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- EMDB-5954: Protruding Knob-like Proteins Violate Local Symmetries in an Icos... -

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Basic information

Entry
Database: EMDB / ID: EMD-5954
TitleProtruding Knob-like Proteins Violate Local Symmetries in an Icosahedral Marine Virus
Map dataIcosahedral cryo-EM reconstruction of Syn5 marine virus
Sample
  • Sample: Syn5 marine virus, also known as horned cyanophage Syn5
  • Virus: Synechococcus phage Syn5 (virus)
KeywordsSyn5 / marine / cyanophage / capsid proteins / symmetry break
Function / homologyMajor capsid protein
Function and homology information
Biological speciesSynechococcus phage Syn5 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 Å
AuthorsGipson P / Baker ML / Raytcheva D / Haase-Pettingell C / Piret J / King JA / Chiu W
CitationJournal: Nat Commun / Year: 2014
Title: Protruding knob-like proteins violate local symmetries in an icosahedral marine virus.
Authors: Preeti Gipson / Matthew L Baker / Desislava Raytcheva / Cameron Haase-Pettingell / Jacqueline Piret / Jonathan A King / Wah Chiu /
Abstract: Marine viruses play crucial roles in shaping the dynamics of oceanic microbial communities and in the carbon cycle on Earth. Here we report a 4.7-Å structure of a cyanobacterial virus, Syn5, by ...Marine viruses play crucial roles in shaping the dynamics of oceanic microbial communities and in the carbon cycle on Earth. Here we report a 4.7-Å structure of a cyanobacterial virus, Syn5, by electron cryo-microscopy and modelling. A Cα backbone trace of the major capsid protein (gp39) reveals a classic phage protein fold. In addition, two knob-like proteins protruding from the capsid surface are also observed. Using bioinformatics and structure analysis tools, these proteins are identified to correspond to gp55 and gp58 (each with two copies per asymmetric unit). The non 1:1 stoichiometric distribution of gp55/58 to gp39 breaks all expected local symmetries and leads to non-quasi-equivalence of the capsid subunits, suggesting a role in capsid stabilization. Such a structural arrangement has not yet been observed in any known virus structures.
History
DepositionMay 11, 2014-
Header (metadata) releaseJul 9, 2014-
Map releaseJul 9, 2014-
UpdateJul 16, 2014-
Current statusJul 16, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.24
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.24
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4bml
  • Surface level: 0.24
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4bml
  • Imaged by Jmol
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_5954.gif

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Map

FileDownload / File: emd_5954.map.gz / Format: CCP4 / Size: 599.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedral cryo-EM reconstruction of Syn5 marine virus
Voxel sizeX=Y=Z: 1.32 Å
Density
Contour LevelBy AUTHOR: 0.24 / Movie #1: 0.24
Minimum - Maximum-0.81437606 - 1.06154096
Average (Standard dev.)0.00496094 (±0.06635214)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-272-272-272
Dimensions544544544
Spacing544544544
CellA=B=C: 718.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z544544544
origin x/y/z0.0000.0000.000
length x/y/z718.080718.080718.080
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ969680
MAP C/R/S123
start NC/NR/NS-272-272-272
NC/NR/NS544544544
D min/max/mean-0.8141.0620.005

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Supplemental data

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Sample components

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Entire : Syn5 marine virus, also known as horned cyanophage Syn5

EntireName: Syn5 marine virus, also known as horned cyanophage Syn5
Components
  • Sample: Syn5 marine virus, also known as horned cyanophage Syn5
  • Virus: Synechococcus phage Syn5 (virus)

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Supramolecule #1000: Syn5 marine virus, also known as horned cyanophage Syn5

SupramoleculeName: Syn5 marine virus, also known as horned cyanophage Syn5
type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Synechococcus phage Syn5

SupramoleculeName: Synechococcus phage Syn5 / type: virus / ID: 1 / Name.synonym: Horned marine virus / NCBI-ID: 438482 / Sci species name: Synechococcus phage Syn5 / Sci species strain: Syn5 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: Horned marine virus
Host (natural)Organism: Synechococcus sp. WH 8109 (bacteria) / Strain: WH 8109 / synonym: ALGAE
Virus shellShell ID: 1 / Diameter: 655 Å / T number (triangulation number): 7

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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

GridDetails: R1.2/1.3 Quantifoil grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: 3 uL sample blotted once for 2.7 seconds

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Electron microscopy

MicroscopeJEOL 3200FSC
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 80000
Specialist opticsEnergy filter - Name: Omega
Sample stageSpecimen holder model: JEOL 3200FSC CRYOHOLDER
DateOct 10, 2010
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 10000 (10k x 10k)

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Image processing

Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: OTHER / Software - Name: MPSA / Number images used: 12000

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