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- PDB-3j7l: Full virus map of brome mosaic virus -

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Basic information

Entry
Database: PDB / ID: 3j7l
TitleFull virus map of brome mosaic virus
ComponentsCapsid proteinCapsid
KeywordsVIRUS / capsid protein / BMV / beta barrel
Function / homologyBromovirus coat protein / Bromovirus coat protein / T=3 icosahedral viral capsid / host cell endoplasmic reticulum / viral nucleocapsid / structural molecule activity / RNA binding / Capsid protein
Function and homology information
Specimen sourceBrome mosaic virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.8 Å resolution
AuthorsWang, Z. / Hryc, C. / Bammes, B. / Afonine, P.V. / Jakana, J. / Chen, D.H. / Liu, X. / Baker, M.L. / Kao, C. / Ludtke, S.J. / Schmid, M.F. / Adams, P.D. / Chiu, W.
CitationJournal: Nat Commun / Year: 2014
Title: An atomic model of brome mosaic virus using direct electron detection and real-space optimization.
Authors: Zhao Wang / Corey F Hryc / Benjamin Bammes / Pavel V Afonine / Joanita Jakana / Dong-Hua Chen / Xiangan Liu / Matthew L Baker / Cheng Kao / Steven J Ludtke / Michael F Schmid / Paul D Adams / Wah Chiu
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Jul 18, 2014 / Release: Sep 10, 2014
RevisionDateData content typeGroupCategoryItemProviderType
1.0Sep 10, 2014Structure modelrepositoryInitial release
1.1Sep 17, 2014Structure modelDatabase references
1.2May 18, 2016Structure modelDerived calculations
1.3Jul 18, 2018Structure modelData collectionem_image_scans / em_software_em_software.image_processing_id

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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
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  • Simplified surface model + fitted atomic model
  • EMDB-6000
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  • Superimposition on EM map
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Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein


Theoretical massNumber of molelcules
Total (without water)61,2353
Polyers61,2353
Non-polymers00
Water0
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)3,674,075180
Polyers3,674,075180
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: Capsid protein
B: Capsid protein
C: Capsid protein
x 5


  • icosahedral pentamer
  • 306 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)306,17315
Polyers306,17315
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 6


  • icosahedral 23 hexamer
  • 367 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)367,40718
Polyers367,40718
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: Protein/peptide Capsid protein / Capsid / CP / Coat protein


Mass: 20411.525 Da / Num. of mol.: 3 / Source: (natural) Brome mosaic virus / References: UniProt: P03602

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / Reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Brome mosaic virus / Type: VIRUS
Details of virusEmpty: NO / Enveloped: NO / Virus host category: PLANTAE(HIGHER PLANTS) / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Triticum aestivum
Buffer solutionpH: 5.2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 293 kelvins / Details: Plunged into liquid ethane (FEI VITROBOT MARK IV).

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Electron microscopy imaging

MicroscopyMicroscope model: JEOL 3200FSC / Date: Jan 10, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 / Nominal defocus max: 2000 nm / Nominal defocus min: 500 nm / Camera length: 0 mm
Specimen holderSpecimen holder model: JEOL 3200FSC CRYOHOLDER
Image recordingFilm or detector model: DIRECT ELECTRON DE-12 (4k x 3k)

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Processing

EM software
IDNameCategory
1EMAN3D reconstruction
2MPSA3D reconstruction
SymmetryPoint symmetry: I
3D reconstructionMethod: Single ParticleSingle particle analysis / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 30000 / Nominal pixel size: 0.93 / Actual pixel size: 0.99 / Details: (Single particle--Applied symmetry: I) / Symmetry type: POINT
Number of atoms included #LASTProtein: 3613 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 3613

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