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Rpd3S histone deacetylase complex
Resolution: 3.46 Å
EM Method: Single-particle
Fitted PDBs: 8kc7
Q-score: 0.375
Dong S, Li H, Wang M, Rasheed N, Zou B, Gao X, Guan J, Li W, Zhang J, Wang C, Zhou N, Shi X, Li M, Zhou M, Huang J, Li H, Zhang Y, Wong KH, Zhang X, Chao WCH, He J
Cell Res (2023) 33 pp. 790-801 [ DOI: doi:10.1038/s41422-023-00869-1 Pubmed: 37666978 ]
- Transcriptional regulatory protein rco1 (84 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Transcriptional regulatory protein sin3 (157 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Chromatin modification-related protein eaf3 (45 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone deacetylase complex rpd3s in its apo form (527 kDa, Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone deacetylase rpd3 (48 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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 [ Pubmed: 36828833 DOI: doi:10.1038/s41467-023-36761-0 ]
- Sars-cov-2 omicron ba.1 spike trimer with one rbd up in complex with one yb9-258 fab (Complex)
- Sars-cov-2 omicron ba.1 spike trimer (Complex from Severe acute respiratory syndrome coronavirus 2)
- Heavy chain of yb9-258 fab (23 kDa, Protein from Homo sapiens)
- Light chain of yb9-258 fab (23 kDa, Protein from Homo sapiens)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Yb9-258 fab (Complex from Homo sapiens)
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 [ Pubmed: 36828833 DOI: doi:10.1038/s41467-023-36761-0 ]
- Sars-cov-2 omicron ba.1 spike trimer with two rbd up in complex with two yb9-258 fab (Complex)
- Sars-cov-2 omicron ba.1 spike trimer (Complex from Severe acute respiratory syndrome coronavirus 2)
- Heavy chain of yb9-258 (23 kDa, Protein from Homo sapiens)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Light chain of yb9-258 (23 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Yb9-258 fab (Complex from Homo sapiens)
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 [ Pubmed: 36828833 DOI: doi:10.1038/s41467-023-36761-0 ]
- Spike protein s1 (30 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 omicron ba.1 spike (6p) in complex with yb13-292 fab, focused refinement of rbd region (Complex)
- Yb13-292 fab (Complex from Homo sapiens)
- Sars-cov-2 omicron ba.1 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike protein s1 (31 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)
- 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 [ Pubmed: 36828833 DOI: doi:10.1038/s41467-023-36761-0 ]
- Spike protein s1 (30 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Light chain variable region of yb9-258 (11 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron ba.1 spike trimer with in complex with yb9-258 fab, focused refinement of 2 rbd region (Complex)
- Sars-cov_2 omicron ba.1 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Heavy chain variable region of yb9-258 (12 kDa, Protein 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)
- Yb9-258 fab (Complex from Homo sapiens)
Resolution: 3.95 Å
EM Method: Single-particle
Fitted PDBs: 8hc8
Q-score: 0.367
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 [ Pubmed: 36828833 DOI: doi:10.1038/s41467-023-36761-0 ]
- Spike protein s1 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Yb13-292 fab (Complex from Homo sapiens)
- Sars-cov-2 omicron ba.1 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 omicron ba.1 spike trimer with in complex with yb13-292 fab, focused refinement of fab region (Complex)
- Light chain of yb13-292 fab (23 kDa, Protein from Homo sapiens)
- Heavy chain of yb13-292 fab (25 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 3 YB13-292 Fabs (3 RBD down)
Resolution: 6.03 Å
EM Method: Single-particle
Fitted PDBs: 8hc9
Q-score: 0.156
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 [ Pubmed: 36828833 DOI: doi:10.1038/s41467-023-36761-0 ]
- Yb13-292 fab (Complex from Homo sapiens)
- Sars-cov-2 omicron ba.1 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 omicron ba.1 spike trimer with three rbd down in complex with three yb13-292 fab (Complex)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Light chain of yb13-292 fab (23 kDa, Protein from Homo sapiens)
- Heavy chain of yb13-292 fab (25 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 3 YB13-292 Fabs (1 RBD up)
Resolution: 4.35 Å
EM Method: Single-particle
Fitted PDBs: 8hca
Q-score: 0.217
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 [ Pubmed: 36828833 DOI: doi:10.1038/s41467-023-36761-0 ]
- Sars-cov-2 ba.1 variant spike protein with one rbd up in complex with three yb13-292 fab (Complex)
- Light chain of yb13-292 fab (23 kDa, Protein from Homo sapiens)
- Yb13-292 fab (Complex from Homo sapiens)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 ba.1 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Heavy chain of yb13-292 fab (25 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
SARS-CoV-2 Omicron BA.1 spike trimer (6P) in complex with 3 YB13-292 Fabs (2 RBD up)
Resolution: 4.18 Å
EM Method: Single-particle
Fitted PDBs: 8hcb
Q-score: 0.256
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 [ Pubmed: 36828833 DOI: doi:10.1038/s41467-023-36761-0 ]
- Yb13-292 fab (Complex from Homo sapiens)
- Sars-cov-2 omicron ba.1 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 omicron ba.1 spike trimer with two rbd up in complex with three yb13-292 fab (Complex)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Light chain of yb13-292 fab (23 kDa, Protein from Homo sapiens)
- Heavy chain of yb13-292 fab (25 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Type VI secretion system effector RhsP in its post-autoproteolysis and monomeric form
Resolution: 3.25 Å
EM Method: Single-particle
Fitted PDBs: 8h8a
Q-score: 0.49
Tang L, Dong S, Rasheed N, Wu HW, Zhou N, Li H, Wang M, Zheng J, He J, Chao WCH
Cell Rep (2022) 41 pp. 111732-111732 [ Pubmed: 36476863 DOI: doi:10.1016/j.celrep.2022.111732 ]
- Putative rhs-family protein (131 kDa, Protein from Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633))
- Type vi secretion system effector rhsp in its post-autoproteolysis form (Complex from Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633))
- C-terminal peptide from putative rhs-family protein (28 kDa, Protein from Vibrio parahaemolyticus serotype O3:K6 (strain RIMD 2210633))