Breaking Symmetry in Viral Icosahedral Capsids as Seen through the Lenses of X-ray Crystallography and Cryo-Electron Microscopy
Abstract
:1. Principles of Icosahedral Virus Assembly
2. Asymmetric Cryo-EM Reconstructions Reveal the Portal Protein Occupies a Unique 5-Fold Vertex
3. Cryo-Electron Tomography Identifies a Portal Protein in Herpesviruses
4. The Challenge of Visualizing Symmetry Mismatches at the Portal Vertex in Genome Packaging Motors
5. Unique Capsid Vertices that Break Icosahedral Symmetry without a Portal Protein
6. Bubblegrams and Cryo-ET Reveal Asymmetrically Organized Proteins inside Icosahedral Capsids
7. Trimeric Fiber-Penton Base Interaction in the Adenovirus Lineage
8. Conclusive Remarks: The Evolution of Structural Methods to “Observe” Asymmetric Features in Icosahedral Capsids
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Virus | Protomer M.W. (kDa) | Accession Number(s) | Cryo-EM | X-ray | ||
---|---|---|---|---|---|---|
EMDB | PDB | |||||
Bacteriophages | P22 (MV) | 82.7 | 5049, 5050, 5051, 1482, 1483 | 5JJ3, 4V4K | +++ | +++ |
P22 (PC) | 82.7 | 5375 * | 5JJ1 | +++ | +++ | |
Phi29 | 35.9 | 1IJG, 1JNB, 1H5W, 1FOU | +++ | |||
T7 | 59.1 | 1231, 2356, 2717, 5690 | 3J4A | +++ | ||
SPP1 | 57.3 | 2993, 2994 1021 | 2JES | +++ | +++ | |
HK97-like | 32.9 | 3KDR | +++ | |||
G20C | 49.7 | 4ZJN | +++ | |||
T4 | 61.0 | 6324 | 3JA7 | +++ | ||
p2 | 39.1 | 2463 | +++ | |||
Herpes | HSV-1 | 74.2 | 5260 ** 5261 *** | +++ |
Virus | EMDB Accession Number(s) | Cryo-EM | Cryo-ET | Year | |
---|---|---|---|---|---|
Podoviridae | Phi29 | 1506, 5010 | +++ | 2009 | |
Phi29 | 1419, 1420 | +++ | 2008 | ||
Phi29 | 6560 | +++ | 2016 | ||
CUS-3 | 5946 | +++ | 2014 | ||
Sf6 | 5730 | +++ | 2013 | ||
T7 | 5566–5573 | +++ | 2013 | ||
T7 | 5534–5537 | +++ | 2013 | ||
C1 | 5446 | +++ | 2012 | ||
P22 | 1119 | +++ | 2005 | ||
P22 | 1220 | +++ | 2006 | ||
P22 | 1222 | +++ | 2006 | ||
P22 | 1827 | +++ | 2011 | ||
P22 | 5348, 5231 | +++ | 2011 | ||
P22 | 8258–6261 | +++ | 2016 | ||
P22 | 8005 | +++ | 2016 | ||
P-SSP7 | 1707 | +++ | 2010 | ||
P-SSP7 | 6427 | +++ | 2016 | ||
P-SSP7 | 1714, 1715 | +++ | 2010 | ||
P-SSP7 | 3131 | +++ | TBP | ||
Syn5 | 5743–5746 | +++ | 2013 | ||
ε15 | 1175 | +++ | 2005 | ||
ε15 | 5203, 5204 | +++ | 2010 | ||
ε15 | 5207–5209 | +++ | 2010 | ||
ε15 | 5216–5219 | +++ | 2010 | ||
BPP-1 | 1619 | +++ | 2010 | ||
N4 | 1475 | +++ | 2009 | ||
PRD-1 | 3548–3550 | +++ | 2017 | ||
PRD-1 | 2438–2440 | +++ | 2013 | ||
K1E | 1336 | +++ | 2007 | ||
K1-5 | 1337 | +++ | 2007 | ||
Myo | PhiKZ | 1415 | +++ | 2007 | |
T4 | 1572, 1573 | +++ | 2008 | ||
T4 | 6323 | +++ | 2015 | ||
T4 | 2774, 6078–6083 | +++ | 2015 | ||
Sipho | P2 | 2463, 2464 | +++ | 2013 | |
Araucaria | 2335–2338 | +++ | 2013 | ||
1358 | 2820 | +++ | 2016 | ||
TW1 | 7070, 8854, 8867, 8868 | +++ | 2017 | ||
ssDNA | ΦX174 | 7033, 8862 | +++ | 2017 |
Virus | EMDB Accession Number(s) | Cryo-EM | Cryo-ET | Year | |
---|---|---|---|---|---|
Archeal | APBV1 * | 3857–3859 | +++ | 2017 | |
His1 * | 6220–6222 | +++ | 2015 | ||
Eukaryotic | HSV-1 | 5452, 5453 | +++ | 2012 | |
HSV-1 | 5255, 5260, 5261 | +++ | 2011 | ||
HSV-1 | 1305–1308 | +++ | 2007 | ||
KSHV | 1320 | +++ | 2007 | ||
Faustovirus | 8144, 8145 | +++ | 2016 | ||
PBCV-1 | 1597 | +++ | 2009 | ||
PBCV-1 | 5384 | +++ | 2012 | ||
CroV ** | 8748 | +++ | 2017 | ||
Mimivirus ** | 5039 | +++ | 2009 | ||
Samba virus ** | 8599 | +++ | 2017 | ||
Chilo Iridescent Virus ** | 1580 | +++ | 2009 |
© 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
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Parent, K.N.; Schrad, J.R.; Cingolani, G. Breaking Symmetry in Viral Icosahedral Capsids as Seen through the Lenses of X-ray Crystallography and Cryo-Electron Microscopy. Viruses 2018, 10, 67. https://doi.org/10.3390/v10020067
Parent KN, Schrad JR, Cingolani G. Breaking Symmetry in Viral Icosahedral Capsids as Seen through the Lenses of X-ray Crystallography and Cryo-Electron Microscopy. Viruses. 2018; 10(2):67. https://doi.org/10.3390/v10020067
Chicago/Turabian StyleParent, Kristin N., Jason R. Schrad, and Gino Cingolani. 2018. "Breaking Symmetry in Viral Icosahedral Capsids as Seen through the Lenses of X-ray Crystallography and Cryo-Electron Microscopy" Viruses 10, no. 2: 67. https://doi.org/10.3390/v10020067