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Yorodumi- EMDB-1752: 3D reconstruction of the rotavirus VP6 trimer using the Fast Proj... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1752 | |||||||||
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Title | 3D reconstruction of the rotavirus VP6 trimer using the Fast Projection Matching (FPM) algorithm. | |||||||||
Map data | Map of rotavirus VP6 trimer (from EMD-1461) after icosahedral averaging and 13-fold non-icosahedral averaging | |||||||||
Sample |
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Keywords | Rotavirus VP6 protein / Methods / Projection Matching | |||||||||
Biological species | Bovine rotavirus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Estrozi LF / Navaza J | |||||||||
Citation | Journal: J Struct Biol / Year: 2010 Title: Ab initio high-resolution single-particle 3D reconstructions: the symmetry adapted functions way. Authors: Leandro F Estrozi / Jorge Navaza / Abstract: A protocol to attain high-resolution single-particle reconstructions is presented. The protocol is the concatenation of two procedures: one to obtain an ab initio low-resolution reconstruction, the ...A protocol to attain high-resolution single-particle reconstructions is presented. The protocol is the concatenation of two procedures: one to obtain an ab initio low-resolution reconstruction, the other to determine a fixed point of the consecutive applications of fast projection matching and 3D reconstruction. It is a reciprocal space formulation where the Fourier coefficients of the 3D scattering density are expressed in terms of symmetry adapted functions and the 2D particle images are represented by their Fourier-Bessel transforms. The new protocol shows advantages in terms of speed and accuracy when compared to other methods currently in use. We illustrate its performance as applied to high-resolution cryo-electron micrographs of rotavirus. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1752.map.gz | 2.2 MB | EMDB map data format | |
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Header (meta data) | emd-1752-v30.xml emd-1752.xml | 11.4 KB 11.4 KB | Display Display | EMDB header |
Images | emd_1752.png | 65 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1752 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1752 | HTTPS FTP |
-Validation report
Summary document | emd_1752_validation.pdf.gz | 236.2 KB | Display | EMDB validaton report |
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Full document | emd_1752_full_validation.pdf.gz | 235.3 KB | Display | |
Data in XML | emd_1752_validation.xml.gz | 5.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1752 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1752 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1752.map.gz / Format: CCP4 / Size: 5.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Map of rotavirus VP6 trimer (from EMD-1461) after icosahedral averaging and 13-fold non-icosahedral averaging | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.14 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Rotavirus VP6 protein
Entire | Name: Rotavirus VP6 protein |
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Components |
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-Supramolecule #1000: Rotavirus VP6 protein
Supramolecule | Name: Rotavirus VP6 protein / type: sample / ID: 1000 Oligomeric state: 780 molecules of VP6 form a DLP particle with 12 molecules of VP1, 120 molecules of VP2, 12 molecules of VP3 and 11 dsRNA molecules Number unique components: 5 |
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-Macromolecule #1: VP6
Macromolecule | Name: VP6 / type: protein_or_peptide / ID: 1 / Name.synonym: VP6 / Recombinant expression: No |
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Source (natural) | Organism: Bovine rotavirus / synonym: Rotavirus |
Molecular weight | Theoretical: 41 KDa |
-Macromolecule #2: VP1
Macromolecule | Name: VP1 / type: protein_or_peptide / ID: 2 / Name.synonym: VP1 / Recombinant expression: No |
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Source (natural) | Organism: Bovine rotavirus / synonym: Rotavirus |
-Macromolecule #3: VP2
Macromolecule | Name: VP2 / type: protein_or_peptide / ID: 3 / Name.synonym: VP2 / Recombinant expression: No |
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Source (natural) | Organism: Bovine rotavirus / synonym: Rotavirus |
-Macromolecule #4: VP3
Macromolecule | Name: VP3 / type: protein_or_peptide / ID: 4 / Name.synonym: VP3 / Recombinant expression: No |
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Source (natural) | Organism: Bovine rotavirus / synonym: Rotavirus |
-Macromolecule #5: dsRNA
Macromolecule | Name: dsRNA / type: rna / ID: 5 / Name.synonym: dsRNA / Classification: OTHER / Structure: OTHER / Synthetic?: No |
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Source (natural) | Organism: Bovine rotavirus / synonym: Rotavirus |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.4 |
Grid | Details: Lacy carbon and C-flat |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 30 % / Instrument: HOMEMADE PLUNGER Details: Vitrification instrument: Home-made. Vitrification carried out in air at room temperature Method: Blot for 3 seconds before plunging |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Temperature | Average: 90 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected |
Date | Jun 1, 2007 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 386 / Average electron dose: 15 e/Å2 / Od range: 1 / Bits/pixel: 8 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 56540 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder: Eucentric, side-entry / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Phase flipping for each particle |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: OTHER / Software - Name: RIco / Number images used: 7000 |
-Atomic model buiding 1
Initial model | PDB ID: Chain - Chain ID: A |
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Software | Name: URO |
Details | PDBEntryID_givenInChain. Protocol: Rigid body |
Refinement | Space: RECIPROCAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient |