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- EMDB-43109: Asymmetric unit of bacteriophage PhiM1 mature capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-43109
TitleAsymmetric unit of bacteriophage PhiM1 mature capsid
Map data
Sample
  • Virus: Pectobacterium phage PhiM1 (virus)
    • Protein or peptide: Major capsid protein (gp38)
    • Protein or peptide: Alpha-claw decoration protein (gp44)
    • Protein or peptide: Alpha-paw decoration protein (gp43)
KeywordsMature capsid / Bacteriophage / Decoration protein / alpha-claw / VIRUS
Function / homologyPutative capsid protein / Uncharacterized protein / Uncharacterized protein
Function and homology information
Biological speciesPectobacterium phage PhiM1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.04 Å
AuthorsEruera A / Hodgkinson-Bean J
Funding support New Zealand, 1 items
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, 2023-
Header (metadata) releaseOct 23, 2024-
Map releaseOct 23, 2024-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43109.png

Downloads & links

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Map

FileDownload / File: emd_43109.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 700 pix.
= 980. Å		1.4 Å/pix.
x 700 pix.
= 980. Å		1.4 Å/pix.
x 700 pix.
= 980. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.5830078 - 3.284967
Average (Standard dev.)0.0077206264 (±0.16179699)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions700700700
Spacing700700700
CellA=B=C: 980.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_43109_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43109_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 : Pectobacterium phage PhiM1

EntireName: Pectobacterium phage PhiM1 (virus)
Components
  • Virus: Pectobacterium phage PhiM1 (virus)
    • Protein or peptide: Major capsid protein (gp38)
    • Protein or peptide: Alpha-claw decoration protein (gp44)
    • Protein or peptide: Alpha-paw decoration protein (gp43)

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Supramolecule #1: Pectobacterium phage PhiM1

SupramoleculeName: Pectobacterium phage PhiM1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Phage sample produced from natural infection of Pectobacterium atrosepticum
NCBI-ID: 1211386 / Sci species name: Pectobacterium phage PhiM1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Pectobacterium atrosepticum (bacteria)
Virus shellShell ID: 1 / Name: Capsid / Diameter: 635.0 Å / T number (triangulation number): 7

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Macromolecule #1: Major capsid protein (gp38)

MacromoleculeName: Major capsid protein (gp38) / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Pectobacterium phage PhiM1 (virus)
Molecular weightTheoretical: 36.44877 KDa
SequenceString: MSDTPYKADL SRVHWAGSNS DVDIHLEIFE GDVDSGFMYN SFFRGNSSYV SVQDQSNQAR IDRMNTVTIK GRTPGQKLDR ESVKNDKLV ITVDTVTYAS TVMDWQDDWT SPDRWAEIGA QHGYQHARLF DTAHLIQIIK ARKWIAPADL KPAFFDGKEY T AAYNADRE ...String:
MSDTPYKADL SRVHWAGSNS DVDIHLEIFE GDVDSGFMYN SFFRGNSSYV SVQDQSNQAR IDRMNTVTIK GRTPGQKLDR ESVKNDKLV ITVDTVTYAS TVMDWQDDWT SPDRWAEIGA QHGYQHARLF DTAHLIQIIK ARKWIAPADL KPAFFDGKEY T AAYNADRE LFAANIIDAH RQGIEEMVRR DLGGSLTEFI TVVSPYVFGL LLDSKKLVNV DYSAGNGNFA ERRVGMVNGV RI VESARFP AAAGTSPLGA AFTVDADDVA CQMVVYHPKM TLVTVEAKPL ATNKYPDNPN FSDILDSFTL YTVGQRRPDT SFA VKLTNL P

UniProtKB: Putative capsid protein

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Macromolecule #2: Alpha-claw decoration protein (gp44)

MacromoleculeName: Alpha-claw decoration protein (gp44) / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Pectobacterium phage PhiM1 (virus)
Molecular weightTheoretical: 6.334274 KDa
SequenceString:
MAITTGTTEA QALNMTMRDA VLKVAPGVQQ LVQNSSQLTA AEIAIIQTNI TALKAAFTAA GA

UniProtKB: Uncharacterized protein

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Macromolecule #3: Alpha-paw decoration protein (gp43)

MacromoleculeName: Alpha-paw decoration protein (gp43) / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Pectobacterium phage PhiM1 (virus)
Molecular weightTheoretical: 17.263197 KDa
SequenceString:
MSLVTATAAQ RIALRNTATN LSEQTQVYAQ SATAPTAAEA AIVQPYIDAA QAAITAVGAG GATVANGATV AVVNSASADS HNATATVTG TTLTNVKLAA TVAFVDNADT ITVQNSAGTA VAGTHTATVA AGVISNVKLA ATIAPVASGL ALTGVTPTGT Y TNTVTFTV AAGVITAIVL S

UniProtKB: Uncharacterized protein

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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: 7.4 / Details: 10 mM Tris-HCl, 10 mM MgSO4, 0.01% w/v gelatine
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: 45 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5279
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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