e Previous human antibody studies have shown that the human V H 1-46 antibody variable gene segment encodes much of the naturally occurring human B cell response to rotavirus and is directed to virus protein 6 (VP6). It is currently unknown why some of the V H 1-46-encoded human VP6 monoclonal antibodies inhibit viral transcription while others do not. In part, there are affinity differences between antibodies that likely affect inhibitory activity, but we also hypothesize that there are differing modes of binding to VP6 that affect the ability to block the transcriptional pore on double-layered particles. Here, we used a hybrid method approach for antibody epitope mapping, including single-particle cryo-electron microscopy (cryo-EM) and enhanced amide hydrogen-deuterium exchange mass spectrometry (DXMS) to determine the location and mode of binding of a V H 1-46-encoded antibody, RV6-25. The structure of the RV6-25 antibody-double-layered particle (DLP) complex indicated a very complex binding pattern that revealed subtle differences in accessibility of the VP6 epitope depending on its position in the type I, II, or III channels. These subtle variations in the presentation or accessibility of the RV VP6 capsid layer led to position-specific differences in occupancy for binding of the RV6-25 antibody. The studies also showed that the location of binding of the noninhibitory antibody RV6-25 on the apical surface of RV VP6 head domain does not obstruct the transcription pore upon antibody binding, in contrast to binding of an inhibitory antibody, RV6-26, deeper in the transcriptional pore. R otaviruses (RVs) are nonenveloped, triple-layered icosahedral viruses that belong to the Reoviridae family, and they are the leading cause of severe diarrheal illness in infants and young children worldwide (1). The inner capsid layer of virus protein 2 (VP2) encloses 11 segments of double-stranded RNA that each encode a single protein, except for segment 11, which codes for two proteins. The VP2 layer is surrounded by 780 molecules of virus protein 6 (VP6). VP6 is arranged into 260 trimers and forms the intermediate viral capsid layer. The VP2 and VP6 layers form the transcriptionally active double-layered particle (DLP). The outer capsid layer is composed of virus protein 7 (VP7) with spikes of virus protein 4 (VP4) and forms the transcriptionally inactive mature infectious virion particle (2-8).RV VP6 is folded into two distinct domains: an ␣-helical base domain with a triangular cross section and a jelly-roll head domain that forms a roughly hexagonal cross section. The Tϭ13 icosahedral symmetry of the VP6 and VP7 layers defines three types of channels that exist within the viral architecture: type I, II, and III channels. Twelve type I channels are located down the icosahedral 5-fold axes and serve as egress points of nascent viral mRNA during viral transcription (6). Sixty type II channels are arranged to surround the type I channels, and 60 type III channels are positioned around the icosahedral 3-fold axes (5, 9-12). W...