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- EMDB-3571: dsRNA bacteriophage phi6 nucleocapsid -

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Basic information

Entry
Database: EMDB / ID: EMD-3571
TitledsRNA bacteriophage phi6 nucleocapsid
Map data
SamplePseudomonas phage phi6 (bacteriophage):
virus / Major inner protein P1 / Packaging enzyme P4 / Major outer capsid protein
Function / homology
Function and homology information


T=13 icosahedral viral capsid / T=2 icosahedral viral capsid / viral inner capsid / viral procapsid / viral outer capsid / nucleoside-triphosphatase activity / viral genome packaging / virion / nucleoside-triphosphate phosphatase / viral capsid ...T=13 icosahedral viral capsid / T=2 icosahedral viral capsid / viral inner capsid / viral procapsid / viral outer capsid / nucleoside-triphosphatase activity / viral genome packaging / virion / nucleoside-triphosphate phosphatase / viral capsid / viral nucleocapsid / RNA binding / ATP binding / identical protein binding
P-loop containing nucleoside triphosphate hydrolase / Packaging enzyme P4
Major outer capsid protein / Packaging enzyme P4 / Major inner protein P1
Biological speciesPseudomonas phage phi6 (bacteriophage)
Methodsingle particle reconstruction / cryo EM / Resolution: 4 Å
AuthorsSun Z / El Omari K / Sun X / Ilca SL / Kotecha A / Stuart DI / Poranen MM / Huiskonen JT
CitationJournal: Nat Commun / Year: 2017
Title: Double-stranded RNA virus outer shell assembly by bona fide domain-swapping.
Authors: Zhaoyang Sun / Kamel El Omari / Xiaoyu Sun / Serban L Ilca / Abhay Kotecha / David I Stuart / Minna M Poranen / Juha T Huiskonen /
Abstract: Correct outer protein shell assembly is a prerequisite for virion infectivity in many multi-shelled dsRNA viruses. In the prototypic dsRNA bacteriophage φ6, the assembly reaction is promoted by ...Correct outer protein shell assembly is a prerequisite for virion infectivity in many multi-shelled dsRNA viruses. In the prototypic dsRNA bacteriophage φ6, the assembly reaction is promoted by calcium ions but its biomechanics remain poorly understood. Here, we describe the near-atomic resolution structure of the φ6 double-shelled particle. The outer T=13 shell protein P8 consists of two alpha-helical domains joined by a linker, which allows the trimer to adopt either a closed or an open conformation. The trimers in an open conformation swap domains with each other. Our observations allow us to propose a mechanistic model for calcium concentration regulated outer shell assembly. Furthermore, the structure provides a prime exemplar of bona fide domain-swapping. This leads us to extend the theory of domain-swapping from the level of monomeric subunits and multimers to closed spherical shells, and to hypothesize a mechanism by which closed protein shells may arise in evolution.
Validation ReportPDB-ID: 5muu

SummaryFull reportAbout validation report
History
DepositionJan 14, 2017-
Header (metadata) releaseJan 25, 2017-
Map releaseMar 22, 2017-
UpdateOct 23, 2019-
Current statusOct 23, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5muu
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5muu
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_3571.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 512 pix.
= 691.2 Å
1.35 Å/pix.
x 512 pix.
= 691.2 Å
1.35 Å/pix.
x 512 pix.
= 691.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.07375267 - 0.14329888
Average (Standard dev.)0.00020935167 (±0.008287506)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 691.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z691.200691.200691.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.0740.1430.000

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Supplemental data

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Sample components

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Entire Pseudomonas phage phi6

EntireName: Pseudomonas phage phi6 (bacteriophage)
Details: The viral envelope was removed by Triton X-114 extraction
Number of components: 4

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Component #1: virus, Pseudomonas phage phi6

VirusName: Pseudomonas phage phi6Pseudomonas virus phi6 / Class: VIRION
Details: The viral envelope was removed by Triton X-114 extraction
Empty: No / Enveloped: Yes / Isolate: SPECIES
SpeciesSpecies: Pseudomonas phage phi6 (bacteriophage)
Source (natural)Host Species: Pseudomonas syringae (bacteria) / Host species strain: pv.phaseolicola HB10Y
Shell #1Name of element: Outer shell / Diameter: 565.0 Å / T number (triangulation number): 13
Shell #2Name of element: Inner shell / Diameter: 500.0 Å / T number (triangulation number): 1

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Component #2: protein, Major inner protein P1

ProteinName: Major inner protein P1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 85.080711 kDa
SourceSpecies: Pseudomonas phage phi6 (bacteriophage)

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Component #3: protein, Packaging enzyme P4

ProteinName: Packaging enzyme P4 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 35.198426 kDa
SourceSpecies: Pseudomonas phage phi6 (bacteriophage)

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Component #4: protein, Major outer capsid protein

ProteinName: Major outer capsid protein / Number of Copies: 10 / Recombinant expression: No
MassTheoretical: 16.018418 kDa
SourceSpecies: Pseudomonas phage phi6 (bacteriophage)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 3 mg/mL / pH: 7.2
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 0.73 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 160000.0 X (nominal), 37037.0 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: - 300.0 nm / Energy filter: GIF Quantum LS / Energy window: 0-20 eV
Specimen HolderModel: OTHER / Temperature: (80.0 - 120.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 900 / Sampling size: 5 µm

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 13291
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Details: The structure of P1 was fitted in the map using COOT as a rigid body in two different positions corresponding to subunits P1A and P1B. P1A and P1B main-chains and side-chains were adjusted ...Details: The structure of P1 was fitted in the map using COOT as a rigid body in two different positions corresponding to subunits P1A and P1B. P1A and P1B main-chains and side-chains were adjusted using manual and real space fitting in COOT. Structure was refined in Phenix.real_space_refine applying secondary structure, rotamer, and Ramachandran plot restraints.
Input PDB model: 4K7H
Chain ID: A
Modeling #2Refinement space: REAL
Details: The structure of P8 (L3 to Y147) was built manually in COOT and side-chains were adjusted using manual and real space fitting in COOT. Structure was refined in Phenix.real_space_refine ...Details: The structure of P8 (L3 to Y147) was built manually in COOT and side-chains were adjusted using manual and real space fitting in COOT. Structure was refined in Phenix.real_space_refine applying secondary structure, rotamer, and Ramachandran plot restraints.
Modeling #3Details: The structure of P4 C-terminus (R292 to L332) was built manually in COOT and side-chains were adjusted using manual and real space fitting in COOT. Structure was refined in Phenix.real_space_ ...Details: The structure of P4 C-terminus (R292 to L332) was built manually in COOT and side-chains were adjusted using manual and real space fitting in COOT. Structure was refined in Phenix.real_space_refine applying secondary structure, rotamer, and Ramachandran plot restraints.
Output model

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