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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
DescriptorMajor capsid protein
KeywordsVIRUS / capsid / major capsid protein / virion / virus
Specimen sourceunidentified phage / virus
MethodElectron microscopy (4 Å resolution / Particle / Single particle)
AuthorsDe Colibus, L. / Stuart, D.I. / Huiskonen, J.T.
CitationProc. Natl. Acad. Sci. U.S.A., 2017, 114, 8378-8383

Proc. Natl. Acad. Sci. U.S.A., 2017, 114, 8378-8383 Yorodumi Papers
Virus found in a boreal lake links ssDNA and dsDNA viruses.
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
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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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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: Polypeptide(L)
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

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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
Details of virusEmpty: NO / Enveloped: YES / Virus isolate: SPECIES / Virus type: VIRION
Natural hostOrganism: Flavobacterium / Strain: sp B330
Virus shellName: Capsid / Diameter: 550 Å / 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 FIELD / 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
IDNameVersionCategoryImage processing IDImaging IDFitting ID
1ETHAN1.2PARTICLE SELECTION1
2SerialEMIMAGE ACQUISITION1
4GctfCTF CORRECTION1
7UCSF ChimeraMODEL FITTING1
8CootMODEL FITTING1
10RELION1.4INITIAL EULER ASSIGNMENT1
11RELION2.0FINAL EULER ASSIGNMENT1
12RELION1.4CLASSIFICATION1
13RELION2.0RECONSTRUCTION1
14PHENIX1.11.1MODEL REFINEMENT1
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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