High-resolution Asymmetric Structure of a Fab-virus Complex Reveals Overlap with the Receptor Binding Site

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2021 Jun 2

PMID 34074770

Citations 9

Authors

Daniel J Goetschius

Samantha R Hartmann

Lindsey J Organtini

Heather Callaway

Kai Huang

Carol M Bator

Robert E Ashley

Alexander M Makhov

James F Conway

Colin R Parrish

Susan L Hafenstein

Affiliations

Soon will be listed here.

Abstract

Canine parvovirus is an important pathogen causing severe diseases in dogs, including acute hemorrhagic enteritis, myocarditis, and cerebellar disease. Overlap on the surface of parvovirus capsids between the antigenic epitope and the receptor binding site has contributed to cross-species transmission, giving rise to closely related variants. It has been shown that Mab 14 strongly binds and neutralizes canine but not feline parvovirus, suggesting this antigenic site also controls species-specific receptor binding. To visualize the conformational epitope at high resolution, we solved the cryogenic electron microscopy (cryo-EM) structure of the Fab-virus complex. We also created custom software, Icosahedral Subparticle Extraction and Correlated Classification, to solve a Fab-virus complex with only a few Fab bound per capsid and visualize local structures of the Fab-bound and -unbound antigenic sites extracted from the same complex map. Our results identified the antigenic epitope that had significant overlap with the receptor binding site, and the structures revealed that binding of Fab induced conformational changes to the virus. We were also able to assign the order and position of attached Fabs to allow assessment of complementarity between the Fabs bound to different positions. This approach therefore provides a method for using cryo-EM to investigate complementarity of antibody binding.

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References

Pettersen E, Goddard T, Huang C, Couch G, Greenblatt D, Meng E . UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004; 25(13):1605-12. DOI: 10.1002/jcc.20084. View

Wang W, Ye W, Yu Q, Jiang C, Zhang J, Luo R . Conformational selection and induced fit in specific antibody and antigen recognition: SPE7 as a case study. J Phys Chem B. 2013; 117(17):4912-23. DOI: 10.1021/jp4010967. View

Govindasamy L, Hueffer K, Parrish C, Agbandje-Mckenna M . Structures of host range-controlling regions of the capsids of canine and feline parvoviruses and mutants. J Virol. 2003; 77(22):12211-21. PMC: 254256. DOI: 10.1128/jvi.77.22.12211-12221.2003. View

Parrish C, Carmichael L . Antigenic structure and variation of canine parvovirus type-2, feline panleukopenia virus, and mink enteritis virus. Virology. 1983; 129(2):401-14. DOI: 10.1016/0042-6822(83)90179-4. View

Gurda B, DiMattia M, Miller E, Bennett A, McKenna R, Weichert W . Capsid antibodies to different adeno-associated virus serotypes bind common regions. J Virol. 2013; 87(16):9111-24. PMC: 3754064. DOI: 10.1128/JVI.00622-13. View

Stucker K, Pagan I, Cifuente J, Kaelber J, Lillie T, Hafenstein S . The role of evolutionary intermediates in the host adaptation of canine parvovirus. J Virol. 2011; 86(3):1514-21. PMC: 3264339. DOI: 10.1128/JVI.06222-11. View

Hafenstein S, Bowman V, Sun T, Nelson C, Palermo L, Chipman P . Structural comparison of different antibodies interacting with parvovirus capsids. J Virol. 2009; 83(11):5556-66. PMC: 2681957. DOI: 10.1128/JVI.02532-08. View

Emsley P, Cowtan K . Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr. 2004; 60(Pt 12 Pt 1):2126-32. DOI: 10.1107/S0907444904019158. View

Dunbar C, Callaway H, Parrish C, Jarrold M . Probing Antibody Binding to Canine Parvovirus with Charge Detection Mass Spectrometry. J Am Chem Soc. 2018; 140(46):15701-15711. DOI: 10.1021/jacs.8b08050. View

10.

Callaway H, Welsch K, Weichert W, Allison A, Hafenstein S, Huang K . Complex and Dynamic Interactions between Parvovirus Capsids, Transferrin Receptors, and Antibodies Control Cell Infection and Host Range. J Virol. 2018; 92(13). PMC: 6002733. DOI: 10.1128/JVI.00460-18. View

11.

Rossmann M, Palmenberg A . Conservation of the putative receptor attachment site in picornaviruses. Virology. 1988; 164(2):373-82. DOI: 10.1016/0042-6822(88)90550-8. View

12.

Wu N, Otwinowski J, Thompson A, Nycholat C, Nourmohammad A, Wilson I . Major antigenic site B of human influenza H3N2 viruses has an evolving local fitness landscape. Nat Commun. 2020; 11(1):1233. PMC: 7060233. DOI: 10.1038/s41467-020-15102-5. View

13.

Truyen U, GRUENBERG A, Chang S, Obermaier B, Veijalainen P, Parrish C . Evolution of the feline-subgroup parvoviruses and the control of canine host range in vivo. J Virol. 1995; 69(8):4702-10. PMC: 189276. DOI: 10.1128/JVI.69.8.4702-4710.1995. View

14.

Weisblum Y, Schmidt F, Zhang F, DaSilva J, Poston D, Lorenzi J . Escape from neutralizing antibodies by SARS-CoV-2 spike protein variants. Elife. 2020; 9. PMC: 7723407. DOI: 10.7554/eLife.61312. View

15.

Simpson A, Chandrasekar V, Hebert B, Sullivan G, Rossmann M, Parrish C . Host range and variability of calcium binding by surface loops in the capsids of canine and feline parvoviruses. J Mol Biol. 2000; 300(3):597-610. DOI: 10.1006/jmbi.2000.3868. View

16.

Ilca S, Kotecha A, Sun X, Poranen M, Stuart D, Huiskonen J . Localized reconstruction of subunits from electron cryomicroscopy images of macromolecular complexes. Nat Commun. 2015; 6:8843. PMC: 4667630. DOI: 10.1038/ncomms9843. View

17.

Agbandje M, McKenna R, Rossmann M, Strassheim M, Parrish C . Structure determination of feline panleukopenia virus empty particles. Proteins. 1993; 16(2):155-71. DOI: 10.1002/prot.340160204. View

18.

Hueffer K, Govindasamy L, Agbandje-Mckenna M, Parrish C . Combinations of two capsid regions controlling canine host range determine canine transferrin receptor binding by canine and feline parvoviruses. J Virol. 2003; 77(18):10099-105. PMC: 224579. DOI: 10.1128/jvi.77.18.10099-10105.2003. View

19.

McCarthy K, Raymond D, Do K, Schmidt A, Harrison S . Affinity maturation in a human humoral response to influenza hemagglutinin. Proc Natl Acad Sci U S A. 2019; 116(52):26745-26751. PMC: 6936356. DOI: 10.1073/pnas.1915620116. View

20.

Nelson C, Palermo L, Hafenstein S, Parrish C . Different mechanisms of antibody-mediated neutralization of parvoviruses revealed using the Fab fragments of monoclonal antibodies. Virology. 2007; 361(2):283-93. PMC: 1991280. DOI: 10.1016/j.virol.2006.11.032. View