Cryo-EM of an Anti-enterovirus Cross Species Neutralizing Antibody
Bibliographic record
Abstract
Enteroviruses (EVs) are common and ubiquitous human pathogens. This genus includes poliovirus, echoviruses, Coxackieviruses A and B, EVs A and D, as well as human rhinovirus (HRV). These single stranded (+) RNA viruses can cause a broad spectrum of serious illness. Infection with these pathogens is known to elicit the production of cross-reactive antibodies to other species of enteroviruses. The significance of these cross-reactive antibodies to antiviral immunity is not well understood. These antibodies are assumed not to neutralize infection as they are thought to recognize shared epitopes that are only exposed when the conformation of the virion is perturbed [1]. Using plaque reduction and enzyme-linked immunosorbent assay (ELISA)-based binding assays, we determined that cross-species anti-EV monospecific polyclonal sera can block infection of cells in culture by a heterologous EV. As polyclonal sera are mixtures of hundreds, if not thousands, of individual mAbs, we performed plaque reduction assays using site specific anti-poliovirus P1/Mahoney mAbs. To determine if known antipoliovirus site-specific mAbs can bind heterologous EVs, murine monoclonal site specific antipoliovirus antibodies were incubated with multiple EVs. The poliovirus mAb that binds the border of two adjacent pentamers, at the three-fold symmetry axis (site 4), interacted with HRV-A1A, multiple isolates of EV-D68, EV-A71 and echovirus 29 while antibodies that recognizes site 2 bound EV-A71 and HRV-A1A but no isolate of EV-D68 tested. Furthermore, mAbs against site 4 of poliovirus were able to protect cells in culture from infection with HRV-A1A. We used cryo-electron microscopy (cryo-EM) to determine the structure of this cross-species neutralizing antibody as a fAb bound to Mahoney strain poliovirus (serotype 1). With our high-resolution cryo-EM map, we used an automated atomic model building tool, Modelangelo [2], to produce an atomic model of the bound fAb which describes the interaction of this cross-reactive antibody bound to poliovirus. We believe this cross-reactive antibody neutralizes infection by stabilizing capsid conformation, thus preventing genome translocation. We will compare the interface this cross-species neutralizing antibody forms with poliovirus and HRV-A1A. The results from this study will provide further insight into the antigenic relationship of EVs and mechanisms of antibody mediated protection. (A) Cryo-EM density map of poliovirus bound by cross-species neutralizing antibody (gray). (B) Surface representation of cross-species neutralizing fAb atomic model (violet). (C) This cross-species neutralizing antibody binds the three-fold axis of the poliovirus capsid, interfacing with VP2 (yellow) and VP3 (red). (D) Surface representation of the previously described crystal structure of Mahoney strain poliovirus (1HXS) [3] fit within our cryo-EM density map. Viral proteins are colored by radial distance from the center of the capsid. (A) Cross-species neutralizing antibody atomic model and the previously described crystal structure of Mahoney strain poliovirus (1HXS) fit within our cryo-EM density map, color coded to depict the distance between capsid and fAb residues. (B) Close up of color-coded atomic models and cryo-EM density map within box of panel A. (C) Capsid proteins are labeled to show that the interface between fAb and Mahoney strain poliovirus is formed between two copies of VP2 and one copy of VP3.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.001 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.001 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.005 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".