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- PDB-7z47: Tail of bacteriophage SU10 -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 7z47
TitleTail of bacteriophage SU10
Components
  • Adaptor protein
  • Putative structural protein
  • Putative tail fiber
  • Surface protein
KeywordsVIRUS / bacteriophage / tail / base plate / nozzle / tail fibers
Function / homology
Function and homology information


: / Baseplate structural protein Gp10, C-terminal domain / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Putative tail fiber / Surface protein / Uncharacterized protein / Putative structural protein
Similarity search - Component
Biological speciesEscherichia phage vB_EcoP_SU10 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 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 10, 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
Revision 1.2Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)506,4769
Polymers506,4769
Non-polymers00
Water00
1
A: Adaptor protein
B: Adaptor protein
G: Surface protein
D: Putative tail fiber
E: Putative tail fiber
F: Putative tail fiber
I: Putative structural protein
H: Putative structural protein
C: Putative structural protein
x 6


Theoretical massNumber of molelcules
Total (without water)3,038,85654
Polymers3,038,85654
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5

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Components

#1: 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
#2: Protein Surface protein


Mass: 110352.617 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Nozzle protein / Source: (natural) Escherichia phage vB_EcoP_SU10 (virus) / References: UniProt: A0A0B4N0C1
#3: Protein Putative tail fiber


Mass: 83558.227 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: Long tail fiber / Source: (natural) Escherichia phage vB_EcoP_SU10 (virus) / References: UniProt: A0A0B4N0B9
#4: Protein Putative structural protein


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

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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: NO / 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 chlorideNaCl1
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 FIELD / 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: 49 e/Å2 / Detector mode: COUNTING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1
Image scansMovie frames/image: 40

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Processing

Software
NameVersionClassification
phenix.real_space_refinedev_3700refinement
PHENIXdev_3700refinement
EM software
IDNameVersionCategory
2EPUimage acquisition
4Gctf1.06CTF correction
7Cootmodel fitting
9PHENIXmodel refinement
10ISOLDEmodel refinement
11RELION3.1initial Euler assignment
12RELION3.1final Euler assignment
13RELION3classification
14RELION3.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 25600
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19111 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 48.71 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002415151
ELECTRON MICROSCOPYf_angle_d0.467920620
ELECTRON MICROSCOPYf_chiral_restr0.04712328
ELECTRON MICROSCOPYf_plane_restr0.0032688
ELECTRON MICROSCOPYf_dihedral_angle_d31.71572024

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