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- PDB-5a32: Electron cryo-microscopy of Cowpea Mosaic Virus containing RNA-1 ... -

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Basic information

Entry
Database: PDB / ID: 5a32
TitleElectron cryo-microscopy of Cowpea Mosaic Virus containing RNA-1 (CPMVb)
Components(RNA2 POLYPROTEIN) x 2
KeywordsVIRUS / CPMV / COMOVIRIDAE / PICORNAVIRALES.
Function / homology
Function and homology information


transport of virus in host, cell to cell / host cell plasmodesma / T=3 icosahedral viral capsid / host cell nucleus / structural molecule activity / GTP binding / DNA binding / RNA binding
Similarity search - Function
Large coat protein / RNA2 polyprotein / Large coat protein / Small coat protein / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCOWPEA MOSAIC VIRUS
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.44 Å
AuthorsHesketh, E.L. / Meshcheriakova, Y. / Dent, K.C. / Saxena, P. / Thompson, R. / Cockburn, J.J. / Lomonossoff, G.P. / Ranson, N.A.
CitationJournal: Nat Commun / Year: 2015
Title: Mechanisms of assembly and genome packaging in an RNA virus revealed by high-resolution cryo-EM.
Authors: Emma L Hesketh / Yulia Meshcheriakova / Kyle C Dent / Pooja Saxena / Rebecca F Thompson / Joseph J Cockburn / George P Lomonossoff / Neil A Ranson /
Abstract: Cowpea mosaic virus is a plant-infecting member of the Picornavirales and is of major interest in the development of biotechnology applications. Despite the availability of >100 crystal structures of ...Cowpea mosaic virus is a plant-infecting member of the Picornavirales and is of major interest in the development of biotechnology applications. Despite the availability of >100 crystal structures of Picornavirales capsids, relatively little is known about the mechanisms of capsid assembly and genome encapsidation. Here we have determined cryo-electron microscopy reconstructions for the wild-type virus and an empty virus-like particle, to 3.4 Å and 3.0 Å resolution, respectively, and built de novo atomic models of their capsids. These new structures reveal the C-terminal region of the small coat protein subunit, which is essential for virus assembly and which was missing from previously determined crystal structures, as well as residues that bind to the viral genome. These observations allow us to develop a new model for genome encapsidation and capsid assembly.
History
DepositionMay 27, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 19, 2017Group: Database references / Other
Revision 1.2Aug 30, 2017Group: Data collection / Refinement description / Category: em_3d_fitting / em_software
Item: _em_3d_fitting.target_criteria / _em_software.image_processing_id / _em_software.name

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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
  • EMDB-3013
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: RNA2 POLYPROTEIN
B: RNA2 POLYPROTEIN


Theoretical massNumber of molelcules
Total (without water)61,8202
Polymers61,8202
Non-polymers00
Water0
1
A: RNA2 POLYPROTEIN
B: RNA2 POLYPROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)3,709,200120
Polymers3,709,200120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: RNA2 POLYPROTEIN
B: RNA2 POLYPROTEIN
x 5


  • icosahedral pentamer
  • 309 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)309,10010
Polymers309,10010
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: RNA2 POLYPROTEIN
B: RNA2 POLYPROTEIN
x 6


  • icosahedral 23 hexamer
  • 371 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)370,92012
Polymers370,92012
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 RNA2 POLYPROTEIN / GENOME POLYPROTEIN M / P2 / COAT PROTEIN VP37 / COAT PROTEIN VP23 / COWPEA MOSAIC VIRUS


Mass: 20961.564 Da / Num. of mol.: 1 / Fragment: LARGE COAT PROTEIN / Source method: isolated from a natural source / Details: WILD-TYPE VIRUS CONTAINING RNA-1 / Source: (natural) COWPEA MOSAIC VIRUS / References: UniProt: P03599
#2: Protein RNA2 POLYPROTEIN / GENOME POLYPROTEIN M / P2 / COAT PROTEIN VP37 / COAT PROTEIN VP23 / COWPEA MOSAIC VIRUS


Mass: 40858.434 Da / Num. of mol.: 1 / Fragment: SMALL COAT PROTEIN N-TERMINUS PART / Source method: isolated from a natural source / Details: WILD-TYPE VIRUS CONTAINING RNA-1 / Source: (natural) COWPEA MOSAIC VIRUS / References: UniProt: P03599

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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: COWPEA MOSAIC VIRUS / Type: VIRUS
SpecimenConc.: 5.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Nov 1, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 134615 X / Calibrated magnification: 134615 X / Nominal defocus max: 8000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 1754

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Processing

EM softwareName: RELION / Version: 1.3 / Category: 3D reconstruction
CTF correctionDetails: CTFFIND3 PER MICROGRAPH
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.44 Å / Num. of particles: 4331 / Nominal pixel size: 1.04 Å / Actual pixel size: 1.04 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3013. (DEPOSITION ID: 13382).
Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL / Target criteria: R-factor / Details: REFINEMENT PROTOCOL--EM
RefinementHighest resolution: 3.44 Å
Refinement stepCycle: LAST / Highest resolution: 3.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4333 0 0 0 4333

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