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- PDB-7z4f: Tail of phage SU10 genome release intermediate -

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Basic information

Entry
Database: PDB / ID: 7z4f
TitleTail of phage SU10 genome release intermediate
Components
  • Adaptor protein
  • Portal protein
  • Putative structural proteinProtein
  • Putative tail fiber
  • Surface proteinCell membrane
KeywordsVIRUS / bacteriophage / tail / base plate / nozzle / tail fibers
Function / homologyInvasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Putative tail fiber / Surface protein / Portal protein / Uncharacterized protein / Putative structural protein
Function and homology information
Biological speciesEscherichia phage vB_EcoP_SU10 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsSiborova, M. / Fuzik, T. / Prochazkova, M. / Novacek, J. / Plevka, P.
Funding support Czech Republic, 1items
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, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 17, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative structural protein
B: Putative structural protein
C: Putative structural protein
D: Putative tail fiber
E: Putative tail fiber
F: Putative tail fiber
I: Adaptor protein
H: Adaptor protein
G: Surface protein
K: Portal protein
J: Portal protein


Theoretical massNumber of molelcules
Total (without water)676,58711
Polymers676,58711
Non-polymers00
Water0
1
A: Putative structural protein
B: Putative structural protein
C: Putative structural protein
D: Putative tail fiber
E: Putative tail fiber
F: Putative tail fiber
I: Adaptor protein
H: Adaptor protein
G: Surface protein
K: Portal protein
J: Portal protein
x 6


Theoretical massNumber of molelcules
Total (without water)4,059,52066
Polymers4,059,52066
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5

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Components

#1: Protein Putative structural protein / Protein


Mass: 29258.613 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage vB_EcoP_SU10 (virus) / References: UniProt: A0A0B4N235
#2: Protein Putative tail fiber


Mass: 83558.227 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Escherichia phage vB_EcoP_SU10 (virus) / References: UniProt: A0A0B4N0B9
#3: Protein Adaptor protein


Mass: 28836.395 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia phage vB_EcoP_SU10 (virus) / References: UniProt: A0A0B4N231
#4: Protein Surface protein / Cell membrane


Mass: 110352.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Escherichia phage vB_EcoP_SU10 (virus) / References: UniProt: A0A0B4N0C1
#5: Protein Portal protein


Mass: 85055.344 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Escherichia phage vB_EcoP_SU10 (virus) / References: UniProt: A0A0B4N229

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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: Escherichia phage vB_EcoP_SU10 / Type: VIRUS / Entity ID: all / Source: NATURAL
Molecular weightValue: 3.036 MDa / Experimental value: NO
Source (natural)Organism: Escherichia phage vB_EcoP_SU10 (virus)
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Escherichia coli
Virus shellName: Tail complex
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
150 mMtrisTris1
210 mMsodium chlorideNaClSodium chloride1
310 mMcalcium chlorideCaCl21
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: PFU 10^11
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 59000 X / Nominal defocus max: 2700 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1 sec. / Electron dose: 52 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1
Image scansMovie frames/image: 40

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM software
IDNameVersionCategory
2SerialEMimage acquisition
4Gctf1.06CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10ISOLDEmodel refinement
11RELION3.1initial Euler assignment
12RELION3.1final Euler assignment
13RELION3.1classification
14RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 11780
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8076 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00225206
ELECTRON MICROSCOPYf_angle_d0.62433877
ELECTRON MICROSCOPYf_dihedral_angle_d4.6613719
ELECTRON MICROSCOPYf_chiral_restr0.0433311
ELECTRON MICROSCOPYf_plane_restr0.0054704

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