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- PDB-8vb0: Asymmetric unit of bacteriophage PhiM1 mature capsid -

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Basic information

Entry
Database: PDB / ID: 8vb0
TitleAsymmetric unit of bacteriophage PhiM1 mature capsid
Components
  • Alpha-claw decoration protein (gp44)
  • Alpha-paw decoration protein (gp43)
  • Major capsid protein (gp38)
KeywordsVIRUS / Mature capsid / Bacteriophage / Decoration protein / alpha-claw
Function / homologyPutative capsid protein / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesPectobacterium phage PhiM1 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsEruera, A. / Hodgkinson-Bean, J.
Funding support New Zealand, 1items
OrganizationGrant numberCountry
Other private New Zealand
CitationJournal: PNAS Nexus / Year: 2024
Title: Ejectosome of bacteriophage ΦM1.
Authors: Alice-Roza Eruera / James Hodgkinson-Bean / Georgia L Rutter / Francesca R Hills / Rosheny Kumaran / Alexander J M Crowe / Nickhil Jadav / Fangfang Chang / Klemens McJarrow-Keller / Fátima ...Authors: Alice-Roza Eruera / James Hodgkinson-Bean / Georgia L Rutter / Francesca R Hills / Rosheny Kumaran / Alexander J M Crowe / Nickhil Jadav / Fangfang Chang / Klemens McJarrow-Keller / Fátima Jorge / Jaekyung Hyun / Hyejin Kim / Bumhan Ryu / Mihnea Bostina /
Abstract: Podophages that infect gram-negative bacteria, such as pathogen ΦM1, encode tail assemblies too short to extend across the complex gram-negative cell wall. To overcome this, podophages encode a ...Podophages that infect gram-negative bacteria, such as pathogen ΦM1, encode tail assemblies too short to extend across the complex gram-negative cell wall. To overcome this, podophages encode a large protein complex (ejectosome) packaged inside the viral capsid and correspondingly ejected during infection to form a transient channel that spans the periplasmic space. Here, we describe the ejectosome of bacteriophage ΦM1 to a resolution of 3.32 Å by single-particle cryo-electron microscopy (cryo-EM). The core consists of tetrameric and octameric ejection proteins which form a ∼1.5-MDa ejectosome that must transition through the ∼30 Å aperture created by the short tail nozzle assembly that acts as the conduit for the passage of DNA during infection. The ejectosome forms several grooves into which coils of genomic DNA are fit before the DNA sharply turns and goes down the tunnel and into the portal. In addition, we reconstructed the icosahedral capsid and hybrid tail apparatus to resolutions between 3.04 and 3.23 Å, and note an uncommon fold adopted by the dimerized decoration proteins which further emphasize the structural diversity of podophages. These reconstructions have allowed the generation of a complete atomic model of the ΦM1, uncovering two distinct decoration proteins and highlighting the exquisite structural diversity of tailed bacteriophages.
History
DepositionDec 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major capsid protein (gp38)
B: Major capsid protein (gp38)
C: Major capsid protein (gp38)
D: Major capsid protein (gp38)
E: Major capsid protein (gp38)
F: Major capsid protein (gp38)
G: Major capsid protein (gp38)
H: Alpha-claw decoration protein (gp44)
I: Alpha-claw decoration protein (gp44)
J: Alpha-paw decoration protein (gp43)
K: Alpha-claw decoration protein (gp44)
L: Alpha-claw decoration protein (gp44)
M: Alpha-claw decoration protein (gp44)
N: Alpha-paw decoration protein (gp43)


Theoretical massNumber of molelcules
Total (without water)321,33914
Polymers321,33914
Non-polymers00
Water00
1
A: Major capsid protein (gp38)
B: Major capsid protein (gp38)
C: Major capsid protein (gp38)
D: Major capsid protein (gp38)
E: Major capsid protein (gp38)
F: Major capsid protein (gp38)
G: Major capsid protein (gp38)
H: Alpha-claw decoration protein (gp44)
I: Alpha-claw decoration protein (gp44)
J: Alpha-paw decoration protein (gp43)
K: Alpha-claw decoration protein (gp44)
L: Alpha-claw decoration protein (gp44)
M: Alpha-claw decoration protein (gp44)
N: Alpha-paw decoration protein (gp43)
x 60


Theoretical massNumber of molelcules
Total (without water)19,280,349840
Polymers19,280,349840
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Major capsid protein (gp38)
B: Major capsid protein (gp38)
C: Major capsid protein (gp38)
D: Major capsid protein (gp38)
E: Major capsid protein (gp38)
F: Major capsid protein (gp38)
G: Major capsid protein (gp38)
H: Alpha-claw decoration protein (gp44)
I: Alpha-claw decoration protein (gp44)
J: Alpha-paw decoration protein (gp43)
K: Alpha-claw decoration protein (gp44)
L: Alpha-claw decoration protein (gp44)
M: Alpha-claw decoration protein (gp44)
N: Alpha-paw decoration protein (gp43)
x 5


  • icosahedral pentamer
  • 1.61 MDa, 70 polymers
Theoretical massNumber of molelcules
Total (without water)1,606,69670
Polymers1,606,69670
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Major capsid protein (gp38)
B: Major capsid protein (gp38)
C: Major capsid protein (gp38)
D: Major capsid protein (gp38)
E: Major capsid protein (gp38)
F: Major capsid protein (gp38)
G: Major capsid protein (gp38)
H: Alpha-claw decoration protein (gp44)
I: Alpha-claw decoration protein (gp44)
J: Alpha-paw decoration protein (gp43)
K: Alpha-claw decoration protein (gp44)
L: Alpha-claw decoration protein (gp44)
M: Alpha-claw decoration protein (gp44)
N: Alpha-paw decoration protein (gp43)
x 6


  • icosahedral 23 hexamer
  • 1.93 MDa, 84 polymers
Theoretical massNumber of molelcules
Total (without water)1,928,03584
Polymers1,928,03584
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
Major capsid protein (gp38)


Mass: 36448.770 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Pectobacterium phage PhiM1 (virus) / References: UniProt: A0A1P7WG08
#2: Protein
Alpha-claw decoration protein (gp44)


Mass: 6334.274 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Pectobacterium phage PhiM1 (virus) / References: UniProt: A0A1P7WG15
#3: Protein Alpha-paw decoration protein (gp43)


Mass: 17263.197 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pectobacterium phage PhiM1 (virus) / References: UniProt: A0A1P7WG13
Has protein modificationN

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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: Pectobacterium phage PhiM1 / Type: VIRUS
Details: Phage sample produced from natural infection of Pectobacterium atrosepticum
Entity ID: all / Source: NATURAL
Molecular weightUnits: MEGADALTONS / Experimental value: NO
Source (natural)Organism: Pectobacterium phage PhiM1 (virus)
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Pectobacterium atrosepticum
Virus shellName: Capsid / Diameter: 635 nm / Triangulation number (T number): 7
Buffer solutionpH: 7.4 / Details: 10 mM Tris-HCl, 10 mM MgSO4, 0.01% w/v gelatine
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 45 mA / Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5279 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT

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