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- EMDB-14484: Central part (C10) of bacteriophage SU10 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-14484
TitleCentral part (C10) of bacteriophage SU10 capsid
Map data
Sample
  • Virus: Escherichia phage vB_EcoP_SU10 (virus)
    • Protein or peptide: Major head protein
Function / homologyProtein of unknown function DUF5309 / Family of unknown function (DUF5309) / Major head protein
Function and homology information
Biological speciesEscherichia phage vB_EcoP_SU10 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 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 24, 2022-
Map releaseAug 24, 2022-
UpdateOct 12, 2022-
Current statusOct 12, 2022Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14484.png

Downloads & links

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Map

FileDownload / File: emd_14484.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.38 Å
Density
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.058085766 - 0.12626915
Average (Standard dev.)0.0005285299 (±0.006738944)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 706.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_14484_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_14484_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

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 head 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: No
Host (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 9.257 MDa

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Macromolecule #1: Major head protein

MacromoleculeName: Major head protein / type: protein_or_peptide / ID: 1 / Number of copies: 24 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage vB_EcoP_SU10 (virus)
Molecular weightTheoretical: 38.616457 KDa
SequenceString: MANPTLFVSY DQNGKKLSFA NWISVLSPQD TPFVSMTGKE SINQTIFSWQ TDALASVDGN NAHVEGSRAE DGEMKPTVIK SNVTQILRK VVRVSDTANT TANYGRGREL MYQLEKKGKE IKRDLEKILL SGQARTDVLA DQYLTNSAAD PAVAGLNDTH A ARKTGAFQ ...String:
MANPTLFVSY DQNGKKLSFA NWISVLSPQD TPFVSMTGKE SINQTIFSWQ TDALASVDGN NAHVEGSRAE DGEMKPTVIK SNVTQILRK VVRVSDTANT TANYGRGREL MYQLEKKGKE IKRDLEKILL SGQARTDVLA DQYLTNSAAD PAVAGLNDTH A ARKTGAFQ FLCAHGGLAG GVVDKTKNGP ADPDTGAVTV KVAQNASNPT TNIGFDEADI FDMTLQLYTA GSEADIIMIN PA HAKIFAG LQENTQGSRK RIFENTKQFI YEVNSITDPL GQSYKIIVNR WMPTDAVYFF RSADWTQMVL RAPKRTELAK DGS YEKWMI EMEVGLRHRN PYASGVLFTA AGKAAA

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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 chloridesodium 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 - Atmosphere: OTHER
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
DetailsPFU 10^11

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Average exposure time: 1.0 sec. / Average electron dose: 49.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 25689
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: OTHER / Details: SGD
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 3.1)
Final 3D classificationSoftware - Name: RELION (ver. 3)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Point group: D10 (2x10 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 25689
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-7z45:
Central part (C10) of bacteriophage SU10 capsid

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