Journal: eLife

Article Title: Boosting of cross-reactive antibodies to endemic coronaviruses by SARS-CoV-2 infection but not vaccination with stabilized spike

doi: 10.7554/eLife.75228

Figure Lengend Snippet: ( A ) Structural models of the N-terminal domain (NTD) and receptor-binding domain (RBD) as ribbons, colored by strain: SARS-CoV-2 (black), 229E (orange), OC43 (blue), NL63 (green), and HKU1 (yellow). Structural alignments were restricted to the residues of the S1 domain. Right alignments between SARS-CoV2 and the endemic S1 domains shown individually rather than overlayed, with β-CoV at left, and α-CoV at right.

Article Snippet: Peptide, recombinant protein , NL63 S , Sino Biological , 40606-V08B , .

Techniques: Binding Assay

Journal: eLife

Article Title: Boosting of cross-reactive antibodies to endemic coronaviruses by SARS-CoV-2 infection but not vaccination with stabilized spike

doi: 10.7554/eLife.75228

Figure Lengend Snippet:

Article Snippet: Peptide, recombinant protein , NL63 S , Sino Biological , 40606-V08B , .

Techniques: Recombinant, Produced, Plasmid Preparation, Software

Journal: Nature Structural & Molecular Biology

Article Title: Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy

doi: 10.1038/nsmb.3293

Figure Lengend Snippet: ( a ) Representative micrograph of frozen-hydrated HCoV-NL63 S particles (defocus 3.4 μm). Scale bar, 355 Å. ( b ) Five selected class averages showing the particles along different orientations. Scale bar, 60 Å. ( c , d ) 3D map filtered at 3.4-Å resolution and colored by protomer. Two orthogonal views of the S trimer from the side ( c ) and from the top, facing toward the viral membrane, ( d ) are shown. ( e , f ) Ribbon diagrams showing the HCoV-NL63 S atomic model, oriented as in c and d , respectively.

Article Snippet: HCoV-NL63 S was prepared for MS analysis unaltered or subjected to Endo H (NEB), subjected to Endo F3 (Millipore) or subjected to combined Endo H and Endo F3 deglycosylation treatment.

Techniques:

Journal: Nature Structural & Molecular Biology

Article Title: Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy

doi: 10.1038/nsmb.3293

Figure Lengend Snippet: ( a ) Ribbon diagram of the S 2 trimer, colored by protomer with glycans rendered as dark-blue spheres. ( b ) Zoomed-in view of the S 2 ′ trigger-loop region comprising the central helix and the fusion peptide (light blue). N-linked glycans are shown as dark-blue spheres. The polypeptide segment corresponding to the putative cleavage site is poorly resolved in the density, and this part of the model should be considered to be hypothetical. ( c , d ) Ribbon diagrams showing two orthogonal views of the S 2 ′ C-terminal region, which is assembled from the connector domains and stem helices. ( e , f ) Ribbon diagrams of the HCoV-NL63 S 2 subunit ( e ) and of the RSV F protein ( f ). Conserved structural elements are colored identically to highlight the similar 3D organization of these two fusion machineries, whereas nonconserved regions are colored gray. The topology diagrams underscore the similar topology of the HCoV-NL63 S connector domain and the equivalent RSV F domain, although the tertiary structures of these domains are different, and several structural motifs have been added to the latter domain throughout evolution. The RSV F secondary-structural elements are annotated according to ref. . The N- and C-terminal extremities of the polypeptide segments are indicated.

Article Snippet: HCoV-NL63 S was prepared for MS analysis unaltered or subjected to Endo H (NEB), subjected to Endo F3 (Millipore) or subjected to combined Endo H and Endo F3 deglycosylation treatment.

Techniques:

Journal: Nature Structural & Molecular Biology

Article Title: Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy

doi: 10.1038/nsmb.3293

Figure Lengend Snippet: ( a ) Schematic representation of several α-coronavirus S-glycoprotein S1 subunits, highlighting the presence of one or several domains 0 (blue), as compared with β-coronaviruses. HCoV-NL63 (GenBank YP_003767.1 ), 229-rel. CoV 1 (GenBank ALK28775.1 ), 229-rel. CoV 2 (GenBank ALK28765.1 ), HCoV-229E (GenBank NP_073551.1 ), porcine epidemic diarrhea virus (PEDV; GenBank AAK38656.1 ), transmissible gastroenteritis virus strain Purdue P115 (TGEV; GenBank ABG89325.1 ), porcine respiratory coronavirus strain ISU-1 (PRCV; GenBank ABG89317.1 ), feline enteric coronavirus strain UU23 (FECV-UU23; GenBank ADC35472.1 ) and feline infectious peritonitis coronavirus strain UU21 (FIPV-UU21; GenBank ADL71466.1 ). The β-coronavirus MHV S 1 subunit is shown for comparison. Domains A–D are indicated for MHV and HCoV-NL63. ( b ) Ribbon diagram of the HCoV-NL63 S 1 subunit. ( c ) Ribbon diagram of the MHV S 1 subunit. ( d – g ) Ribbon diagrams of HCoV-NL63 domain 0 ( d ), domain A ( e ), MHV domain A ( f ) and rotavirus VP8* ( g ), showing their structural similarity, which suggests common ancestry. HCoV-NL63 domain 0 and A probably arose from a duplication event.

Article Snippet: HCoV-NL63 S was prepared for MS analysis unaltered or subjected to Endo H (NEB), subjected to Endo F3 (Millipore) or subjected to combined Endo H and Endo F3 deglycosylation treatment.

Techniques:

Journal: Nature Structural & Molecular Biology

Article Title: Glycan shield and epitope masking of a coronavirus spike protein observed by cryo-electron microscopy

doi: 10.1038/nsmb.3293

Figure Lengend Snippet: ( a ) Ribbon diagram of the HCoV-NL63 S trimer, highlighting the conformation of the S 1 subunit. Domains 0, A, B, C and D are colored for one protomer. ( b ) The HCoV-NL63 receptor-binding loops are buried via interactions with domain A of the same protomer (including the glycan moiety at Asn358) and are not available to engage host-cell receptors. Superimposition of the HCoV-NL63 (purple) and MHV (light gray) S 1 subunits via their C domains highlights that their B domains feature opposite orientations related by an ∼180° rotation, thus suggesting a putative trajectory for the conformational changes that must occur to engage the host-cell receptor. Only domain B is shown for MHV S. ( c ) Comparison of the HCoV-NL63 domain-B structure in our cryo-EM-derived model (purple) with the crystal structure of the same domain in complex with ACE2 (green and dark gray), showing that the receptor-binding loop containing residues 531–539 substantially changes its conformation after binding. ( d ) ACE2 binding ELISA showing that isolated HCoV-NL63 domain B (HCoV-NL63 S 1 -B-mFc) binds ACE2 with higher affinity than does the full-length S 1 domain (HCoV-NL63 S 1 -mFc). SARS-CoV S 1 (HCoV-NL63 S 1 -mFc) is a positive control. HCoV-NL63 S 1 domain 0 (HCoV-NL63 S 1 -0-mFc) and PEDV S 1 (PEDV S 1 -mFc), which do not bind ACE2, are negative controls. Mean values and s.d. of three independent experiments are shown.

Article Snippet: HCoV-NL63 S was prepared for MS analysis unaltered or subjected to Endo H (NEB), subjected to Endo F3 (Millipore) or subjected to combined Endo H and Endo F3 deglycosylation treatment.

Techniques: Binding Assay, Cryo-EM Sample Prep, Derivative Assay, Enzyme-linked Immunosorbent Assay, Isolation, Positive Control

Journal: medRxiv

Article Title: Decay of Fc-dependent antibody functions after mild to moderate COVID-19

doi: 10.1101/2020.12.13.20248143

Figure Lengend Snippet: (A) Best fit decay slopes of IgG and dimeric FcγR-binding antibodies against S from HCoV strains OC43, HKU1, 229E and NL63. The responses at timepoint 1 for each parameter are set to 100% and the %change over time is shown. (B-C) Kinetics of dimeric FcγRIIIa (V158) and FcγRIIa (H131) binding antibodies against HCoV-OC43 S antigens over time in COVID-19 convalescent individuals (n=53). The best-fit decay slopes (red lines) and estimated half-lives ( t ½ ) are indicated for COVID-19 convalescent individuals. Uninfected controls (n=33) are shown in open circles, with the median and 90% percentile responses presented as thick and thin dashed lines respectively. The limit of detection is shown as the shaded area.

Article Snippet: As previously described , a custom multiplex bead array was designed and coupled with SARS-CoV-2 S trimer, S1 subunit (Sino Biological), S2 subunit (ACRO Biosystems) and RBD (BEI Resources), as well as HCoV (OC43, HKU1, 229E, NL63) S (Sino Biological) (Table S2).

Techniques: Binding Assay