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- PDB-2xea: 4.6 ANGSTROM CRYO-EM RECONSTRUCTION OF TOBACCO MOSAIC VIRUS FROM ... -

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Basic information

Entry
Database: PDB / ID: 2xea
Title4.6 ANGSTROM CRYO-EM RECONSTRUCTION OF TOBACCO MOSAIC VIRUS FROM IMAGES RECORDED AT 300 KEV ON A 4KX4K CCD CAMERA
Components
  • 5'-(*GP*AP*AP)-3'
  • TOBACCO MOSAIC VIRUS
KeywordsVIRUS / SINGLE PARTICLE PROCESSING
Function / homologyTobacco mosaic virus-like, coat protein / Tobacco mosaic virus-like, coat protein superfamily / Virus coat protein (TMV like) / helical viral capsid / structural molecule activity / RNA / Capsid protein
Function and homology information
Biological speciesTOBACCO MOSAIC VIRUS
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsClare, D.K. / Orlova, E.V.
CitationJournal: J Struct Biol / Year: 2010
Title: 4.6A Cryo-EM reconstruction of tobacco mosaic virus from images recorded at 300 keV on a 4k x 4k CCD camera.
Authors: Daniel K Clare / Elena V Orlova /
Abstract: Tobacco mosaic virus (TMV) is a plant virus with a highly ordered organisation and has been described in three different structural states: As stacked disks without RNA (X-ray crystallography), as a ...Tobacco mosaic virus (TMV) is a plant virus with a highly ordered organisation and has been described in three different structural states: As stacked disks without RNA (X-ray crystallography), as a helical form with RNA (X-ray fibre diffraction) and as a second distinct helical form with RNA (cryo-EM). Here we present a structural analysis of TMV as a test object to assess the quality of cryo-EM images recorded at 300 keV on a CCD camera. The 4.6A TMV structure obtained is consistent with the previous cryo-EM structure and confirms that there is a second helical form of TMV. The structure here also shows that with a similar number of TMV segments an equivalent resolution can be achieved with a 4k CCD camera at 300 keV.
History
DepositionMay 12, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 2017Group: Data collection / Refinement description / Structure summary
Category: em_3d_fitting / em_software / entity
Item: _em_3d_fitting.target_criteria / _em_software.fitting_id ..._em_3d_fitting.target_criteria / _em_software.fitting_id / _em_software.image_processing_id / _entity.src_method
Revision 1.4May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as representative helical assembly
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-1730
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  • Superimposition on EM map
  • EMDB-1730
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: TOBACCO MOSAIC VIRUS
R: 5'-(*GP*AP*AP)-3'


Theoretical massNumber of molelcules
Total (without water)18,4642
Polymers18,4642
Non-polymers00
Water00
1
A: TOBACCO MOSAIC VIRUS
R: 5'-(*GP*AP*AP)-3'
x 49


Theoretical massNumber of molelcules
Total (without water)904,74098
Polymers904,74098
Non-polymers00
Water0
TypeNameSymmetry operationNumber
helical symmetry operation48
identity operation1_555x,y,z1
2


  • Idetical with deposited unit
  • helical asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 49 / Rise per n subunits: 1.408 Å / Rotation per n subunits: 22.032 °)

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Components

#1: Protein TOBACCO MOSAIC VIRUS


Mass: 17505.426 Da / Num. of mol.: 1 / Fragment: CP, RESIDUES 2-159 / Source method: isolated from a natural source / Source: (natural) TOBACCO MOSAIC VIRUS / References: UniProt: Q77LT8
#2: RNA chain 5'-(*GP*AP*AP)-3'


Mass: 958.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TOBACCO 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: TOBACCO MOSAIC VIRUS / Type: VIRUS
Buffer solutionName: 50 MM TRIS-HCL, 50 MM KCL, 10 MM MGCL2 / pH: 7.4 / Details: 50 MM TRIS-HCL, 50 MM KCL, 10 MM MGCL2
SpecimenConc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30 / Date: Feb 1, 2009
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 90000 X / Calibrated magnification: 121000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 900 nm / Cs: 2.3 mm
Specimen holderTemperature: 78 K
Image recordingElectron dose: 25 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNum. digital images: 104
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1Cootmodel fitting
2UCSF Chimeramodel fitting
3IMAGIC3D reconstruction
4SPIDER3D reconstruction
CTF correctionDetails: EACH PARTICLE WAS FULLY CTF CORRECTED
3D reconstructionMethod: PROJECTION MATCHING / Resolution: 4.6 Å / Num. of particles: 5300 / Nominal pixel size: 1.24 Å / Actual pixel size: 1.24 Å
Magnification calibration: THE VIRUS DIFFRACTION PATTERN WAS USED TO CALIBRATE THE MICROSCOPE MAGNIFICATION
Details: BPRP WAS USED TO RECONSTRUCT THE 3D VOLUME THE PDB 2OM3 WAS DOCKED INTO THE CRYO-EM DENSITY USING CHIMERA. SOME SIDE CHAIN RESIDUES AND THE INNER LOOP OF THE CP WERE REMODELLED USING COOT. ...Details: BPRP WAS USED TO RECONSTRUCT THE 3D VOLUME THE PDB 2OM3 WAS DOCKED INTO THE CRYO-EM DENSITY USING CHIMERA. SOME SIDE CHAIN RESIDUES AND THE INNER LOOP OF THE CP WERE REMODELLED USING COOT. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1730
Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient
Details: METHOD--RIGID BODY, REAL SPACE REFINEMENT PROTOCOL--CRYO-EM
Atomic model buildingPDB-ID: 2XEA

Accession code: 2XEA / Source name: PDB / Type: experimental model
RefinementHighest resolution: 4.6 Å
Refinement stepCycle: LAST / Highest resolution: 4.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1212 67 0 0 1279

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