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- PDB-5a2t: The Molecular Basis for Flexibility in the Flexible Filamentous P... -

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Basic information

Entry
Database: PDB / ID: 5a2t
TitleThe Molecular Basis for Flexibility in the Flexible Filamentous Plant Viruses
Components
  • BAMBOO MOSAIC VIRUS
  • COAT PROTEIN
KeywordsVIRAL PROTEIN / HELICAL POLYMER / CUMULATIVE DISORDER / PLANT VIRUSES
Function / homologyPotex/carlavirus coat protein / Viral coat protein / helical viral capsid / ribonucleoprotein complex / structural molecule activity / RNA / RNA (> 10) / RNA (> 100) / Coat protein
Function and homology information
Biological speciesBAMBOO MOSAIC VIRUS
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 5.6 Å
AuthorsDiMaio, F. / Chen, C.C. / Yu, X. / Frenz, B. / Hsu, Y.H. / Lin, N.S. / Egelman, E.H.
CitationJournal: Nat Struct Mol Biol / Year: 2015
Title: The molecular basis for flexibility in the flexible filamentous plant viruses.
Authors: Frank DiMaio / Chun-Chieh Chen / Xiong Yu / Brandon Frenz / Yau-Heiu Hsu / Na-Sheng Lin / Edward H Egelman /
Abstract: Flexible filamentous plant viruses cause more than half the viral crop damage in the world but are also potentially useful for biotechnology. Structural studies began more than 75 years ago but have ...Flexible filamentous plant viruses cause more than half the viral crop damage in the world but are also potentially useful for biotechnology. Structural studies began more than 75 years ago but have failed, owing to the virion's extreme flexibility. We have used cryo-EM to generate an atomic model for bamboo mosaic virus, which reveals flexible N- and C-terminal extensions that allow deformation while still maintaining structural integrity.
History
DepositionMay 23, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2015Provider: repository / Type: Initial release
Revision 1.1Aug 19, 2015Group: Database references
Revision 1.2May 8, 2024Group: Author supporting evidence / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_image_scans / em_single_particle_entity
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Movie
  • Deposited structure unit
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  • Superimposition on EM map
  • EMDB-3020
  • Imaged by UCSF Chimera
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  • Superimposition on EM map
  • EMDB-3020
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
D: COAT PROTEIN
E: COAT PROTEIN
F: COAT PROTEIN
G: COAT PROTEIN
H: COAT PROTEIN
I: COAT PROTEIN
J: COAT PROTEIN
K: COAT PROTEIN
L: COAT PROTEIN
M: COAT PROTEIN
N: COAT PROTEIN
O: COAT PROTEIN
P: COAT PROTEIN
Q: COAT PROTEIN
R: COAT PROTEIN
S: COAT PROTEIN
T: COAT PROTEIN
U: COAT PROTEIN
V: COAT PROTEIN
W: COAT PROTEIN
X: COAT PROTEIN
Y: COAT PROTEIN
Z: BAMBOO MOSAIC VIRUS


Theoretical massNumber of molelcules
Total (without water)597,00626
Polymers597,00626
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA

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Components

#1: Protein ...
COAT PROTEIN


Mass: 22351.225 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Source: (natural) BAMBOO MOSAIC VIRUS / References: UniProt: O37178
#2: RNA chain BAMBOO MOSAIC VIRUS


Mass: 38225.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) BAMBOO MOSAIC VIRUS

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: BAMV / Type: VIRUS
SpecimenEmbedding 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 FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionDetails: IMAGES
3D reconstructionMethod: IHRSR / Resolution: 5.6 Å / Num. of particles: 104433 / Nominal pixel size: 1.05 Å / Actual pixel size: 1.05 Å
Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3020. (DEPOSITION ID: 13412).
Symmetry type: HELICAL
RefinementHighest resolution: 5.6 Å
Refinement stepCycle: LAST / Highest resolution: 5.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39425 2500 0 0 41925

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