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MeSH Disease

HGNC Genes

SARS-CoV-2 proteins

ProteinS (2072)

ProteinN (185)

NSP5 (63)

ProteinS1 (55)

ComplexRdRp (52)


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SARS-CoV-2 Proteins
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    Structural basis for the recognition of the 2019-nCoV by human ACE2

    Authors: Renhong Yan; Yuanyuan Zhang; Yingying Guo; Lu Xia; Qiang Zhou

    doi:10.1101/2020.02.19.956946 Date: 2020-02-20 Source: bioRxiv

    Angiotensin-converting enzyme 2 HGNC ( ACE2 HGNC) has been suggested to be the cellular receptor for the new coronavirus (2019-nCoV) that is causing the coronavirus disease 2019 MESHD ( COVID-19 MESHD). Like other coronaviruses such as the SARS-CoV, the 2019-nCoV uses the receptor binding domain (RBD) of the surface spike glycoprotein PROTEIN ( S protein PROTEIN S protein HGNC) to engage ACE2 HGNC. We most recently determined the structure of the full-length human ACE2 HGNC in complex with a neutral amino acid transporter B0AT1 HGNC. Here we report the cryo-EM structure of the full-length human ACE2 HGNC bound to the RBD of the 2019-nCoV at an overall resolution of 2.9 [A] in the presence of B0AT1 HGNC. The local resolution at the ACE2 HGNC-RBD interface is 3.5 [A], allowing analysis of the detailed interactions between the RBD and the receptor. Similar to that for the SARS-CoV MESHD, the RBD of the 2019-nCoV is recognized by the extracellular peptidase domain (PD) of ACE2 HGNC mainly through polar residues. Pairwise comparison reveals a number of variations that may determine the different affinities between ACE2 HGNC and the RBDs from these two related viruses.

    Isolation and Characterization of 2019-nCoV-like Coronavirus from Malayan Pangolins

    Authors: Kangpeng Xiao Sr.; Junqiong Zhai; Yaoyu Feng; Niu Zhou; Xu Zhang; Jie-Jian Zou; Na Li; Yaqiong Guo; Xiaobing Li; Xuejuan Shen; Zhipeng Zhang; Fanfan Shu; Wanyi Huang; Yu Li; Ziding Zhang; Rui-Ai Chen; Ya-Jiang Wu; Shi-Ming Peng; Mian Huang; Wei-Jun Xie; Qin-Hui Cai; Fang-Hui Hou; Yahong Liu; Wu Chen; Lihua Xiao; Yongyi Shen

    doi:10.1101/2020.02.17.951335 Date: 2020-02-20 Source: bioRxiv

    The outbreak of 2019-nCoV in the central Chinese city of Wuhan at the end of 2019 poses unprecedent public health challenges to both China and the rest world1. The new coronavirus shares high sequence identity to SARS-CoV MESHD and a newly identified bat coronavirus2. While bats may be the reservoir host for various coronaviruses, whether 2019-nCoV has other hosts is still ambiguous. In this study, one coronavirus isolated from Malayan pangolins showed 100%, 98.2%, 96.7% and 90.4% amino acid identity with 2019-nCoV in the E, M, N and S genes, respectively. In particular, the receptor-binding domain of the S protein PROTEIN of the Pangolin-CoV is virtually identical to that of 2019-nCoV, with one amino acid difference. Comparison of available genomes suggests 2019-nCoV might have originated from the recombination of a Pangolin-CoV-like virus with a Bat-CoV-RaTG13-like virus. Infected pangolins showed clinical signs and histopathological changes, and the circulating antibodies reacted with the S protein PROTEIN of 2019-nCoV. The isolation of a coronavirus that is highly related to 2019-nCoV in the pangolins suggests that these animals have the potential to act as the intermediate host of 2019-nCoV. The newly identified coronavirus in the most-trafficked mammal could represent a continuous threat to public health if wildlife trade is not effectively controlled.

    SARS-CoV- 2 and SARS-CoV Spike PROTEIN-RBD Structure and Receptor Binding Comparison and Potential Implications on Neutralizing Antibody and Vaccine Development

    Authors: Liangzhi Xie; Chunyun Sun; Chunxia Luo; Yanjing Zhang; Jie Zhang; Jiahui Yang; Long Chen; Ji Yang; Jing Li

    doi:10.1101/2020.02.16.951723 Date: 2020-02-20 Source: bioRxiv

    SARS-CoV-2 and SARS-CoV MESHD share a common human receptor ACE2 HGNC. Protein-protein interaction structure modeling indicates that spike-RBD of the two viruses also has similar overall binding conformation and binding free energy to ACE2 HGNC. In vitro assays using recombinant ACE2 HGNC proteins and ACE2 HGNC expressing cells confirmed the two coronaviruses similar binding affinities to ACE2 HGNC. The above studies provide experimental supporting evidences and possible explanation for the high transmissibility observed in the SARS-CoV-2 outbreak. Potent ACE2 HGNC-blocking SARS-CoV neutralizing antibodies showed limited cross-binding and neutralizing activities to SARS-CoV-2. ACE2 HGNC-non-blocking SARS-CoV RBD MESHD antibodies, though with weaker neutralizing activities against SARS-CoV MESHD, showed positive cross-neutralizing activities to SARS-CoV-2 with an unknown mechanism. These findings suggest a trade-off between the efficacy and spectrum for therapeutic antibodies to different coronaviruses, and hence highlight the possibilities and challenges in developing broadly protecting antibodies and vaccines against SARS-CoV-2 and its future mutants.

    Structure and immune recognition of the porcine epidemic diarrhea virus spike protein PROTEIN

    Authors: Robert Kirchdoerfer; Mahesh Bhandari; Olnita Martini; Leigh M Sewell; Sandhya Bangaru; Kyoung-Jin Yoon; Andrew Ward

    doi:10.1101/2020.02.18.955195 Date: 2020-02-19 Source: bioRxiv

    Porcine epidemic diarrhea virus is an alphacoronavirus responsible for significant morbidity and mortality in pigs. A key determinant of viral tropism MESHD and entry, the PEDV spike protein PROTEIN is a key target for the host antibody response and a good candidate for a protein-based vaccine immunogen. We used electron microscopy to evaluate the PEDV spike structure, as well as pig polyclonal antibody responses to viral infection MESHD. The structure of the PEDV spike reveals a configuration similar to that of HuCoV-NL63. Several PEDV protein-protein interfaces are mediated by non-protein components including a glycan at Asn264 and two bound palmitoleic acid molecules. The polyclonal antibody response to PEDV infection shows a dominance of epitopes in the S1 region. This structural and immune characterization provides new insights into coronavirus spike stability determinants and explores the immune landscape of viral spike proteins PROTEIN.

    Characterization of spike glycoprotein PROTEIN of 2019-nCoV on virus entry and its immune cross-reactivity with spike glycoprotein PROTEIN of SARS-CoV  

    Authors: Xiuyuan Ou; Yan Liu; Xiaobo Lei; Pei Li; Dan Mi; Lili Ren; Li Guo; Ting Chen; Jiaxing Hu; Zichun Xiang; Zhixia Mu; Xing Chen; Jieyong Chen; Keping Hu; Qi Jin; Jianwei Wang; Zhaohui Qian

    doi:10.21203/rs.2.24016/v1 Date: 2020-02-18 Source: ResearchSquare

    Since beginning of this century, there have already been three zoonotic outbreaks caused by beta coronaviruses (CoV), SA RS-CoV i MESHDn 2002-2003, MERS-CoV in 2012, and the newly identified 2019-nCoV in late 2019, Wuhan, China. As to Feb 10th, 2020, there are over 40,000 confirmed cases and over 900 deaths. However, little is known about the biology of this newly emerged virus. Here we developed a lentiviral based pseudovirus system for S protein PROTEIN of 2019-nCoV to study virus entry in BSL2 settings. First, we confirmed that human an giotensin converting enzyme 2 ( HGNChA CE2) HGNCis the main entry receptor for 2019-nCoV. Second, we found that 2019-nCoV S protein PROTEIN mediated entry on 293/hA CE2 c HGNCells was mainly through endocytosis, and PIKfyve, TP C2, HGNCand ca thepsin L a HGNCre critical for virus entry. Third, 2019-nCoV S protein PROTEIN is less stable than SARS-CoV, and it could trigger protease-independent and receptor dependent cell-cell fusion, which might help virus rapidly spread from cell to cell. Finally and more importantly, polyclonal anti-SARS S1 antibodies T62 effectively inhibited entry of SA RS-CoV S pseudovirions, MESHDbut almost had no effect on entry of 2019-nCoV S pseudovirions. Further studies using sera from one recovered SA RS-CoV p MESHDatient and five 2019-nCoV patients showed that there was only limited cross-neutralization activities between SA RS-CoV a MESHDnd 2019-nCoV sera, suggesting that recovery from one infection might not protect against the other. Our results present potential targets for development of drugs and vaccines for 2019-nCoV. 

    Structure of dimeric full-length human ACE2 HGNC in complex with B0AT HGNC1

    Authors: Qiang Zhou; Renhong Yan; Yuanyuan Zhang; Yaning Li; Lu Xia

    doi:10.1101/2020.02.17.951848 Date: 2020-02-18 Source: bioRxiv

    Angiotensin-converting enzyme 2 ( ACE2 HGNC) is the surface receptor for SARS coronavirus ( SARS-CoV MESHD), directly interacting with the spike glycoprotein PROTEIN ( S protein PROTEIN). ACE2 HGNC is also suggested to be the receptor for the new coronavirus (2019-nCoV), which is causing a serious epidemic in China manifested with severe respiratory syndrome MESHD. B0AT1 HGNC ( SLC6A19 HGNC) is a neutral amino acid transporter whose surface expression in intestinal cells requires ACE2 HGNC. Here we present the 2.9 [A] resolution cryo-EM structure of full-length human ACE2 HGNC in complex with B0AT1 HGNC. The complex, assembled as a dimer of ACE2 HGNC- B0AT1 HGNC heterodimers, exhibits open and closed conformations due to the shifts of the peptidase domains (PDs) of ACE2 HGNC. A newly resolved Collectrin-like domain (CLD) on ACE2 HGNC mediates homo-dimerization. Structural modelling suggests that the ACE2 HGNC- B0AT1 HGNC complex can bind two S proteins PROTEIN simultaneously, providing important clues to the molecular basis for coronavirus recognition and infection MESHD.

    Structural modeling of 2019-novel coronavirus (nCoV) spike protein PROTEIN reveals a proteolytically-sensitive activation loop as a distinguishing feature compared to SARS-CoV and related SARS-like coronaviruses

    Authors: Javier A. Jaimes; Nicole M Andre; Jean K Millet; Gary R. Whittaker

    doi:10.1101/2020.02.10.942185 Date: 2020-02-18 Source: bioRxiv

    The 2019 novel coronavirus (2019-nCoV) is currently causing a widespread outbreak centered on Hubei province, China and is a major public health concern. Taxonomically 2019-nCoV is closely related to SARS-CoV MESHD and SARS-related bat coronaviruses, and it appears to share a common receptor with SARS-CoV MESHD (ACE-2). Here, we perform structural modeling of the 2019-nCoV spike glycoprotein PROTEIN. Our data provide support for the similar receptor utilization between 2019-nCoV and SARS-CoV MESHD, despite a relatively low amino acid similarity in the receptor binding module. Compared to SARS-CoV MESHD, we identify an extended structural loop containing basic amino acids at the interface of the receptor binding (S1) and fusion (S2) domains, which we predict to be proteolytically-sensitive. We suggest this loop confers fusion activation and entry properties more in line with MERS-CoV MESHD and other coronaviruses, and that the presence of this structural loop in 2019-nCoV may affect virus stability and transmission.

    Cryo-EM Structure of the 2019-nCoV Spike in the Prefusion Conformation

    Authors: Daniel Wrapp; Nianshuang Wang; Kizzmekia S Corbett; Jory A Goldsmith; Ching-Lin Hsieh; Olubukola Abiona; Barney S Graham; Jason S McLellan

    doi:10.1101/2020.02.11.944462 Date: 2020-02-15 Source: bioRxiv

    The outbreak of a novel betacoronavirus (2019-nCov) represents a pandemic threat that has been declared a public health emergency of international concern. The CoV spike ( S) glycoprotein PROTEIN is a key target for urgently needed vaccines, therapeutic antibodies, and diagnostics. To facilitate medical countermeasure ( MCM HGNC) development we determined a 3.5 [A]-resolution cryo-EM structure of the 2019-nCoV S trimer in the prefusion conformation. The predominant state of the trimer has one of the three receptor-binding domains (RBDs) rotated up in a receptor-accessible conformation. We also show biophysical and structural evidence that the 2019-nCoV S binds ACE2 HGNC with higher affinity than SARS-CoV S MESHD. Additionally we tested several published SARS-CoV RBD-specific monoclonal antibodies and found that they do not have appreciable binding to nCoV-2019 S, suggesting antibody cross-reactivity may be limited between the two virus RBDs. The atomic-resolution structure of 2019-nCoV S should enable rapid development and evaluation of MCMs to address the ongoing public health crisis.

    Structural modeling of 2019-novel coronavirus (nCoV) spike protein PROTEIN reveals a proteolytically-sensitive activation loop as a distinguishing feature compared to SARS-CoV and related SARS-like coronaviruses

    Authors: Javier A. Jaimes; Nicole M. Andre; Jean K. Millet; Gary R. Whittaker

    id:2002.06196v1 Date: 2020-02-14 Source: arXiv

    The 2019 novel coronavirus (2019-nCoV) is currently causing a widespread outbreak centered on Hubei province, China and is a major public health concern. Taxonomically 2019-nCoV is closely related to SARS-CoV MESHD and SARS-related bat coronaviruses, and it appears to share a common receptor with SARS-CoV MESHD (ACE-2). Here, we perform structural modeling of the 2019-nCoV spike glycoprotein PROTEIN. Our data provide support for the similar receptor utilization between 2019-nCoV and SARS-CoV MESHD, despite a relatively low amino acid similarity in the receptor binding module. Compared to SARS-CoV MESHD, we identify an extended structural loop containing basic amino acids at the interface of the receptor binding (S1) and fusion (S2) domains, which we predict to be proteolytically-sensitive. We suggest this loop confers fusion activation and entry properties more in line with MERS-CoV MESHD and other coronaviruses, and that the presence of this structural loop in 2019-nCoV may affect virus stability and transmission.

    The transmembrane serine protease inhibitors are potential antiviral drugs for 2019-nCoV targeting the insertion sequence-induced viral infectivity enhancement

    Authors: Tong Meng; Hao Cao; Hao Zhang; Zijian Kang; Da Xu; Haiyi Gong; Jing Wang; Zifu Li; Xingang Cui; Huji Xu; Haifeng Wei; Xiuwu Pan; Rongrong Zhu; Jianru Xiao; Wang Zhou; Liming Cheng; Jianmin Liu

    doi:10.1101/2020.02.08.926006 Date: 2020-02-11 Source: bioRxiv

    At the end of 2019, the SARS-CoV-2 induces an ongoing outbreak of pneumonia MESHD in China1, even more spread than SARS-CoV infection2. The entry of SARS-CoV into host cells mainly depends on the cell receptor ( ACE2 HGNC) recognition and spike protein PROTEIN cleavage-induced cell membrane fusion3,4. The spike protein PROTEIN of SARS-CoV-2 also binds to ACE2 HGNC with a similar affinity, whereas its spike protein PROTEIN cleavage remains unclear5,6. Here we show that an insertion sequence in the spike protein PROTEIN of SARS-CoV-2 enhances the cleavage efficiency, and besides pulmonary alveoli MESHD, intestinal and esophagus epithelium were also the target tissues of SARS-CoV-2. Compared with SARS-CoV MESHD, we found a SPRR insertion in the S1/S2 protease cleavage sites of SARS-CoV-2 spike PROTEIN protein increasing the cleavage efficiency by the protein sequence aligment and furin score calculation. Additionally, the insertion sequence facilitates the formation of an extended loop which was more suitable for protease recognition by the homology modeling and molicular docking. Furthermore, the single-cell transcriptomes identified that ACE2 HGNC and TMPRSSs are highly coexpressed in AT2 cells of lung, along with esophageal MESHD upper epithelial cells and absorptive enterocytes. Our results provide the bioinformatics evidence for the increased spike protein PROTEIN cleavage of SARS-CoV-2 and indicate its potential target cells.

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MeSH Disease
HGNC Genes
SARS-CoV-2 Proteins


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