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

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Half map: #1

Fileemd_14491_half_map_2.map
Projections & Slices
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Histogram (log scale)

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Sample components

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Entire : Escherichia phage vB_EcoP_SU10

EntireName: Escherichia phage vB_EcoP_SU10 (virus)
Components
  • Virus: Escherichia phage vB_EcoP_SU10 (virus)
    • Protein or peptide: major capsid protein

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Supramolecule #1: Escherichia phage vB_EcoP_SU10

SupramoleculeName: Escherichia phage vB_EcoP_SU10 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 1519788 / Sci species name: Escherichia phage vB_EcoP_SU10 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 3 MDa
Virus shellShell ID: 1 / Name: Capsid cap assymetric

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Macromolecule #1: major capsid protein

MacromoleculeName: major capsid protein / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage vB_EcoP_SU10 (virus)
SequenceString: MANPTLFVSY DQNGKKLSFA NWISVLSPQD TPFVSMTGKE SINQ TIFSW QTDALASVDG NNAHVEGSRA EDGEMKPTVI KSNVTQILRK VVRVSDTANT TAN YGRGRE LMYQLEKKGK EIKRDLEKIL LSGQARTDVL ADQYLTNSAA DPAVAGLNDT HA ARKTGAF ...String:
MANPTLFVSY DQNGKKLSFA NWISVLSPQD TPFVSMTGKE SINQ TIFSW QTDALASVDG NNAHVEGSRA EDGEMKPTVI KSNVTQILRK VVRVSDTANT TAN YGRGRE LMYQLEKKGK EIKRDLEKIL LSGQARTDVL ADQYLTNSAA DPAVAGLNDT HA ARKTGAF QFLCAHGGLA GGVVDKTKNG PADPDTGAVT VKVAQNASNP TTNIGFDEAD I FDMTLQLY TAGSEADIIM INPAHAKIFA GLQENTQGSR KRIFENTKQF IYEVNSITDP LGQSYKIIV NRWMPTDAVY FFRSADWTQM VLRAPKRTEL AKDGSYEKWM IEMEVGLRH RNPYASGVLF TAAGKAAA

GENBANK: GENBANK: NC_027395.1

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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: 8
Component:
ConcentrationFormulaName
50.0 mMTristris
10.0 mMNaClsodium chloride
10.0 mMCaCl2calcium chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
DetailsPFU 10^11

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Average exposure time: 8.0 sec. / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 10500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 11780
Startup modelType of model: OTHER / Details: SGD
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 5974
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL

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