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Yorodumi- PDB-2xea: 4.6 ANGSTROM CRYO-EM RECONSTRUCTION OF TOBACCO MOSAIC VIRUS FROM ... -
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-Basic information
Entry | Database: PDB / ID: 2xea | ||||||
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Title | 4.6 ANGSTROM CRYO-EM RECONSTRUCTION OF TOBACCO MOSAIC VIRUS FROM IMAGES RECORDED AT 300 KEV ON A 4KX4K CCD CAMERA | ||||||
Components |
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Keywords | VIRUS / SINGLE PARTICLE PROCESSING | ||||||
Function / homology | Tobacco 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 species | TOBACCO MOSAIC VIRUS | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.6 Å | ||||||
Authors | Clare, D.K. / Orlova, E.V. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 2xea.cif.gz | 41.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xea.ent.gz | 27.4 KB | Display | PDB format |
PDBx/mmJSON format | 2xea.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xe/2xea ftp://data.pdbj.org/pub/pdb/validation_reports/xe/2xea | HTTPS FTP |
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-Related structure data
Related structure data | 1730MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Helical 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 °) |
-Components
#1: Protein | 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 |
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#2: RNA chain | Mass: 958.660 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TOBACCO MOSAIC VIRUS |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: TOBACCO MOSAIC VIRUS / Type: VIRUS |
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Buffer solution | Name: 50 MM TRIS-HCL, 50 MM KCL, 10 MM MGCL2 / pH: 7.4 / Details: 50 MM TRIS-HCL, 50 MM KCL, 10 MM MGCL2 |
Specimen | Conc.: 3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: LIQUID ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F30 / Date: Feb 1, 2009 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: 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 holder | Temperature: 78 K |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) |
Image scans | Num. digital images: 104 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: EACH PARTICLE WAS FULLY CTF CORRECTED | |||||||||||||||
3D reconstruction | Method: 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 building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient Details: METHOD--RIGID BODY, REAL SPACE REFINEMENT PROTOCOL--CRYO-EM | |||||||||||||||
Atomic model building | PDB-ID: 2XEA Accession code: 2XEA / Source name: PDB / Type: experimental model | |||||||||||||||
Refinement | Highest resolution: 4.6 Å | |||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 4.6 Å
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