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Instruments / Technical Area	Publication Details	Published	Actions
Krios II-Titan Krios II at Diamond Krios IV-Titan Krios IV at Diamond	Application of super-resolution and correlative double sampling in cryo-electron microscopy Yuewen Sheng , Peter J. Harrison , Vinod Vogirala , Zhengyi Yang , Claire Strain-Damerell , Thomas Frosio , Benjamin A. Himes , C. Alistair Siebert , Peijun Zhang , Daniel Clare Faraday Discussions DOI: 10.1039/D2FD00049K Diamond Proposal Number(s): [26464, 28151] Open Access Show Abstract ▼ Abstract: Developments in cryo-EM have allowed atomic or near-atomic resolution structure determination to become routine in single particle analysis (SPA). However, near-atomic resolution structures determined using cryo-electron tomography and sub-tomogram averaging (cryo-ET STA) are much less routine. In this paper, we show that by collecting cryo-ET STA data using the same conditions as SPA, with both Correlated Double Sampling (CDS) and super-resolution mode, allowed apoferritin to be reconstructed out to the physical Nyquist frequency of the images. Even with just two tilt series, STA yields an apoferritin map at 2.9 Å resolution. These results highlight the exciting potential of cryo-ET STA in the future of protein structure determination. While processing SPA data recorded in super-resolution mode may yield structures surpassing the physical Nyquist limit, processing cryo-ET STA data in super-resolution mode gave no additional resolution benefit. We further show that collecting SPA data in super-resolution mode, with CDS activated, reduces the estimated B-factor, leading to a reduction in the number of particles required to reach a target resolution without compromising data size on disk and area imaged in SerialEM. However, collecting SPA data in CDS does reduce throughput, given that a similar resolution structure, with a slightly larger B-factor, is achievable with optimised parameters for speed in EPU (without CDS).	Apr 2022
Krios I-Titan Krios I at Diamond Krios II-Titan Krios II at Diamond Krios IV-Titan Krios IV at Diamond	Structure of native HIV-1 cores and their interactions with IP6 and CypA Tao Ni , Yanan Zhu , Zhengyi Yang , Chaoyi Xu , Yuriy Chaban , Tanya Nesterova , Jiying Ning , Till Böcking , Michael W. Parker , Christina Monnie , Jinwoo Ahn , Juan R. Perilla , Peijun Zhang Science Advances 7 DOI: 10.1126/sciadv.abj5715 Diamond Proposal Number(s): [21004, 20223] Open Access Show Abstract ▼ Abstract: The viral capsid plays essential roles in HIV replication and is a major platform engaging host factors. To overcome challenges in study native capsid structure, we used the perfringolysin O to perforate the membrane of HIV-1 particles, thus allowing host proteins and small molecules to access the native capsid while improving cryo–electron microscopy image quality. Using cryo–electron tomography and subtomogram averaging, we determined the structures of native capsomers in the presence and absence of inositol hexakisphosphate (IP6) and cyclophilin A and constructed an all-atom model of a complete HIV-1 capsid. Our structures reveal two IP6 binding sites and modes of cyclophilin A interactions. Free energy calculations substantiate the two binding sites at R18 and K25 and further show a prohibitive energy barrier for IP6 to pass through the pentamer. Our results demonstrate that perfringolysin O perforation is a valuable tool for structural analyses of enveloped virus capsids and interactions with host cell factors.	Nov 2021

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