Cryo-EM structure of the SARS-CoV-2 Spike bound to TMEM106B
Baggen J, Jacquemyn M, Persoons L, Vanstreels E, Pye VE, Wrobel AG, Calvaresi V, Martin SR, Roustan C, Cronin NB, Reading E, Thibaut HJ, Vercruysse T, Maes P, De Smet F, Yee A, Nivitchanyong T, Roell M, Franco-Hernandez N, Rhinn H, Mamchak AA, Ah Young-Chapon M, Brown E, Cherepanov P, Daelemans D
Cell (2023) 186 pp. 3427-3442.e22 [ DOI: doi:10.1016/j.cell.2023.06.005 Pubmed: 37421949 ]
- Tmem106b lumenal domain (Complex from Homo sapiens)
- Trimeric sars-cov-2 spike bound to one molecule of tmem106b (450 kDa, Complex)
- Sars-cov-2 spike ectodomain, hexa-pro stabilized; belgium/ghb-03021 variant (asp-484) (Complex from Severe acute respiratory syndrome coronavirus 2)
- Tmem106b lumenal domain (Protein from Homo sapiens)
- Sars-cov-2 spike ectodomain, hexa-pro stabilized; belgium/ghb-03021 variant (asp-484) (Protein from Severe acute respiratory syndrome coronavirus 2)
Local refinement of the SARS-CoV-2 Spike RBD bound to TMEM106B
Baggen J, Jacquemyn M, Persoons L, Vanstreels E, Pye VE, Wrobel AG, Calvaresi V, Martin SR, Roustan C, Cronin NB, Reading E, Thibaut HJ, Vercruysse T, Maes P, De Smet F, Yee A, Nivitchanyong T, Roell M, Franco-Hernandez N, Rhinn H, Mamchak AA, Ah Young-Chapon M, Brown E, Cherepanov P, Daelemans D
Cell (2023) 186 pp. 3427-3442.e22 [ DOI: doi:10.1016/j.cell.2023.06.005 Pubmed: 37421949 ]
- Sars-cov-2 spike ectodomain (belgium/ghb-03021) stabilized in trimeric pre-fusion state (Protein from Severe acute respiratory syndrome coronavirus 2)
- Trimeric sars-cov-2 spike bound to one molecule of tmem106b (450 kDa, Complex)
- Sars-cov-2 spike ectodomain (belgium/ghb-03021) stabilized in trimeric pre-fusion state (Complex from Severe acute respiratory syndrome coronavirus 2)
- Tmem106b lumenall domain (Protein from Homo sapiens)
- Tmem106b lumenall domain (Complex from Homo sapiens)
Resolution: 2.76 Å
EM Method: Single-particle
Fitted PDBs: 6cv1
Q-score: 0.619
Baggen J, Liu Y, Lyoo H, van Vliet ALW, Wahedi M, de Bruin JW, Roberts RW, Overduin P, Meijer A, Rossmann MG, Thibaut HJ, van Kuppeveld FJM
Nat Commun (2019) 10 pp. 3171-3171 [ DOI: doi:10.1038/s41467-019-11256-z Pubmed: 31320648 ]
- Enterovirus d68 (Virus from Enterovirus D68)
- Viral protein 1 (32 kDa, Protein from Enterovirus D68)
- Viral protein 3 (27 kDa, Protein from Enterovirus D68)
- Viral protein 2 (27 kDa, Protein from Enterovirus D68)
- Viral protein 4 (7 kDa, Protein from Enterovirus D68)
- Water (18 Da, Ligand)
CryoEM structure of human enterovirus D68 full virion
Resolution: 2.86 Å
EM Method: Single-particle
Fitted PDBs: 6cv2
Q-score: 0.608
Baggen J, Liu Y, Lyoo H, van Vliet ALW, Wahedi M, de Bruin JW, Roberts RW, Overduin P, Meijer A, Rossmann MG, Thibaut HJ, van Kuppeveld FJM
Nat Commun (2019) 10 pp. 3171-3171 [ DOI: doi:10.1038/s41467-019-11256-z Pubmed: 31320648 ]
- Enterovirus d68 (Virus from Enterovirus D68)
- Viral protein 1 (32 kDa, Protein from Enterovirus D68)
- Viral protein 3 (27 kDa, Protein from Enterovirus D68)
- Viral protein 2 (27 kDa, Protein from Enterovirus D68)
- Viral protein 4 (7 kDa, Protein from Enterovirus D68)
CryoEM structure of human enterovirus D68 emptied particle
Resolution: 3.56 Å
EM Method: Single-particle
Fitted PDBs: 6cv3
Q-score: 0.472
Baggen J, Liu Y, Lyoo H, van Vliet ALW, Wahedi M, de Bruin JW, Roberts RW, Overduin P, Meijer A, Rossmann MG, Thibaut HJ, van Kuppeveld FJM
Nat Commun (2019) 10 pp. 3171-3171 [ DOI: doi:10.1038/s41467-019-11256-z Pubmed: 31320648 ]
- Enterovirus d68 (Virus from Enterovirus D68)
- Viral protein 1 (32 kDa, Protein from Enterovirus D68)
- Viral protein 3 (27 kDa, Protein from Enterovirus D68)
- Viral protein 2 (27 kDa, Protein from Enterovirus D68)
Resolution: 3.03 Å
EM Method: Single-particle
Fitted PDBs: 6cv4
Q-score: 0.55
Baggen J, Liu Y, Lyoo H, van Vliet ALW, Wahedi M, de Bruin JW, Roberts RW, Overduin P, Meijer A, Rossmann MG, Thibaut HJ, van Kuppeveld FJM
Nat Commun (2019) 10 pp. 3171-3171 [ DOI: doi:10.1038/s41467-019-11256-z Pubmed: 31320648 ]
- Enterovirus d68 (Virus from Enterovirus D68)
- Viral protein 1 (32 kDa, Protein from Enterovirus D68)
- Viral protein 3 (27 kDa, Protein from Enterovirus D68)
- Viral protein 2 (27 kDa, Protein from Enterovirus D68)
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 6cv5
Q-score: 0.622
Baggen J, Liu Y, Lyoo H, van Vliet ALW, Wahedi M, de Bruin JW, Roberts RW, Overduin P, Meijer A, Rossmann MG, Thibaut HJ, van Kuppeveld FJM
Nat Commun (2019) 10 pp. 3171-3171 [ DOI: doi:10.1038/s41467-019-11256-z Pubmed: 31320648 ]
- Enterovirus d68 (Virus from Enterovirus D68)
- Viral protein 1 (32 kDa, Protein from Enterovirus D68)
- Viral protein 3 (27 kDa, Protein from Enterovirus D68)
- Viral protein 2 (27 kDa, Protein from Enterovirus D68)
- Viral protein 4 (7 kDa, Protein from Enterovirus D68)
- Water (18 Da, Ligand)
CryoEM structure of human enterovirus D68 in complex with 6'-sialyl-N-acetyllactosamine
Resolution: 2.43 Å
EM Method: Single-particle
Fitted PDBs: 6cvb
Q-score: 0.678
Baggen J, Liu Y, Lyoo H, van Vliet ALW, Wahedi M, de Bruin JW, Roberts RW, Overduin P, Meijer A, Rossmann MG, Thibaut HJ, van Kuppeveld FJM
Nat Commun (2019) 10 pp. 3171-3171 [ DOI: doi:10.1038/s41467-019-11256-z Pubmed: 31320648 ]
- Enterovirus d68 (Virus from Enterovirus D68)
- Viral protein 1 (32 kDa, Protein from Enterovirus D68)
- Viral protein 3 (27 kDa, Protein from Enterovirus D68)
- Viral protein 2 (27 kDa, Protein from Enterovirus D68)
- Viral protein 4 (7 kDa, Protein from Enterovirus D68)
- Water (18 Da, Ligand)
Structure of the EVA71 strain 11316 capsid
Sun L, Lee H, Thibaut HJ, Lanko K, Rivero-Buceta E, Bator C, Martinez-Gualda B, Dallmeier K, Delang L, Leyssen P, Gago F, San-Felix A, Hafenstein S, Mirabelli C, Neyts J
PLoS Pathog (2019) 15 pp. e1007760-e1007760 [ DOI: doi:10.1371/journal.ppat.1007760 Pubmed: 31071193 ]
- Vp1 (32 kDa, Protein from Enterovirus A71)
- Sphingosine (299 Da, Ligand)
- Vp4 (7 kDa, Protein from Enterovirus A71)
- Vp3 (26 kDa, Protein from Enterovirus A71)
- Vp2 (26 kDa, Protein from Enterovirus A71)
- Enterovirus a71 (Virus from Enterovirus A71)
EV-A71 strain 11316 complexed with tryptophan dendrimer MADAL_0385
Resolution: 3.59 Å
EM Method: Single-particle
Fitted PDBs: 6diz
Q-score: 0.509
Sun L, Lee H, Thibaut HJ, Lanko K, Rivero-Buceta E, Bator C, Martinez-Gualda B, Dallmeier K, Delang L, Leyssen P, Gago F, San-Felix A, Hafenstein S, Mirabelli C, Neyts J
PLoS Pathog (2019) 15 pp. e1007760-e1007760 [ DOI: doi:10.1371/journal.ppat.1007760 Pubmed: 31071193 ]
- Vp1 (32 kDa, Protein from Enterovirus A71)
- Sphingosine (299 Da, Ligand)
- Vp3 (26 kDa, Protein from Enterovirus A71)
- Vp2 (26 kDa, Protein from Enterovirus A71)
- Enterovirus a71 (Virus from Enterovirus A71)
- Vp4 (8 kDa, Protein from Enterovirus A71)