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- PDB-5oac: FLiP major capsid protein -

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Basic information

Entry
Database: PDB / ID: 5oac
TitleFLiP major capsid protein
ComponentsMajor capsid protein
KeywordsVIRUS / capsid / major capsid protein / virion
Function / homologyMajor capsid protein
Function and homology information
Biological speciesunidentified phage (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsDe Colibus, L. / Stuart, D.I. / Huiskonen, J.T.
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, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 9, 2017Group: Data collection / Database references / Refinement description
Category: citation / em_3d_fitting / em_imaging_optics
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _em_3d_fitting.target_criteria / _em_imaging_optics.energyfilter_name
Revision 1.2Nov 13, 2019Group: Data collection / Other / Category: cell / symmetry
Item: _cell.Z_PDB / _symmetry.Int_Tables_number / _symmetry.space_group_name_H-M

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • EMDB-3771
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-3771
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Major capsid protein


Theoretical massNumber of molelcules
Total (without water)345,33910
Polymers345,33910
Non-polymers00
Water0
1
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Major capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)20,720,360600
Polymers20,720,360600
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
Buried area35630 Å2
ΔGint-81 kcal/mol
Surface area122490 Å2
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Major capsid protein
x 5


  • icosahedral pentamer
  • 1.73 MDa, 50 polymers
Theoretical massNumber of molelcules
Total (without water)1,726,69750
Polymers1,726,69750
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
E: Major capsid protein
F: Major capsid protein
G: Major capsid protein
H: Major capsid protein
I: Major capsid protein
J: Major capsid protein
x 6


  • icosahedral 23 hexamer
  • 2.07 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)2,072,03660
Polymers2,072,03660
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
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


Mass: 34533.934 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) unidentified phage (virus) / References: UniProt: A0A2D0TC94*PLUS

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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: unidentified phage / Type: VIRUS
Details: Flavobacterium infecting lipid-containing phage FLiP
Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: unidentified phage (virus)
Details of virusEmpty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Flavobacterium / Strain: sp B330
Virus shellName: Capsid / Diameter: 550 nm / Triangulation number (T number): 25
Buffer solutionpH: 7.2 / Details: 20 mM PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: C-flat-2/2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyModel: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 160000 X / Calibrated magnification: 37037 X / Calibrated defocus min: 700 nm / Calibrated defocus max: 2500 nm / Cs: 2 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: OTHER
Image recordingElectron dose: 22 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: GIF Quantum LS / Energyfilter upper: 20 eV / Energyfilter lower: 0 eV
Image scansSampling size: 5 µm / Movie frames/image: 22 / Used frames/image: 1-22

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameVersionCategory
1ETHAN1.2particle selection
2SerialEMimage acquisition
4GctfCTF correction
7UCSF Chimeramodel fitting
8Cootmodel fitting
10RELION1.4initial Euler assignment
11RELION2final Euler assignment
12RELION1.4classification
13RELION23D reconstruction
14PHENIX1.11.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 934 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingB value: 84.31 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0061478400
ELECTRON MICROSCOPYf_angle_d0.9562005800
ELECTRON MICROSCOPYf_dihedral_angle_d5.042900600
ELECTRON MICROSCOPYf_chiral_restr0.061235200
ELECTRON MICROSCOPYf_plane_restr0.006258600

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