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- PDB-6hy0: Atomic models of P1, P4 C-terminal fragment and P8 fitted in the ... -

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Entry
Database: PDB / ID: 6hy0
TitleAtomic models of P1, P4 C-terminal fragment and P8 fitted in the bacteriophage phi6 nucleocapsid reconstructed with icosahedral symmetry
Components
  • Major Outer Capsid Protein P8
  • Major inner protein P1
  • Packaging Enzyme P4
KeywordsVIRUS / virus / dsRNA / capsid
Function / homologyT=2 icosahedral viral capsid / viral inner capsid / virion / viral nucleocapsid / RNA binding / identical protein binding / Major inner protein P1
Function and homology information
Biological speciesPseudomonas phage phi6 (bacteriophage)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsEl Omari, K. / Ilca, S.L. / Stuart, D.I. / Huiskonen, J.T.
CitationJournal: Nature / Year: 2019
Title: Multiple liquid crystalline geometries of highly compacted nucleic acid in a dsRNA virus.
Authors: Serban L Ilca / Xiaoyu Sun / Kamel El Omari / Abhay Kotecha / Felix de Haas / Frank DiMaio / Jonathan M Grimes / David I Stuart / Minna M Poranen / Juha T Huiskonen /
Abstract: Characterizing the genome of mature virions is pivotal to understanding the highly dynamic processes of virus assembly and infection. Owing to the different cellular fates of DNA and RNA, the life ...Characterizing the genome of mature virions is pivotal to understanding the highly dynamic processes of virus assembly and infection. Owing to the different cellular fates of DNA and RNA, the life cycles of double-stranded (ds)DNA and dsRNA viruses are dissimilar. In terms of nucleic acid packing, dsDNA viruses, which lack genome segmentation and intra-capsid transcriptional machinery, predominantly display single-spooled genome organizations. Because the release of dsRNA into the cytoplasm triggers host defence mechanisms, dsRNA viruses retain their genomes within a core particle that contains the enzymes required for RNA replication and transcription. The genomes of dsRNA viruses vary greatly in the degree of segmentation. In members of the Reoviridae family, genomes consist of 10-12 segments and exhibit a non-spooled arrangement mediated by RNA-dependent RNA polymerases. However, whether this arrangement is a general feature of dsRNA viruses remains unknown. Here, using cryo-electron microscopy to resolve the dsRNA genome structure of the tri-segmented bacteriophage ɸ6 of the Cystoviridae family, we show that dsRNA viruses can adopt a dsDNA-like single-spooled genome organization. We find that in this group of viruses, RNA-dependent RNA polymerases do not direct genome ordering, and the dsRNA can adopt multiple conformations. We build a model that encompasses 90% of the genome, and use this to quantify variation in the packing density and to characterize the different liquid crystalline geometries that are exhibited by the tightly compacted nucleic acid. Our results demonstrate that the canonical model for the packing of dsDNA can be extended to dsRNA viruses.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 18, 2018 / Release: Jun 12, 2019
RevisionDateData content typeProviderType
1.0Jun 12, 2019Structure modelrepositoryInitial release

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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  • Superimposition on EM map
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  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Major inner protein P1
B: Major inner protein P1
C: Packaging Enzyme P4
D: Major Outer Capsid Protein P8
E: Major Outer Capsid Protein P8
F: Major Outer Capsid Protein P8
G: Major Outer Capsid Protein P8
H: Major Outer Capsid Protein P8
I: Major Outer Capsid Protein P8
J: Major Outer Capsid Protein P8
K: Major Outer Capsid Protein P8
L: Major Outer Capsid Protein P8
M: Major Outer Capsid Protein P8


Theoretical massNumber of molelcules
Total (without water)365,54413
Polymers365,54413
Non-polymers00
Water0
1
A: Major inner protein P1
B: Major inner protein P1
C: Packaging Enzyme P4
D: Major Outer Capsid Protein P8
E: Major Outer Capsid Protein P8
F: Major Outer Capsid Protein P8
G: Major Outer Capsid Protein P8
H: Major Outer Capsid Protein P8
I: Major Outer Capsid Protein P8
J: Major Outer Capsid Protein P8
K: Major Outer Capsid Protein P8
L: Major Outer Capsid Protein P8
M: Major Outer Capsid Protein P8
x 60


Theoretical massNumber of molelcules
Total (without water)21,932,642780
Polymers21,932,642780
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
Buried area34010 Å2
ΔGint-189 kcal/mol
Surface area159930 Å2
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: Major inner protein P1
B: Major inner protein P1
C: Packaging Enzyme P4
D: Major Outer Capsid Protein P8
E: Major Outer Capsid Protein P8
F: Major Outer Capsid Protein P8
G: Major Outer Capsid Protein P8
H: Major Outer Capsid Protein P8
I: Major Outer Capsid Protein P8
J: Major Outer Capsid Protein P8
K: Major Outer Capsid Protein P8
L: Major Outer Capsid Protein P8
M: Major Outer Capsid Protein P8
x 5


  • icosahedral pentamer
  • 1.83 MDa, 65 polymers
Theoretical massNumber of molelcules
Total (without water)1,827,72065
Polymers1,827,72065
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Major inner protein P1
B: Major inner protein P1
C: Packaging Enzyme P4
D: Major Outer Capsid Protein P8
E: Major Outer Capsid Protein P8
F: Major Outer Capsid Protein P8
G: Major Outer Capsid Protein P8
H: Major Outer Capsid Protein P8
I: Major Outer Capsid Protein P8
J: Major Outer Capsid Protein P8
K: Major Outer Capsid Protein P8
L: Major Outer Capsid Protein P8
M: Major Outer Capsid Protein P8
x 6


  • icosahedral 23 hexamer
  • 2.19 MDa, 78 polymers
Theoretical massNumber of molelcules
Total (without water)2,193,26478
Polymers2,193,26478
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/peptide Major inner protein P1 / Major Inner Capsid Protein P1


Mass: 85080.711 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage phi6 (bacteriophage) / References: UniProt: P11126
#2: Protein/peptide Packaging Enzyme P4


Mass: 35198.426 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage phi6 (bacteriophage)
#3: Protein/peptide
Major Outer Capsid Protein P8


Mass: 16018.418 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Pseudomonas phage phi6 (bacteriophage)

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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: Pseudomonas phage phi6Cystovirus / Type: VIRUS / Entity ID: 1, 2, 3 / Source: NATURAL
Source (natural)Organism: Pseudomonas phage phi6 (bacteriophage)
Details of virusEmpty: NO / Enveloped: YES / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Pseudomonas syringae
Virus shell

Entity assembly-ID: 1

IDNameTriangulation number (T number)
1Outer Capsid Shell13
2Inner Capsid Shell1
Buffer solutionpH: 7.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 33 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.13_2998: / Classification: refinement
EM software
IDNameVersionCategory
1ETHANparticle selection
4RELIONCTF correction
7UCSF Chimeramodel fitting
12RELION2.0.33D reconstruction
13REFMAC5model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55265 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model buildingPDB-ID: 5MUU

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