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Yorodumi- EMDB-5584: Life in the extremes: atomic structure of Sulfolobus Turreted Ico... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5584 | |||||||||
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Title | Life in the extremes: atomic structure of Sulfolobus Turreted Icosahedral Virus | |||||||||
Map data | Reconstruction of mature STIV | |||||||||
Sample |
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Keywords | Virus assembly / Evolution / Electron microscopy / Archaea | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Sulfolobus turreted icosahedral virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||
Authors | Veesler D / Ng TS / Sendamarai AK / Eilers BJ / Lawrence CM / Lok SM / Young MJ / Johnson JE / Fu CY | |||||||||
Citation | Journal: Proc Natl Acad Sci U S A / Year: 2013 Title: Atomic structure of the 75 MDa extremophile Sulfolobus turreted icosahedral virus determined by CryoEM and X-ray crystallography. Authors: David Veesler / Thiam-Seng Ng / Anoop K Sendamarai / Brian J Eilers / C Martin Lawrence / Shee-Mei Lok / Mark J Young / John E Johnson / Chi-yu Fu / Abstract: Sulfolobus turreted icosahedral virus (STIV) was isolated in acidic hot springs where it infects the archeon Sulfolobus solfataricus. We determined the STIV structure using near-atomic resolution ...Sulfolobus turreted icosahedral virus (STIV) was isolated in acidic hot springs where it infects the archeon Sulfolobus solfataricus. We determined the STIV structure using near-atomic resolution electron microscopy and X-ray crystallography allowing tracing of structural polypeptide chains and visualization of transmembrane proteins embedded in the viral membrane. We propose that the vertex complexes orchestrate virion assembly by coordinating interactions of the membrane and various protein components involved. STIV shares the same coat subunit and penton base protein folds as some eukaryotic and bacterial viruses, suggesting that they derive from a common ancestor predating the divergence of the three kingdoms of life. One architectural motif (β-jelly roll fold) forms virtually the entire capsid (distributed in three different gene products), indicating that a single ancestral protein module may have been at the origin of its evolution. | |||||||||
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_5584.map.gz | 2.9 GB | EMDB map data format | |
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Header (meta data) | emd-5584-v30.xml emd-5584.xml | 11.7 KB 11.7 KB | Display Display | EMDB header |
Images | emd_5584_1.png | 340.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5584 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5584 | HTTPS FTP |
-Validation report
Summary document | emd_5584_validation.pdf.gz | 188.4 KB | Display | EMDB validaton report |
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Full document | emd_5584_full_validation.pdf.gz | 187.9 KB | Display | |
Data in XML | emd_5584_validation.xml.gz | 500 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5584 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5584 | HTTPS FTP |
-Related structure data
Related structure data | 3j31MC 4il7C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5584.map.gz / Format: CCP4 / Size: 3.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of mature STIV | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.37 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 : Mature Sulfolobus Turreted Icosahedral Virus
Entire | Name: Mature Sulfolobus Turreted Icosahedral Virus |
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Components |
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-Supramolecule #1000: Mature Sulfolobus Turreted Icosahedral Virus
Supramolecule | Name: Mature Sulfolobus Turreted Icosahedral Virus / type: sample / ID: 1000 / Number unique components: 5 |
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Molecular weight | Theoretical: 75 MDa |
-Supramolecule #1: Sulfolobus turreted icosahedral virus
Supramolecule | Name: Sulfolobus turreted icosahedral virus / type: virus / ID: 1 / NCBI-ID: 269145 / Sci species name: Sulfolobus turreted icosahedral virus / Sci species strain: Isolate YNPRC179 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No |
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Host (natural) | Organism: Sulfolobus solfataricus (archaea) / Strain: 2-2-12 / synonym: ARCHAEA |
Molecular weight | Theoretical: 75 MDa |
Virus shell | Shell ID: 1 / Name: B345-A223 / Diameter: 730 Å / T number (triangulation number): 31 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 3.5 Details: 23 mM KH2PO4, 19 mM (NH4)2SO4, 1 mM MgSO4, 2 mM CaCl2 |
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Grid | Details: glow-discharged C-flat holey carbon grids (CF-2/2-4C, Protochips) |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 94 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification carried out at room temperature |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Average: 90 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 103,000 times magnification |
Details | Nanoprobe mode was used |
Date | Mar 30, 2011 |
Image recording | Category: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Number real images: 878 / Average electron dose: 18 e/Å2 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 102189 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 µm |
Sample stage | Specimen holder: Nitrogen cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Each particle |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: OTHER / Software - Name: Frealign Details: The final reconstruction was sharpened with a negative temperature factor of 400A2. Number images used: 8903 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: CNS |
Details | Positional (xyz) minimization and isotropic B factor refinement. Real space refinement was also carried out using Coot. |
Refinement | Space: RECIPROCAL |
Output model | PDB-3j31: |
-Atomic model buiding 2
Initial model | PDB ID: |
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Software | Name: CNS |
Details | Positional (xyz) minimization and isotropic B factor refinement. Real space refinement was also carried out using Coot. Only the N-terminal domain was refined using CNS (residues 3-134). The C-terminal domain (residues 135-222) was only rigid-body fit using Coot and an arbitrary B-factor value of 150 A2 was assigned to it. |
Refinement | Space: RECIPROCAL |
Output model | PDB-3j31: |