Twenty-Five Years of Structural Parvovirology
Abstract
:1. Introduction
2. Parvovirinae
2.1. Expression of the Parvovirinae VPs Utilizes Different Transcription Strategies
2.2. Parvovirinae Genera Display Distinct Capsid Surface Morphologies
2.3. Nucleotides Are Ordered Inside Parvovirinae Capsids Despite Lack of Icosahedral Symmetry
2.4. The Structure of Capsid Variants Provide Insight into Function
2.5. Capsid-Receptor Complex Structures
2.6. Capsid-Antibody Complex Structures
2.7. Engineering of Parvovirus Capsids to Create Biologics
3. Densovirinae
3.1. The Densovirinae Utilize Diverse Strategies for VP Expression
3.2. Densovirinae Capsid Structures Display Distinct Surface Morphology
3.3. Functions Associated with Densoviral Capsid Proteins
4. Summary
Funding
Conflicts of Interest
References
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Virus | Empty/Full | Structure Determination Method | Year | Resolution in Å | PDB-ID | Reference |
---|---|---|---|---|---|---|
Protoparvovirus | ||||||
BuV1 | Empty | Cryo-EM | 2018 | 2.8 | 6BWX | Ilyas et al. [39] |
BuV2 | Empty | Cryo-EM | 2018 | 3.8 | 6BX0 | Ilyas et al. [39] |
BuV3 | Empty | Cryo-EM | 2018 | 3.3 | 6BX1 | Ilyas et al. [39] |
CPV | Empty | X-Ray Crystallography | 1993 | 3.0 | 2CAS | Wu et al. [38] |
CPV | Full | X-Ray Crystallography | 1996 | 2.9 | 4DPV | Xie et al. [40] |
CPV-N93D | Full | X-Ray Crystallography | 2003 | 3.3 | 1P5Y | Govindasamy et al. [41] |
CPV-N93R | Full | X-Ray Crystallography | 2003 | 3.3 | 1P5W | Govindasamy et al. [41] |
CPV-d-A300D | Empty | X-Ray Crystallography | 2000 | 3.3 | 1C8D | Simpson et al. [42] |
CPV-d-A300D | Full | X-Ray Crystallography | 1996 | 3.3 | 1IJS | Llamas-Saiz et al. [43] |
CPV-d pH5.5 | Empty | X-Ray Crystallography | 2000 | 3.5 | 1C8H | Simpson et al. [42] |
CPV2a | Full | X-Ray Crystallography | 2014 | 3.3 | 4QYK | Organtini et al. [44] |
FPV | Empty | X-Ray Crystallography | 1993 | 3.3 | 1FPV | Agbandje et al. [45] |
FPV | Empty | X-Ray Crystallography | 2000 | 3.0 | 1C8F | Simpson et al. [42] |
FPV low pH | Empty | X-Ray Crystallography | 2000 | 3.0 | 1C8G | Simpson et al. [42] |
FPV no CaCl2 | Empty | X-Ray Crystallography | 2000 | 3.0 | 1C8E | Simpson et al. [42] |
H-1PV | Full | X-Ray Crystallography | 2013 | 2.7 | 4G0R | Halder et al. [46] |
H-1PV | Empty | X-Ray Crystallography | 2013 | 3.2 | 4GBT | Halder et al. [46] |
LuIII | Empty | Cryo-EM | 2017 | 3.2 | 6B9Q | Pittman et al. [47] |
M. Spretus EVE | Empty | Cryo-EM | 2018 | 3.9 | 6NF9 | Callaway et al. [48] |
MVMi | Full | X-Ray Crystallography | 1997 | 3.5 | 1MVM | Llamas-Saiz et al. [49] |
MVMi | Empty | X-Ray Crystallography | 2005 | 3.5 | 1Z1C | Kontou et al. [50] |
MVMi-L172W | Empty | X-Ray Crystallography | 2011 | 4.2 | 2XGK | Plevka et al. [51] |
MVMp | Full | X-Ray Crystallography | 2005 | 3.3 | 1Z14 | Kontou et al. [50] |
MVMp-N170A | Empty | X-Ray Crystallography | 2015 | 3.8 | 4ZPY | Guerra et al. [52] |
PPV | Empty | X-Ray Crystallography | 2001 | 3.5 | 1K3V | Simpson et al. [53] |
Bocaparvovirus | ||||||
BPV | Empty | X-Ray Crystallography | 2015 | 3.2 | 4QC8 | Kailasan et al. [5] |
HBoV1 | Empty | Cryo-EM | 2017 | 2.9 | 5URF | Mietzsch et al. [54] |
HBoV3 | Empty | Cryo-EM | 2017 | 2.8 | 5US7 | Mietzsch et al. [54] |
HBoV4 | Empty | Cryo-EM | 2017 | 3.0 | 5US9 | Mietzsch et al. [54] |
Dependoparvovirus | ||||||
AAV1 | Full | X-Ray Crystallography | 2011 | 2.5 | 3NG9 | Ng et al. [55] |
AAV2 | Full | X-Ray Crystallography | 2002 | 3.0 | 1LP3 | Xie et al. [3] |
AAV2 | Empty | Cryo-EM | 2016 | 3.8 | 5IPI | Drouin et al. [56] |
AAV2-L336C | Empty | Cryo-EM | 2018 | 1.9 | 6E9D | Tan et al. [57] |
AAV2-R432A | Empty | Cryo-EM | 2016 | 3.7 | 5IPK | Drouin et al. [56] |
AAV2.5 | Full | Cryo-EM | 2018 | 2.8 | 6CBE | Burg et al. [58] |
AAV3 | Full | X-Ray Crystallography | 2010 | 2.6 | 3KIC | Lerch et al. [59] |
AAV4 | Full | X-Ray Crystallography | 2007 | 3.2 | 2G8G | Govindasamy et al. [60] |
AAV5 | Empty | X-Ray Crystallography | 2010 | 3.5 | 3NTT | Govindasamy et al. [61] |
AAV6 | Empty | X-Ray Crystallography | 2010 | 3.0 | 3OAH | Ng et al. [55] |
AAV6 | Full | X-Ray Crystallography | 2011 | 3.0 | 4V86 | Xie et al. [62] |
AAV8 | Empty | X-Ray Crystallography | 2007 | 2.6 | 2QA0 | Nam et al. [63] |
AAV8 pH7.5 | Full | X-Ray Crystallography | 2011 | 2.7 | 3RA4 | Nam et al. [64] |
AAV8 pH6.0 | Full | X-Ray Crystallography | 2011 | 2.7 | 3RA9 | Nam et al. [64] |
AAV8 pH5.5 | Full | X-Ray Crystallography | 2011 | 2.7 | 3RA8 | Nam et al. [64] |
AAV8 pH4.0 | Full | X-Ray Crystallography | 2011 | 2.7 | 3RA2 | Nam et al. [64] |
AAV8 pH4/7.5 | Full | X-Ray Crystallography | 2011 | 3.2 | 3RAA | Nam et al. [64] |
AAV9 | Empty | X-Ray Crystallography | 2011 | 2.8 | 3UX1 | Dimattia et al. [65] |
AAV9-L001 | Full | Cryo-EM | 2019 | 3.2 | 6NXE | Guenther et al. [66] |
AAV-DJ | Empty | Cryo-EM | 2012 | 4.5 | 3J1Q | Lerch et al. [67] |
AAVrh.8 | Full | X-Ray Crystallography | 2014 | 3.5 | 4RSO | Halder et al. [68] |
AAVrh.32.33 | Full | X-Ray Crystallography | 2013 | 3.5 | 4IOV | Mikals et al. [69] |
Erythroparvovirus | ||||||
B19 | Empty | X-Ray Crystallography | 2004 | 3.5 | 1S58 | Kaufmann et al. [4] |
Virus | Receptor | Structure Determination Method | Year | Resolution in Å | Reference |
---|---|---|---|---|---|
AAV2 | AAVR | Cryo-EM | 2019 | 2.8 | Zhang et al. [102] |
AAV-DJ | heparinoid pentasaccharide | Cryo-EM | 2017 | 2.8 | Xie et al. [97] |
AAV1 | SIA | X-Ray Crystallography | 2016 | 3.0 | Huang et al. [100] |
AAV5 | SIA | X-Ray Crystallography | 2015 | 3.5 | Afione et al. [98] |
AAV3 | sucrose octasulfate | X-Ray Crystallography | 2012 | 6.5 | Lerch et al. [99] |
AAV2 | heparin | Cryo-EM | 2009 | 8.3 | O’Donnell et al. [95] |
AAV2 | heparin | Cryo-EM | 2009 | 18.0 | Levy et al. [96] |
CPV | transferrin receptor | Cryo-EM | 2007 | 25.0 | Hafenstein et al. [83] |
MVMp | SIA | X-Ray Crystallography | 2006 | 3.5 | López-Bueno et al. [101] |
Virus | Antibody Name | Year | Binding Region | Neutralizing for Infection | Resolution in Å | Reference |
---|---|---|---|---|---|---|
Protoparvovirus | ||||||
CPV | Fab-E | 2012 | side of 3-fold protrusions across 2-fold axis | Yes | 4.1 | Organtini et al. [111] |
CPV | Fab-14 | 2009 | 3-fold protrusions | Yes | 12.4 | Hafenstein et al. [84] |
FPV | Fab-6 | 2009 | 3-fold protrusions | Yes | 18.0 | Hafenstein et al. [84] |
FPV | Fab-8 | 2009 | 2/5-fold wall | Yes | 8.5 | Hafenstein et al. [84] |
FPV | Fab-15 | 2009 | 2/5-fold wall | Yes | 10.5 | Hafenstein et al. [84] |
FPV | Fab-16 | 2009 | 2/5-fold wall | Yes | 13.0 | Hafenstein et al. [84] |
FPV | Fab-B | 2009 | 3-fold protrusions | Yes | 14.0 | Hafenstein et al. [84] |
FPV | Fab-E | 2009 | side of 3-fold protrusions across 2-fold axis | Yes | 12.0 | Hafenstein et al. [84] |
FPV | Fab-F | 2009 | side of 3-fold protrusions across 2-fold axis | Yes | 14.0 | Hafenstein et al. [84] |
MVMi | B7 | 2007 | center of 3-fold symmetry axis | Yes | 7.0 | Kaufmann et al. [112] |
Bocaparvovirus | ||||||
HBoV1 | 4C2 | 2016 | 3-fold protrusions | unknown | 16.0 | Kailasan et al. [113] |
HBoV1 | 9G12 | 2016 | 3-fold protrusions | unknown | 8.5 | Kailasan et al. [113] |
HBoV1 | 12C1 | 2016 | 3-fold protrusions | unknown | 11.9 | Kailasan et al. [113] |
HBoV1 | 15C6 | 2016 | around 5-fold symmetry axis | unknown | 18.6 | Kailasan et al. [113] |
HBoV2 | 15C6 | 2016 | around 5-fold symmetry axis | unknown | 17.8 | Kailasan et al. [113] |
HBoV4 | 15C6 | 2016 | around 5-fold symmetry axis | unknown | 9.5 | Kailasan et al. [113] |
Dependoparvovirus | ||||||
AAV1 | ADK1a | 2015 | 3-fold protrusions | Yes | 11.0 | Tseng et al. [114] |
AAV1 | ADK1b | 2015 | 2/5-fold wall | Yes | 11.0 | Tseng et al. [114] |
AAV1 | 4E4 | 2013 | side of 3-fold protrusions across 2-fold axis | Yes | 12.0 | Gurda et al. [115] |
AAV1 | 5H7 | 2013 | center of 3-fold symmetry axis | Yes | 23.0 | Gurda et al. [115] |
AAV2 | C37-B | 2013 | 3-fold protrusions | Yes | 11.0 | Gurda et al. [115] |
AAV2 | A20 | 2012 | 2/5-fold wall | Yes | 8.5 | McCraw et al. [116] |
AAV5 | ADK5a | 2015 | 2/5-fold wall | Yes | 11.0 | Tseng et al. [114] |
AAV5 | ADK5b | 2015 | 2/5-fold wall to 5-fold symmetry axis | Yes | 12.0 | Tseng et al. [114] |
AAV5 | HL2476 | 2018 | 3-fold protrusions | Yes | 3.1 | Jose et al. [108] |
AAV5 | 3C5 | 2013 | 2/5-fold wall in a tangential orientation | No | 16.0 | Gurda et al. [115] |
AAV6 | 5H7 | 2013 | center of 3-fold symmetry axis | unknown | 15.0 | Gurda et al. [115] |
AAV6 | ADK6 | 2018 | 3-fold protrusions & 2/5-fold wall | Yes | 13.0 | Bennett et al. [117] |
AAV8 | ADK8 | 2011 | 3-fold protrusions | Yes | 18.7 | Gurda et al. [118] |
AAV9 | PAV9.1 | 2018 | center of 3-fold symmetry axis | Yes | 4.2 | Giles et al. [119] |
Erythroparvovirus | ||||||
B19 | human Fab | 2018 | around 5-fold symmetry axis | Yes | 3.2 | Sun et al. [120] |
Virus | Empty / Full | Structure Determination Method | Year | Resolution in Å | PDB-ID | Reference |
---|---|---|---|---|---|---|
Ambidensovirus | ||||||
AdDV | Full | X-Ray Crystallography | 2013 | 3.5 | 4MGU | Meng et al. [8] |
GmDV | Full | X-Ray Crystallography | 1998 | 3.6 | 1DNV | Simpson et al. [7] |
JcDV | Empty | Cryo-EM | 2005 | 8.7 | N/A | Bruemmer et al. [158] |
Brevidensovirus | ||||||
AalDV2 | Full | Cryo-EM | 2004 | 15.6 | N/A | Chen et al. [159] |
Iteradensovirus | ||||||
BmDV1 | Empty | X-Ray Crystallography | 2011 | 3.1 | 3P0S | Kaufmann et al. [9] |
Penstyldensovirus | ||||||
PstDV | Empty | X-Ray Crystallography | 2010 | 2.5 | 3N7X | Kaufmann et al. [157] |
Inner Radius (Å) | Inner Surface Area (nm2) | Inner Volume (nm3) | Genome Size (nt) | Genus | |
---|---|---|---|---|---|
GmDV | 98.7 | 1223.2 | 4022.6 | 6039 | Ambidensovirus |
AdDV | 91.7 | 1056.2 | 3227.8 | 5425 | Ambidensovirus |
BmDV1 | 98.7 | 1224 | 4027.5 | 5076 | Iteradensovirus |
PstDV | 87.6 | 963.3 | 2811.5 | 3914 | Penstyldensovirus |
CPV | 92.9 | 1084.8 | 3359.5 | 5323 | Protoparvovirus |
AAV2 | 89.9 | 1014.9 | 3040.4 | 4679 | Dependoparvovirus |
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Mietzsch, M.; Pénzes, J.J.; Agbandje-McKenna, M. Twenty-Five Years of Structural Parvovirology. Viruses 2019, 11, 362. https://doi.org/10.3390/v11040362
Mietzsch M, Pénzes JJ, Agbandje-McKenna M. Twenty-Five Years of Structural Parvovirology. Viruses. 2019; 11(4):362. https://doi.org/10.3390/v11040362
Chicago/Turabian StyleMietzsch, Mario, Judit J. Pénzes, and Mavis Agbandje-McKenna. 2019. "Twenty-Five Years of Structural Parvovirology" Viruses 11, no. 4: 362. https://doi.org/10.3390/v11040362