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Open data
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Basic information
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Title | Near-atomic structure of five-fold averaged PBCV-1 capsid | |||||||||
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![]() | giant virus / nucleocytoplasmic large DNA viruses (NCLDVs) / viral assembly / Paramecium bursaria chlorella virus 1 (PBCV-1) / chlorovirus / major capsid protein / minor capsid protein / VIRUS / VIRAL PROTEIN | |||||||||
Function / homology | ![]() viral capsid / membrane => GO:0016020 / structural molecule activity / membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
![]() | Shao Q / Agarkova IV / Noel EA / Dunigan DD / Liu Y / Wang A / Guo M / Xie L / Zhao X / Rossmann MG ...Shao Q / Agarkova IV / Noel EA / Dunigan DD / Liu Y / Wang A / Guo M / Xie L / Zhao X / Rossmann MG / Van Etten JL / Klose T / Fang Q | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Near-atomic, non-icosahedrally averaged structure of giant virus Paramecium bursaria chlorella virus 1. Authors: Qianqian Shao / Irina V Agarkova / Eric A Noel / David D Dunigan / Yunshu Liu / Aohan Wang / Mingcheng Guo / Linlin Xie / Xinyue Zhao / Michael G Rossmann / James L Van Etten / Thomas Klose / Qianglin Fang / ![]() ![]() Abstract: Giant viruses are a large group of viruses that infect many eukaryotes. Although components that do not obey the overall icosahedral symmetry of their capsids have been observed and found to play ...Giant viruses are a large group of viruses that infect many eukaryotes. Although components that do not obey the overall icosahedral symmetry of their capsids have been observed and found to play critical roles in the viral life cycles, identities and high-resolution structures of these components remain unknown. Here, by determining a near-atomic-resolution, five-fold averaged structure of Paramecium bursaria chlorella virus 1, we unexpectedly found the viral capsid possesses up to five major capsid protein variants and a penton protein variant. These variants create varied capsid microenvironments for the associations of fibers, a vesicle, and previously unresolved minor capsid proteins. Our structure reveals the identities and atomic models of the capsid components that do not obey the overall icosahedral symmetry and leads to a model for how these components are assembled and initiate capsid assembly, and this model might be applicable to many other giant viruses. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 6.1 GB | ![]() | |
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Header (meta data) | ![]() ![]() | 47 KB 47 KB | Display Display | ![]() |
Images | ![]() | 203.4 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8h2iMC C: citing same article ( M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.62 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : Paramecium bursaria Chlorella virus 1
+Supramolecule #1: Paramecium bursaria Chlorella virus 1
+Macromolecule #1: Major capsid protein (MCP)
+Macromolecule #2: MCPv1
+Macromolecule #3: MCPv2
+Macromolecule #4: MCPv3
+Macromolecule #5: MCPv4
+Macromolecule #6: P1v1
+Macromolecule #7: P2
+Macromolecule #8: P3
+Macromolecule #9: P4
+Macromolecule #10: P5
+Macromolecule #11: P6
+Macromolecule #12: P8
+Macromolecule #13: P9
+Macromolecule #14: P11
+Macromolecule #15: P12
+Macromolecule #16: P13
+Macromolecule #17: P15
+Macromolecule #18: P16
+Macromolecule #19: P17
+Macromolecule #20: P18
+Macromolecule #21: P19
+Macromolecule #22: P20
+Macromolecule #23: P21
+Macromolecule #24: MCPv5
+Macromolecule #25: P22
+Macromolecule #26: P23
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average exposure time: 8.0 sec. / Average electron dose: 24.4 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 56500 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: jspr |