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- EMDB-3771: Three-dimensional reconstruction of FLiP virion -

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Basic information

Entry
Database: EMDB / ID: EMD-3771
TitleThree-dimensional reconstruction of FLiP virion
Map dataReconstruction of Flavobacterium infecting lipid-containing phage FLiP
Sample
  • Virus: unidentified phage (virus)
    • Protein or peptide: Major capsid protein
Function / homologyMajor capsid protein
Function and homology information
Biological speciesunidentified phage (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsDe Colibus L / Gillum A / Stuart DI / Huiskonen JT
CitationJournal: Proc Natl Acad Sci U S A / Year: 2017
Title: Virus found in a boreal lake links ssDNA and dsDNA viruses.
Authors: Elina Laanto / Sari Mäntynen / Luigi De Colibus / Jenni Marjakangas / Ashley Gillum / David I Stuart / Janne J Ravantti / Juha T Huiskonen / Lotta-Riina Sundberg /
Abstract: Viruses have impacted the biosphere in numerous ways since the dawn of life. However, the evolution, genetic, structural, and taxonomic diversity of viruses remain poorly understood, in part because ...Viruses have impacted the biosphere in numerous ways since the dawn of life. However, the evolution, genetic, structural, and taxonomic diversity of viruses remain poorly understood, in part because sparse sampling of the virosphere has concentrated mostly on exploring the abundance and diversity of dsDNA viruses. Furthermore, viral genomes are highly diverse, and using only the current sequence-based methods for classifying viruses and studying their phylogeny is complicated. Here we describe a virus, FLiP (-infecting, lipid-containing phage), with a circular ssDNA genome and an internal lipid membrane enclosed in the icosahedral capsid. The 9,174-nt-long genome showed limited sequence similarity to other known viruses. The genetic data imply that this virus might use replication mechanisms similar to those found in other ssDNA replicons. However, the structure of the viral major capsid protein, elucidated at near-atomic resolution using cryo-electron microscopy, is strikingly similar to that observed in dsDNA viruses of the PRD1-adenovirus lineage, characterized by a major capsid protein bearing two β-barrels. The strong similarity between FLiP and another member of the structural lineage, bacteriophage PM2, extends to the capsid organization (pseudo = 21 ) despite the difference in the genetic material packaged and the lack of significant sequence similarity.
History
DepositionJun 21, 2017-
Header (metadata) releaseJul 5, 2017-
Map releaseJul 26, 2017-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
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  • Surface view colored by radius
  • Surface level: 0.04
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  • Surface view with fitted model
  • Atomic models: PDB-5oac
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5oac
  • Imaged by Jmol
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3771.png

Downloads & links

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Map

FileDownload / File: emd_3771.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Flavobacterium infecting lipid-containing phage FLiP
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.08169098 - 0.16613102
Average (Standard dev.)0.0012641506 (±0.0115462085)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-349-349-349
Dimensions700700700
Spacing700700700
CellA=B=C: 945.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z700700700
origin x/y/z0.0000.0000.000
length x/y/z945.000945.000945.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-349-349-349
NC/NR/NS700700700
D min/max/mean-0.0820.1660.001

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Supplemental data

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Mask #1

Fileemd_3771_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_3771_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_3771_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 : unidentified phage

EntireName: unidentified phage (virus)
Components
  • Virus: unidentified phage (virus)
    • Protein or peptide: Major capsid protein

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Supramolecule #1: unidentified phage

SupramoleculeName: unidentified phage / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Flavobacterium infecting lipid-containing phage FLiP
NCBI-ID: 38018 / Sci species name: unidentified phage / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Flavobacterium (bacteria) / Strain: sp B330
Virus shellShell ID: 1 / Name: Capsid / Diameter: 550.0 Å / T number (triangulation number): 25

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Macromolecule #1: Major capsid protein

MacromoleculeName: Major capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 10 / Enantiomer: LEVO
Source (natural)Organism: unidentified phage (virus)
Molecular weightTheoretical: 34.533934 KDa
SequenceString: MTIKYLSSET EKLMNQTVSG IDVCFTLIGV DDDSFASGSK NDYISDTPKF LDPSNVHIKA TLKRGGKDYV LFSENLALLA KYSTITQGR DQWEEGVKLA AKEMVHLVYI PFSGNTNWPA HINLKDNDVL EVYVNVVRGA YGAELDANAC ICDVRTSPSI G VEKFIPFM ...String:
MTIKYLSSET EKLMNQTVSG IDVCFTLIGV DDDSFASGSK NDYISDTPKF LDPSNVHIKA TLKRGGKDYV LFSENLALLA KYSTITQGR DQWEEGVKLA AKEMVHLVYI PFSGNTNWPA HINLKDNDVL EVYVNVVRGA YGAELDANAC ICDVRTSPSI G VEKFIPFM TSYSIRANQA TDLVNLGNDV TRIALLSMTN DVSNIPNAFT DVTLSSDRLD KNFNSNQLIL EHSKCIEDSV RS HANEVDS YLIHEDIEID SAKVHLKMNP AKIRENTIYL VRSHFQTSLE ILQKAVAMEE KHQSADIAKV PAT

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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: 7.2 / Details: 20 mM PBS
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.5 µm / Calibrated defocus min: 0.7 µm / Calibrated magnification: 37037 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal magnification: 160000
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Sample stageSpecimen holder model: OTHER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Sampling interval: 5.0 µm / Digitization - Frames/image: 1-22 / Average electron dose: 22.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: EMDB MAP
EMDB ID:

1082

Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 4 / Avg.num./class: 551 / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.0)
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 934
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 84.31 / Target criteria: Cross-correlation coefficient
Output model

PDB-5oac:
FLiP major capsid protein

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