+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0436 | |||||||||
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Title | Near-atomic structure of icosahedrally averaged PBCV-1 capsid | |||||||||
Map data | icosahedrally averaged PBCV-1 capsid | |||||||||
Sample |
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Function / homology | Function and homology information viral capsid / membrane => GO:0016020 / structural molecule activity / membrane Similarity search - Function | |||||||||
Biological species | PBCV-1 (virus) / Paramecium bursaria Chlorella virus 1 | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Fang Q / Rossmann MG | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Commun / Year: 2019 Title: Near-atomic structure of a giant virus. Authors: Qianglin Fang / Dongjie Zhu / Irina Agarkova / Jagat Adhikari / Thomas Klose / Yue Liu / Zhenguo Chen / Yingyuan Sun / Michael L Gross / James L Van Etten / Xinzheng Zhang / Michael G Rossmann / Abstract: Although the nucleocytoplasmic large DNA viruses (NCLDVs) are one of the largest group of viruses that infect many eukaryotic hosts, the near-atomic resolution structures of these viruses have ...Although the nucleocytoplasmic large DNA viruses (NCLDVs) are one of the largest group of viruses that infect many eukaryotic hosts, the near-atomic resolution structures of these viruses have remained unknown. Here we describe a 3.5 Å resolution icosahedrally averaged capsid structure of Paramecium bursaria chlorella virus 1 (PBCV-1). This structure consists of 5040 copies of the major capsid protein, 60 copies of the penton protein and 1800 minor capsid proteins of which there are 13 different types. The minor capsid proteins form a hexagonal network below the outer capsid shell, stabilizing the capsid by binding neighboring capsomers together. The size of the viral capsid is determined by a tape-measure, minor capsid protein of which there are 60 copies in the virion. Homologs of the tape-measure protein and some of the other minor capsid proteins exist in other NCLDVs. Thus, a similar capsid assembly pathway might be used by other NCLDVs. | |||||||||
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_0436.map.gz | 1.2 GB | EMDB map data format | |
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Header (meta data) | emd-0436-v30.xml emd-0436.xml | 23.5 KB 23.5 KB | Display Display | EMDB header |
Images | emd_0436.png | 289.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0436 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0436 | HTTPS FTP |
-Validation report
Summary document | emd_0436_validation.pdf.gz | 467.9 KB | Display | EMDB validaton report |
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Full document | emd_0436_full_validation.pdf.gz | 467.5 KB | Display | |
Data in XML | emd_0436_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | emd_0436_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0436 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0436 | HTTPS FTP |
-Related structure data
Related structure data | 6nclMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0436.map.gz / Format: CCP4 / Size: 6.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | icosahedrally averaged PBCV-1 capsid | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.62 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 : Paramecium bursaria Chlorella virus 1
+Supramolecule #1: Paramecium bursaria Chlorella virus 1
+Macromolecule #1: P14
+Macromolecule #2: P9
+Macromolecule #3: P10
+Macromolecule #4: P7
+Macromolecule #5: P6
+Macromolecule #6: P1
+Macromolecule #7: P12
+Macromolecule #8: P5
+Macromolecule #9: P11
+Macromolecule #10: P2
+Macromolecule #11: P4
+Macromolecule #12: P3
+Macromolecule #13: P8
+Macromolecule #14: Major capsid protein
+Macromolecule #15: P13
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
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Grid | Support film - Material: CARBON / Support film - topology: LACEY / Details: unspecified |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 85 % / Instrument: GATAN CRYOPLUNGE 3 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 24.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13000 |
Initial angle assignment | Type: PROJECTION MATCHING |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |