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- EMDB-8689: Sinorhizobium meliloti Phage Phi M5 -

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Basic information

Entry
Database: EMDB / ID: EMD-8689
TitleSinorhizobium meliloti Phage Phi M5
Map dataS. Meliloti Phage Phi M5
SampleSinorhizobium meliloti Phage Phi M5 != Sinorhizobium meliloti

Sinorhizobium meliloti Phage Phi M5

  • Virus: Sinorhizobium meliloti (bacteria)
Biological speciesSinorhizobium meliloti (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsJohnson MC / Sena Valez M / Washburn BK / Lu S / Platt GN / Brewer TE / Lynn JS / Stroupe ME / Jones KM
CitationJournal: J Struct Biol / Year: 2017
Title: Structure, proteome and genome of Sinorhizobium meliloti phage ΦM5: A virus with LUZ24-like morphology and a highly mosaic genome.
Authors: Matthew C Johnson / Marta Sena-Velez / Brian K Washburn / Georgia N Platt / Stephen Lu / Tess E Brewer / Jason S Lynn / M Elizabeth Stroupe / Kathryn M Jones /
Abstract: Bacteriophages of nitrogen-fixing rhizobial bacteria are revealing a wealth of novel structures, diverse enzyme combinations and genomic features. Here we report the cryo-EM structure of the phage ...Bacteriophages of nitrogen-fixing rhizobial bacteria are revealing a wealth of novel structures, diverse enzyme combinations and genomic features. Here we report the cryo-EM structure of the phage capsid at 4.9-5.7Å-resolution, the phage particle proteome, and the genome of the Sinorhizobium meliloti-infecting Podovirus ΦM5. This is the first structure of a phage with a capsid and capsid-associated structural proteins related to those of the LUZ24-like viruses that infect Pseudomonas aeruginosa. Like many other Podoviruses, ΦM5 is a T=7 icosahedron with a smooth capsid and short, relatively featureless tail. Nonetheless, this group is phylogenetically quite distinct from Podoviruses of the well-characterized T7, P22, and epsilon 15 supergroups. Structurally, a distinct bridge of density that appears unique to ΦM5 reaches down the body of the coat protein to the extended loop that interacts with the next monomer in a hexamer, perhaps stabilizing the mature capsid. Further, the predicted tail fibers of ΦM5 are quite different from those of enteric bacteria phages, but have domains in common with other rhizophages. Genomically, ΦM5 is highly mosaic. The ΦM5 genome is 44,005bp with 357bp direct terminal repeats (DTRs) and 58 unique ORFs. Surprisingly, the capsid structural module, the tail module, the DNA-packaging terminase, the DNA replication module and the integrase each appear to be from a different lineage. One of the most unusual features of ΦM5 is its terminase whose large subunit is quite different from previously-described short-DTR-generating packaging machines and does not fit into any of the established phylogenetic groups.
History
DepositionApr 17, 2017-
Header (metadata) releaseMay 3, 2017-
Map releaseApr 25, 2018-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8689.png

Downloads & links

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Map

FileDownload / File: emd_8689.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationS. Meliloti Phage Phi M5
Voxel sizeX=Y=Z: 1.26 Å
Density
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.037418 - 0.09340415
Average (Standard dev.)0.00009753447 (±0.007466093)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-400-400-400
Dimensions800800800
Spacing800800800
CellA=B=C: 1008.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.261.261.26
M x/y/z800800800
origin x/y/z0.0000.0000.000
length x/y/z1008.0001008.0001008.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-400-400-400
NC/NR/NS800800800
D min/max/mean-0.0370.0930.000

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Supplemental data

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Sample components

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Entire : Sinorhizobium meliloti Phage Phi M5

EntireName: Sinorhizobium meliloti Phage Phi M5
Components
  • Virus: Sinorhizobium meliloti (bacteria)

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Supramolecule #1: Sinorhizobium meliloti

SupramoleculeName: Sinorhizobium meliloti / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 562 / Sci species name: Sinorhizobium meliloti / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: Yes
Host (natural)Organism: Sinorhizobium meliloti (bacteria)

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 15895
FSC plot (resolution estimation)

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