Stabilised BA.1 SARS-CoV-2 spike with H6 nanobodies in '3 up' RBD conformation
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8oyt
Q-score: 0.161
Cornish K, Huo J, Jones L, Sharma P, Thrush JW, Abdelkarim S, Kipar A, Ramadurai S, Weckener M, Mikolajek H, Liu S, Buckle I, Bentley E, Kirby A, Han X, Laidlaw SM, Hill M, Eyssen L, Norman C, Le Bas A, Clarke J, James W, Stewart JP, Carroll M, Naismith JH, Owens RJ
Open Biol (2024) 14 pp. 230252-230252 [ DOI: doi:10.1098/rsob.230252 Pubmed: 38835241 ]
- H6 nanobody (14 kDa, Protein from Lama glama)
- Stabilised hexapro omicron ba.1 spike trimer (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein,fibritin (140 kDa, Protein from Tequatrovirus T4)
- Complex of stabilised hexapro omicron ba.1 spike trimer with three h6 nanobodies (Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- H6 nanobody (Complex from Lama glama)
Stabilised BA.1 SARS-CoV-2 spike with H6 nanobodies in '2 up 1 down' RBD conformation
Resolution: 4.0 Å
EM Method: Single-particle
Fitted PDBs: 8oyu
Q-score: 0.145
Cornish K, Huo J, Jones L, Sharma P, Thrush JW, Abdelkarim S, Kipar A, Ramadurai S, Weckener M, Mikolajek H, Liu S, Buckle I, Bentley E, Kirby A, Han X, Laidlaw SM, Hill M, Eyssen L, Norman C, Le Bas A, Clarke J, James W, Stewart JP, Carroll M, Naismith JH, Owens RJ
Open Biol (2024) 14 pp. 230252-230252 [ Pubmed: 38835241 DOI: doi:10.1098/rsob.230252 ]
- Complex of stabilised hexapro omicron ba.1 spike trimer with two h6 nanobodies (Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- H6 nanobody (Complex from Lama glama)
- Stabilised hexapro omicron ba.1 spike trimer (Complex from Severe acute respiratory syndrome coronavirus 2)
- H6 nanobody (13 kDa, Protein from Lama glama)
- Spike glycoprotein,fibritin (139 kDa, Protein from Enterobacteria phage T4)
SARS-CoV-2 Spike ectodomain with Fab FI3A
Resolution: 4.8 Å
EM Method: Single-particle
Fitted PDBs: 7q0a
Q-score: 0.18
Huang KA, Zhou D, Tan TK, Chen C, Duyvesteyn HME, Zhao Y, Ginn HM, Qin L, Rijal P, Schimanski L, Donat R, Harding A, Gilbert-Jaramillo J, James W, Tree JA, Buttigieg K, Carroll M, Charlton S, Lien CE, Lin MY, Chen CP, Cheng SH, Chen X, Lin TY, Fry EE, Ren J, Ma C, Townsend AR, Stuart DI
Theranostics (2022) 12 pp. 1-17 [ Pubmed: 34987630 DOI: doi:10.7150/thno.65563 ]
- Fi3a fab light chain (11 kDa, Protein from Homo sapiens)
- Fi3a fab (Complex from Homo sapiens)
- Sars-cov2 spike ectodomain with fi3a fab (21 GDa, Complex)
- Fi3a fab heavy chain (12 kDa, Protein from Homo sapiens)
- Spike glycoprotein,spike ectodomain,spike protein s2' (145 kDa, Protein from Bat coronavirus Rp3/2004)
- Sars-cov2 spike ectodomain (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7oan
Q-score: 0.45
Huo J, Mikolajek H, Le Bas A, Clark JJ, Sharma P, Kipar A, Dormon J, Norman C, Weckener M, Clare DK, Harrison PJ, Tree JA, Buttigieg KR, Salguero FJ, Watson R, Knott D, Carnell O, Ngabo D, Elmore MJ, Fotheringham S, Harding A, Moynie L, Ward PN, Dumoux M, Prince T, Hall Y, Hiscox JA, Owen A, James W, Carroll MW, Stewart JP, Naismith JH, Owens RJ
Nat Commun (2021) 12 pp. 5469-5469 [ DOI: doi:10.1038/s41467-021-25480-z Pubmed: 34552091 ]
- Spike glycoprotein (139 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Immunoglobulin mu heavy chain (13 kDa, Protein from Vicugna pacos)
- Nanobody complex (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Tilt-series taken from SARS-CoV-2 infected Vero cells.
Mendonça L, Howe A, Gilchrist JB, Sheng Y, Sun D, Knight ML, Zanetti-Domingues LC, Bateman B, Krebs AS, Chen L, Radecke J, Li VD, Ni T, Kounatidis I, Koronfel MA, Szynkiewicz M, Harkiolaki M, Martin-Fernandez ML, James W, Zhang P
Nat Commun (2021) 12 [ DOI: 10.1038/s41467-021-24887-y Pubmed: 34330917 ]
Image sets:
SARS-CoV-2 spike subtomogram average from extracelullar viruses
Mendonca L, Howe A, Gilchrist JB, Sheng Y, Sun D, Knight ML, Zanetti-Domingues LC, Bateman B, Krebs AS, Chen L, Radecke J, Li VD, Ni T, Kounatidis I, Koronfel MA, Szynkiewicz M, Harkiolaki M, Martin-Fernandez ML, James W, Zhang P
Nat Commun (2021) 12 pp. 4629-4629 [ DOI: doi:10.1038/s41467-021-24887-y Pubmed: 34330917 ]
SARS-CoV-2 spike subtomogram average from intracelullar viruses
Mendonca L, Howe A, Gilchrist JB, Sheng Y, Sun D, Knight ML, Zanetti-Domingues LC, Bateman B, Krebs AS, Chen L, Radecke J, Li VD, Ni T, Kounatidis I, Koronfel MA, Szynkiewicz M, Harkiolaki M, Martin-Fernandez ML, James W, Zhang P
Nat Commun (2021) 12 pp. 4629-4629 [ DOI: doi:10.1038/s41467-021-24887-y Pubmed: 34330917 ]
EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-40 Fab
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7nd3
Q-score: 0.363
Dejnirattisai W, Zhou D, Ginn HM, Duyvesteyn HME, Supasa P, Case JB, Zhao Y, Walter TS, Mentzer AJ, Liu C, Wang B, Paesen GC, Slon-Campos J, Lopez-Camacho C, Kafai NM, Bailey AL, Chen RE, Ying B, Thompson C, Bolton J, Fyfe A, Gupta S, Tan TK, Gilbert-Jaramillo J, James W, Knight M, Carroll MW, Skelly D, Dold C, Peng Y, Levin R, Dong T, Pollard AJ, Knight JC, Klenerman P, Temperton N, Hall DR, Williams MA, Paterson NG, Bertram FKR, Siebert CA, Clare DK, Howe A, Radecke J, Song Y, Townsend AR, Huang KA, Fry EE, Mongkolsapaya J, Diamond MS, Ren J, Stuart DI, Screaton GR
Cell (2021) 184 pp. 2183- [ DOI: doi:10.1016/j.cell.2021.02.032 Pubmed: 33756110 ]
- Complex of sars-cov-2 spike glycoprotein with covox-40 fab (488 kDa, Complex)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Covox-40 fab (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Covox-40 light chain (24 kDa, Protein from Homo sapiens)
- Covox-40 heavy chain (25 kDa, Protein from Homo sapiens)
EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-88 Fab
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 7nd4
Q-score: 0.355
Dejnirattisai W, Zhou D, Ginn HM, Duyvesteyn HME, Supasa P, Case JB, Zhao Y, Walter TS, Mentzer AJ, Liu C, Wang B, Paesen GC, Slon-Campos J, Lopez-Camacho C, Kafai NM, Bailey AL, Chen RE, Ying B, Thompson C, Bolton J, Fyfe A, Gupta S, Tan TK, Gilbert-Jaramillo J, James W, Knight M, Carroll MW, Skelly D, Dold C, Peng Y, Levin R, Dong T, Pollard AJ, Knight JC, Klenerman P, Temperton N, Hall DR, Williams MA, Paterson NG, Bertram FKR, Siebert CA, Clare DK, Howe A, Radecke J, Song Y, Townsend AR, Huang KA, Fry EE, Mongkolsapaya J, Diamond MS, Ren J, Stuart DI, Screaton GR
Cell (2021) 184 pp. 2183- [ DOI: doi:10.1016/j.cell.2021.02.032 Pubmed: 33756110 ]
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Covox-88 fab heavy chain (25 kDa, Protein from Homo sapiens)
- Sars-cov-2 spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Complex of sars-cov-2 spike glycoprotein with covox-88 fab (593 kDa, Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Covox-88 fab (Complex from Homo sapiens)
- Covox-88 fab light chain (24 kDa, Protein from Homo sapiens)
EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-150 Fab
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7nd5
Q-score: 0.309
Dejnirattisai W, Zhou D, Ginn HM, Duyvesteyn HME, Supasa P, Case JB, Zhao Y, Walter TS, Mentzer AJ, Liu C, Wang B, Paesen GC, Slon-Campos J, Lopez-Camacho C, Kafai NM, Bailey AL, Chen RE, Ying B, Thompson C, Bolton J, Fyfe A, Gupta S, Tan TK, Gilbert-Jaramillo J, James W, Knight M, Carroll MW, Skelly D, Dold C, Peng Y, Levin R, Dong T, Pollard AJ, Knight JC, Klenerman P, Temperton N, Hall DR, Williams MA, Paterson NG, Bertram FKR, Siebert CA, Clare DK, Howe A, Radecke J, Song Y, Townsend AR, Huang KA, Fry EE, Mongkolsapaya J, Diamond MS, Ren J, Stuart DI, Screaton GR
Cell (2021) 184 pp. 2183- [ DOI: doi:10.1016/j.cell.2021.02.032 Pubmed: 33756110 ]
- Covox-150 fab light chain (24 kDa, Protein from Homo sapiens)
- Covox-150 fab heavy chain (24 kDa, Protein from Homo sapiens)
- Spike glycoprotein (142 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Covox-150 fab (Complex from Homo sapiens)
- Complex of sars-cov-2 spike glycoprotein with covox-150 fab (487 kDa, Complex)