Structure Determination of an Fab Fragment that Neutralizes Human Rhinovirus 14 and Analysis of the Fab-Virus Complex

Liu, Hansong; Smith, Thomas J.; Lee, Wai Ming; Mosser, Anne G.; Rueckert, Roland R.; Olson, Norman H.; Cheng, R. Holland; Baker, Timothy S.

doi:10.1006/jmbi.1994.1427

Cited by 50 publications

(35 citation statements)

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“…These observations suggest that NIm-III-binding neutralizing antibodies might use a common neutralizing mechanism by triggering genome release of EVs. In contrast, previous structural studies on antibodies that target other NIm sites on RV-B14 or homologous sites on other EVs have not shown that these antibodies cause virus uncoating (28)(29)(30)(31)(32).…”

Section: Resultsmentioning

confidence: 84%

Antibody-induced uncoating of human rhinovirus B14

Dong

Liu

Jiang

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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Rhinoviruses (RVs) are the major causes of common colds in humans. They have a nonenveloped, icosahedral capsid surrounding a positive-strand RNA genome. Here we report that the antigenbinding (Fab) fragment of a neutralizing antibody (C5) can trigger genome release from RV-B14 to form emptied particles and neutralize virus infection. Using cryo-electron microscopy, structures of the C5 Fab in complex with the full and emptied particles have been determined at 2.3 Å and 3.0 Å resolution, respectively. Each of the 60 Fab molecules binds primarily to a region on viral protein 3 (VP3). Binding of the C5 Fabs to RV-B14 results in significant conformational changes around holes in the capsid through which the viral RNA might exit. These results are so far the highest resolution view of an antibody-virus complex and elucidate a mechanism whereby antibodies neutralize RVs and related viruses by inducing virus uncoating.rhinovirus | antibody | cryo-electron microscopy | genome release | atomic structure

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Section: Resultsmentioning

confidence: 84%

Antibody-induced uncoating of human rhinovirus B14

Dong

Liu

Jiang

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

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“…For this analysis, the MNV-1-Fab model was constructed using the pseudo-atomic model described in the accompanying paper (24), the ϳ22-Å resolution 3D image reconstruction of the MNV-1-Fab A6.2 complex previously described (25), an MNV-1 P-domain dimer, and the structure of Fab17 (31,52,54). As detailed in the accompanying paper (24), the highresolution image reconstruction of MNV-1 has marked "horns" (protrusions made by loops AЈ-BЈ and EЈ-FЈ) at the top of the P domains that closely match the closed conformation.…”

Section: Resultsmentioning

confidence: 99%

“…The structure of Fab17 is only an approximation for that of the bound A6.2, and as was seen in the case of Fab17 (31,52), flexibility of the hypervariable region may allow the antibody to mold itself to the epitope region. As was shown in our previous studies, where the structures of human rhinovirus 14, the Fab, and the Fab-virus complex were all known (52), pseudo-atomic models made from 3D reconstructions at this resolution can be off by several angstroms (8), and this can have a significant effect on predicted contact points.…”

Section: Resultsmentioning

confidence: 99%

“…MNV-1-Fab complex previously described (25), the crystal structure of the MNV-1 P-domain dimer in the "closed" conformation, and the structure of Fab17 (31,52,54). The electron density from the previous 3D image reconstruction of the MNV-1-Fab complex was then overlaid onto this pseudo-atomic model of MNV-1, and the structure of the antibody, Fab17, was manually placed into the envelope corresponding to the bound Fab.…”

Section: Methodsmentioning

confidence: 99%

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High-Resolution X-Ray Structure and Functional Analysis of the Murine Norovirus 1 Capsid Protein Protruding Domain

Taube

Rubin

Katpally

et al. 2010

J Virol

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127

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Murine noroviruses (MNV) are closely related to the human noroviruses (HuNoV), which cause the majority of nonbacterial gastroenteritis. Unlike HuNoV, MNV grow in culture and in a small-animal model that represents a tractable model to study norovirus biology. To begin a detailed investigation of molecular events that occur during norovirus binding to cells, the crystallographic structure of the murine norovirus 1 (MNV-1) capsid protein protruding (P) domain has been determined. Crystallization of the bacterially expressed protein yielded two different crystal forms (Protein Data Bank identifiers [PDB ID], 3LQ6 and 3LQE). Comparison of the structures indicated a large degree of structural mobility in loops on the surface of the P2 subdomain. Specifically, the A-B and E-F loops were found in open and closed conformations. These regions of high mobility include the known escape mutation site for the neutralizing antibody A6.2 and an attenuation mutation site, which arose after serial passaging in culture and led to a loss in lethality in STAT1 ؊/؊ mice, respectively. Modeling of a Fab fragment and crystal structures of the P dimer into the cryoelectron microscopy three-dimensional (3D) image reconstruction of the A6.2/ MNV-1 complex indicated that the closed conformation is most likely bound to the Fab fragment and that the antibody contact is localized to the A-B and E-F loops. Therefore, we hypothesize that these loop regions and the flexibility of the P domains play important roles during MNV-1 binding to the cell surface.Murine noroviruses (MNV) are members of the family Caliciviridae, which contains small icosahedral viruses with positive-sense, single-stranded RNA genomes (18). MNV is related to human noroviruses (HuNoV), which cause most of the sporadic cases and outbreaks of infectious nonbacterial gastroenteritis worldwide in people of all ages (4,15,28,36,38,64). However, noroviruses are an understudied group of viruses due to the previous lack of a tissue culture system and small-animal model. Since its discovery in 2003 (23), MNV has become an increasingly important model to study norovirus biology (66). The availability of a small-animal model, cell culture, and reverse-genetics system, combined with many shared characteristics of human and murine noroviruses, allows detailed studies of norovirus biology (7,23,63,65,66).The norovirus genome is organized into 3 major open reading frames (ORFs), which encode the nonstructural polyprotein (ϳ200 kDa) and the major (VP1; ϳ58-kDa) and minor (VP2; ϳ20-kDa) capsid proteins (18). Recently, a putative ORF-4 was identified in MNV, but the existence of that product and its function remain unknown (60). Norovirus capsids are formed from 180 copies of VP1 arranged with Tϭ3 icosahedral symmetry (9,25,(46)(47)(48). Each capsid protein is divided into an N-terminal arm (N), a shell (S), and a C-terminal protruding (P) domain, with the last two domains connected by a short hinge. VP1 self-assembles into virus-like particles (VLPs) in baculovirus, mammalian, and plant e...

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“…Thus, Fab 22A12 does not act as a canyon-binding receptor to trigger A-particle formation. Alternatively, antibodies bound at the canyons of other picornaviruses have been shown to neutralize by capsid stabilization and/or blocking receptor binding (50,51). However, the low affinity of Fab 22A12 argues against the ability of antibody to stabilize capsids or outcompete the receptor effectively.…”

Section: Discussionmentioning

confidence: 99%

The Enterovirus 71 Procapsid Binds Neutralizing Antibodies and Rescues Virus Infection In Vitro

Shingler

Cifuente

Ashley

et al. 2015

J Virol

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Enterovirus 71 (EV71) is responsible for seasonal outbreaks of hand, foot, and mouth disease in the Asia-Pacific region. The virus has the capability to cause severe disease and death, especially in young children. Although several vaccines are currently in clinical trials, no vaccines or therapeutics have been approved for use. Previous structural studies have revealed that two antigenically distinct capsid forms are produced in EV71-infected cells: an expanded empty capsid, sometimes called a procapsid, and the infectious virus. Specifically, an immunodominant epitope of EV71 that maps to the virus canyon is structurally different in the procapsid and virus. This structure-function study shows that the procapsid can sequester antibodies, thus enhancing EV71 infection in vitro. The results presented here suggest that, due to conformational differences between the EV71 procapsid and virus, the presence of the procapsid in natural virus infections should be considered in the future design of vaccines or therapeutics. IMPORTANCEIn a picornavirus infection, both an infectious and a noninfectious empty capsid, sometimes referred to as a procapsid, are produced. It was novel to discover that the procapsid form of EV71 was expanded and antigenically distinct from the infectious virus. Previously, it had been supposed that this empty capsid was an off-pathway dead end or at best served for storage of pentameric subunits, which was later shown to be unlikely. It remains unexplained why picornaviruses evolutionarily conserve the wasteful production of so much noninfectious capsid. Here, we demonstrate that the EV71 procapsid has different antigenic properties than the infectious virus. Thus, the procapsid has the capacity to sequester neutralizing antibody and protect the virus, promoting or restoring a successful infection in vitro. This important observation should be considered in the future design and development of vaccines and therapeutics.

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Structure Determination of an Fab Fragment that Neutralizes Human Rhinovirus 14 and Analysis of the Fab-Virus Complex

Cited by 50 publications

References 0 publications

Antibody-induced uncoating of human rhinovirus B14

Antibody-induced uncoating of human rhinovirus B14

High-Resolution X-Ray Structure and Functional Analysis of the Murine Norovirus 1 Capsid Protein Protruding Domain

The Enterovirus 71 Procapsid Binds Neutralizing Antibodies and Rescues Virus Infection In Vitro

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