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- PDB-7z49: The capsid of bacteriophage SU10. -

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Basic information

Entry
Database: PDB / ID: 7z49
TitleThe capsid of bacteriophage SU10.
ComponentsMajor head protein
KeywordsVIRUS / bacteriophage / capsid / major capsid 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)
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 1.0Oct 5, 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 1.2Nov 23, 2022Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Apr 19, 2023Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: Major head protein
AB: Major head protein
AC: Major head protein
AD: Major head protein
AE: Major head protein
AF: Major head protein
AG: Major head protein
AH: Major head protein
AI: Major head protein
AJ: Major head protein
AK: Major head protein
AL: Major head protein
AM: Major head protein
AN: Major head protein
AO: Major head protein
AP: Major head protein
AQ: Major head protein
AR: Major head protein
AS: Major head protein
AT: Major head protein
AU: Major head protein
AV: Major head protein
AW: Major head protein
AX: Major head protein
AY: Major head protein
AZ: Major head protein
BA: Major head protein
BB: Major head protein
BC: Major head protein
BD: Major head protein
BE: Major head protein
BF: Major head protein
BG: Major head protein
BH: Major head protein
BI: Major head protein
BJ: Major head protein
BK: Major head protein
BL: Major head protein
BM: Major head protein
BN: Major head protein
BO: Major head protein
BP: Major head protein
BQ: Major head protein
BR: Major head protein
BS: Major head protein
BT: Major head protein
BU: Major head protein
BV: Major head protein
BW: Major head protein
BX: Major head protein
BY: Major head protein
BZ: Major head protein
CA: Major head protein
CB: Major head protein
CC: Major head protein
CD: Major head protein
CE: Major head protein
CF: Major head protein
CG: Major head protein
CH: Major head protein
CI: Major head protein
CJ: Major head protein
CK: Major head protein
CL: Major head protein
CM: Major head protein
CN: Major head protein
CO: Major head protein
CP: Major head protein
CQ: Major head protein
CR: Major head protein
CS: Major head protein
CT: Major head protein
CU: Major head protein
CV: Major head protein
CW: Major head protein
CX: Major head protein
CY: Major head protein
CZ: Major head protein
DA: Major head protein
DB: Major head protein
DC: Major head protein
DD: Major head protein
DE: Major head protein
DF: Major head protein
DG: Major head protein
DH: Major head protein
DI: Major head protein
DJ: Major head protein
DK: Major head protein
DL: Major head protein
DM: Major head protein
DN: Major head protein
DO: Major head protein
DP: Major head protein
DQ: Major head protein


Theoretical massNumber of molelcules
Total (without water)3,668,56395
Polymers3,668,56395
Non-polymers00
Water00
1
AA: Major head protein
AB: Major head protein
AC: Major head protein
AD: Major head protein
AE: Major head protein
AF: Major head protein
AG: Major head protein
AH: Major head protein
AI: Major head protein
AJ: Major head protein
AK: Major head protein
AL: Major head protein
AM: Major head protein
AN: Major head protein
AO: Major head protein
AP: Major head protein
AQ: Major head protein
AR: Major head protein
AS: Major head protein
AT: Major head protein
AU: Major head protein
AV: Major head protein
AW: Major head protein
AX: Major head protein
AY: Major head protein
AZ: Major head protein
BA: Major head protein
BB: Major head protein
BC: Major head protein
BD: Major head protein
BE: Major head protein
BF: Major head protein
BG: Major head protein
BH: Major head protein
BI: Major head protein
BJ: Major head protein
BK: Major head protein
BL: Major head protein
BM: Major head protein
BN: Major head protein
BO: Major head protein
BP: Major head protein
BQ: Major head protein
BR: Major head protein
BS: Major head protein
BT: Major head protein
BU: Major head protein
BV: Major head protein
BW: Major head protein
x 10
BX: Major head protein
BY: Major head protein
BZ: Major head protein
CA: Major head protein
CB: Major head protein
CC: Major head protein
CD: Major head protein
CE: Major head protein
CF: Major head protein
CG: Major head protein
CH: Major head protein
CI: Major head protein
CJ: Major head protein
CK: Major head protein
CL: Major head protein
CM: Major head protein
CN: Major head protein
CO: Major head protein
CP: Major head protein
CQ: Major head protein
CR: Major head protein
CS: Major head protein
CT: Major head protein
CU: Major head protein
CV: Major head protein
CW: Major head protein
CX: Major head protein
CY: Major head protein
CZ: Major head protein
DA: Major head protein
DB: Major head protein
DC: Major head protein
DD: Major head protein
DE: Major head protein
DF: Major head protein
DG: Major head protein
DH: Major head protein
DI: Major head protein
DJ: Major head protein
DK: Major head protein
DL: Major head protein
DM: Major head protein
DN: Major head protein
DO: Major head protein
DP: Major head protein
DQ: Major head protein
x 5


  • defined by author
  • Evidence: electron microscopy, C10 sym, electron microscopy, C5 sym
  • 27.8 MDa, 720 polymers
Theoretical massNumber of molelcules
Total (without water)27,803,849720
Polymers27,803,849720
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_5552
point symmetry operation13

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Components

#1: Protein ...
Major head protein


Mass: 38616.457 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Source: (natural) Escherichia phage vB_EcoP_SU10 (virus) / References: UniProt: A0A0B4N1Q7
Has protein modificationY

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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: 27.6 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
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 II (4k x 4k) / Num. of grids imaged: 1
Image scansMovie frames/image: 40

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Processing

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: 25689
SymmetryPoint symmetry: C5 (5 fold cyclic)
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 9418 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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