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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 / virus
Specimen sourceunidentified phage (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 4 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jun 21, 2017 / Release: Jul 26, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Jul 26, 2017Structure modelrepositoryInitial release
1.1Aug 9, 2017Structure modelData collection / Database references / Refinement descriptioncitation / em_3d_fitting / em_imaging_optics_citation.journal_volume / _citation.page_first / _citation.page_last / _em_3d_fitting.target_criteria / _em_imaging_optics.energyfilter_name

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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
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  • Simplified surface model + fitted atomic model
  • EMDB-3771
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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
Polyers345,33910
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
Polyers20,720,360600
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
Buried area (Å2)35630
ΔGint (kcal/M)-81
Surface area (Å2)122490
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
Polyers1,726,69750
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
Polyers2,072,03660
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

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Components

#1: Protein/peptide
Major capsid protein


Mass: 34533.934 Da / Num. of mol.: 10 / Source: (natural) unidentified phage (virus)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 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: 1 / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: unidentified phage (virus)
Details of virusEmpty: NO / Enveloped: YES / Virus isolate: SPECIES / Virus type: VIRION
Natural hostOrganism: Flavobacterium / Strain: sp B330
Virus shellName: Capsid / Diameter: 550 nm / Triangulation number (T number): 25
Buffer solutionDetails: 20 mM PBS / pH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 / 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
MicroscopyMicroscope model: 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 / Calibrated magnification: 37037 / Calibrated defocus min: 700 nm / Calibrated defocus max: 2500 nm / Cs: 2 mm / C2 aperture diameter: 50 mm / 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 microns / 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
11RELION2.0final Euler assignment
12RELION1.4classification
13RELION2.03D reconstruction
14PHENIX1.11.1model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I
3D reconstructionResolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 934 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingOverall b value: 84.31 / Ref protocol: AB INITIO MODEL / Ref 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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