SARS-CoV-2 BA.1 RBD with UT28-RD
Resolution: 3.41 Å
EM Method: Single-particle
Fitted PDBs: 8k5g
Q-score: 0.522
Ozawa T, Ikeda Y, Chen L, Suzuki R, Hoshino A, Noguchi A, Kita S, Anraku Y, Igarashi E, Saga Y, Inasaki N, Taminishi S, Sasaki J, Kirita Y, Fukuhara H, Maenaka K, Hashiguchi T, Fukuhara T, Hirabayashi K, Tani H, Kishi H, Niimi H
Structure (2024) 32 pp. 263-272.e7 [ DOI: doi:10.1016/j.str.2023.12.013 Pubmed: 38228146 ]
- Ut28k-rd fab heavy chain (27 kDa, Protein from Homo sapiens)
- Spike protein s1 (25 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Ut28k-rd fab (Complex from Homo sapiens)
- Sars-cov-2 ba.1 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Ut28k-rd fab light chain (25 kDa, Protein from Homo sapiens)
- Sars-cov-2 ba.1 spike protein with ut28k-rd complex (50 kDa, Complex)
SARS-CoV-2 BA.1 spike with UT28-RD
Resolution: 3.22 Å
EM Method: Single-particle
Fitted PDBs: 8k5h
Q-score: 0.497
Ozawa T, Ikeda Y, Chen L, Suzuki R, Hoshino A, Noguchi A, Kita S, Anraku Y, Igarashi E, Saga Y, Inasaki N, Taminishi S, Sasaki J, Kirita Y, Fukuhara H, Maenaka K, Hashiguchi T, Fukuhara T, Hirabayashi K, Tani H, Kishi H, Niimi H
Structure (2024) 32 pp. 263-272.e7 [ DOI: doi:10.1016/j.str.2023.12.013 Pubmed: 38228146 ]
- Spike glycoprotein (133 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Ut28k-rd fab light chain (25 kDa, Protein from Homo sapiens)
- Ut28k-rd fab (Complex from Homo sapiens)
- Sars-cov-2 ba.1 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 ba.1 spike protein with ut28k-rd complex (50 kDa, Complex)
- Ut28k-rd fab heavy chain (27 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8b6v
Q-score: 0.45
Marini G, Poland B, Leininger C, Lukoyanova N, Spielbauer D, Barry JK, Altier D, Lum A, Scolaro E, Ortega CP, Yalpani N, Sandahl G, Mabry T, Klever J, Nowatzki T, Zhao JZ, Sethi A, Kassa A, Crane V, Lu AL, Nelson ME, Eswar N, Topf M, Saibil HR
Nat Commun (2023) 14 pp. 4171-4171 [ DOI: doi:10.1038/s41467-023-39891-7 Pubmed: 37443175 ]
- Mpf2ba1 (49 kDa, Protein from Pseudomonas monteilii)
- Magnesium ion (24 Da, Ligand)
- Mpf2ba1 22-mer pre-pore (Complex from Pseudomonas monteilii)
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 8b6w
Q-score: 0.446
Marini G, Poland B, Leininger C, Lukoyanova N, Spielbauer D, Barry JK, Altier D, Lum A, Scolaro E, Ortega CP, Yalpani N, Sandahl G, Mabry T, Klever J, Nowatzki T, Zhao JZ, Sethi A, Kassa A, Crane V, Lu AL, Nelson ME, Eswar N, Topf M, Saibil HR
Nat Commun (2023) 14 pp. 4171-4171 [ DOI: doi:10.1038/s41467-023-39891-7 Pubmed: 37443175 ]
- Mpf2ba1 (49 kDa, Protein from Pseudomonas monteilii)
- Magnesium ion (24 Da, Ligand)
- Mpf2ba1 21-mer pore (Complex from Pseudomonas monteilii)
SARS-CoV-2 BA.1 variants S ectodomain trimer in complex with neutralizing antibody 10-5B and 6-2C
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8h08
Q-score: 0.3
Liu Y, Wang Z, Zhuang X, Zhang S, Chen Z, Zou Y, Sheng J, Li T, Tai W, Yu J, Wang Y, Zhang Z, Chen Y, Tong L, Yu X, Wu L, Chen D, Zhang R, Jin N, Shen W, Zhao J, Tian M, Wang X, Cheng G
Nat Commun (2023) 14 pp. 2179-2179 [ Pubmed: 37069158 DOI: doi:10.1038/s41467-023-37926-7 ]
- Sars-cov-2 ba.1 variants spike (Complex)
- Sars-cov-2 ba.1 variants spike (Cellular component from Severe acute respiratory syndrome coronavirus 2)
- 10-5b h chain (12 kDa, Protein from Homo sapiens)
- 10-5b l chain (11 kDa, Protein from Homo sapiens)
- 6-2c h chain (13 kDa, Protein from Homo sapiens)
- 6-2c l chain (11 kDa, Protein from Homo sapiens)
- Antibody (Cellular component from Homo sapiens)
- Spike glycoprotein (144 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 6.04 Å
EM Method: Single-particle
Fitted PDBs: 8bgg
Q-score: 0.168
To Be Published
- Nanobody w25 (17 kDa, Protein from Vicugna pacos)
- Spike glycoprotein (133 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 spike (omicron ba.1 variant) in complex with nanobody w25 (100 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 1 YB9-258 Fab (1 RBD up)
Resolution: 6.21 Å
EM Method: Single-particle
Fitted PDBs: 8hc2
Q-score: 0.154
Yu H, Liu B, Zhang Y, Gao X, Wang Q, Xiang H, Peng X, Xie C, Wang Y, Hu P, Shi J, Shi Q, Zheng P, Feng C, Tang G, Liu X, Guo L, Lin X, Li J, Liu C, Huang Y, Yang N, Chen Q, Li Z, Su M, Yan Q, Pei R, Chen X, Liu L, Hu F, Liang D, Ke B, Ke C, Li F, He J, Wang M, Chen L, Xiong X, Tang X
Nat Commun (2023) 14 pp. 1058-1058 [ DOI: doi:10.1038/s41467-023-36761-0 Pubmed: 36828833 ]
- Light chain of yb9-258 fab (23 kDa, Protein from Homo sapiens)
- Heavy chain of yb9-258 fab (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron ba.1 spike trimer with one rbd up in complex with one yb9-258 fab (Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Yb9-258 fab (Complex from Homo sapiens)
- Sars-cov-2 omicron ba.1 spike trimer (Complex from Severe acute respiratory syndrome coronavirus 2)
SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 2 YB9-258 Fabs (2 RBD up)
Resolution: 4.35 Å
EM Method: Single-particle
Fitted PDBs: 8hc3
Q-score: 0.224
Yu H, Liu B, Zhang Y, Gao X, Wang Q, Xiang H, Peng X, Xie C, Wang Y, Hu P, Shi J, Shi Q, Zheng P, Feng C, Tang G, Liu X, Guo L, Lin X, Li J, Liu C, Huang Y, Yang N, Chen Q, Li Z, Su M, Yan Q, Pei R, Chen X, Liu L, Hu F, Liang D, Ke B, Ke C, Li F, He J, Wang M, Chen L, Xiong X, Tang X
Nat Commun (2023) 14 pp. 1058-1058 [ DOI: doi:10.1038/s41467-023-36761-0 Pubmed: 36828833 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Light chain of yb9-258 (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron ba.1 spike trimer with two rbd up in complex with two yb9-258 fab (Complex)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Yb9-258 fab (Complex from Homo sapiens)
- Heavy chain of yb9-258 (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron ba.1 spike trimer (Complex from Severe acute respiratory syndrome coronavirus 2)
Resolution: 4.69 Å
EM Method: Single-particle
Fitted PDBs: 8hc6
Q-score: 0.221
Yu H, Liu B, Zhang Y, Gao X, Wang Q, Xiang H, Peng X, Xie C, Wang Y, Hu P, Shi J, Shi Q, Zheng P, Feng C, Tang G, Liu X, Guo L, Lin X, Li J, Liu C, Huang Y, Yang N, Chen Q, Li Z, Su M, Yan Q, Pei R, Chen X, Liu L, Hu F, Liang D, Ke B, Ke C, Li F, He J, Wang M, Chen L, Xiong X, Tang X
Nat Commun (2023) 14 pp. 1058-1058 [ DOI: doi:10.1038/s41467-023-36761-0 Pubmed: 36828833 ]
- Spike protein s1 (31 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Spike protein s1 (30 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Heavy chain of yb9-258 fab (23 kDa, Protein from Homo sapiens)
- Light chain of yb9-258 (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron ba.1 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Yb13-292 fab (Complex from Homo sapiens)
- Sars-cov-2 omicron ba.1 spike (6p) in complex with yb13-292 fab, focused refinement of rbd region (Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 4.54 Å
EM Method: Single-particle
Fitted PDBs: 8hc7
Q-score: 0.234
Yu H, Liu B, Zhang Y, Gao X, Wang Q, Xiang H, Peng X, Xie C, Wang Y, Hu P, Shi J, Shi Q, Zheng P, Feng C, Tang G, Liu X, Guo L, Lin X, Li J, Liu C, Huang Y, Yang N, Chen Q, Li Z, Su M, Yan Q, Pei R, Chen X, Liu L, Hu F, Liang D, Ke B, Ke C, Li F, He J, Wang M, Chen L, Xiong X, Tang X
Nat Commun (2023) 14 pp. 1058-1058 [ DOI: doi:10.1038/s41467-023-36761-0 Pubmed: 36828833 ]
- Spike protein s1 (30 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 omicron ba.1 spike trimer with in complex with yb9-258 fab, focused refinement of 2 rbd region (Complex)
- Light chain variable region of yb9-258 (11 kDa, Protein from Homo sapiens)
- Yb9-258 fab (Complex from Homo sapiens)
- Spike protein s1 (58 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Heavy chain variable region of yb9-258 (12 kDa, Protein from Homo sapiens)
- Sars-cov_2 omicron ba.1 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)