JN.1 RBD with Q493E in complex with ACE2
Resolution: 3.29 Å
EM Method: Single-particle
Fitted PDBs: 9iuu
Q-score: 0.509
Feng L, Sun Z, Zhang Y, Jian F, Yang S, Xia K, Yu L, Wang J, Shao F, Wang X, Cao Y
Cell Discov (2024) 10 pp. 123-123 [ Pubmed: 39616168 DOI: doi:10.1038/s41421-024-00752-2 ]
- Spike protein s1 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Ace2 (Complex from Homo sapiens)
- Angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Jn.1 rbd q493e (Complex from Severe acute respiratory syndrome coronavirus 2)
- Jn.1 rbd with q493e in complex with ace2 (Complex)
- Zinc ion (65 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Spike Trimer of BA.2.86 in complex with one hACE2
Resolution: 3.33 Å
EM Method: Single-particle
Fitted PDBs: 8whs
Q-score: 0.272
Liu P, Yue C, Meng B, Xiao T, Yang S, Liu S, Jian F, Zhu Q, Yu Y, Ren Y, Wang P, Li Y, Wang J, Mao X, Shao F, Wang Y, Gupta RK, Cao Y, Wang X
Natl Sci Rev (2024) 11 pp. nwae206-nwae206 [ Pubmed: 39071099 DOI: doi:10.1093/nsr/nwae206 ]
- Processed angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Spike glycoprotein (134 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- Severe acute respiratory syndrome coronavirus 2 (Virus from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Spike Trimer of BA.2.86 in complex with two hACE2s
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8whu
Q-score: 0.261
Liu P, Yue C, Meng B, Xiao T, Yang S, Liu S, Jian F, Zhu Q, Yu Y, Ren Y, Wang P, Li Y, Wang J, Mao X, Shao F, Wang Y, Gupta RK, Cao Y, Wang X
Natl Sci Rev (2024) 11 pp. nwae206-nwae206 [ Pubmed: 39071099 DOI: doi:10.1093/nsr/nwae206 ]
- Processed angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Spike glycoprotein (134 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- Severe acute respiratory syndrome coronavirus 2 (Virus from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
BA.2.86 Spike Trimer in complex with heparan sulfate
Resolution: 3.85 Å
EM Method: Single-particle
Fitted PDBs: 8xur
Q-score: 0.247
Liu P, Yue C, Meng B, Xiao T, Yang S, Liu S, Jian F, Zhu Q, Yu Y, Ren Y, Wang P, Li Y, Wang J, Mao X, Shao F, Wang Y, Gupta RK, Cao Y, Wang X
Natl Sci Rev (2024) 11 pp. nwae206-nwae206 [ Pubmed: 39071099 DOI: doi:10.1093/nsr/nwae206 ]
- Spike glycoprotein (134 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Ba.2.86 spike trimer in complex with heparan sulfate (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-o-sulfo-beta-l-altropyranuronic acid (274 Da, Ligand)
JN.1 Spike Trimer in complex with heparan sulfate
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 8xus
Q-score: 0.372
Liu P, Yue C, Meng B, Xiao T, Yang S, Liu S, Jian F, Zhu Q, Yu Y, Ren Y, Wang P, Li Y, Wang J, Mao X, Shao F, Wang Y, Gupta RK, Cao Y, Wang X
Natl Sci Rev (2024) 11 pp. nwae206-nwae206 [ Pubmed: 39071099 DOI: doi:10.1093/nsr/nwae206 ]
- Spike glycoprotein (134 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Jn.1 spike trimer in complex with heparan sulfate (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-o-sulfo-beta-l-altropyranuronic acid (274 Da, Ligand)
XBB.1.5 Spike Trimer in complex with heparan sulfate
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8xut
Q-score: 0.398
Liu P, Yue C, Meng B, Xiao T, Yang S, Liu S, Jian F, Zhu Q, Yu Y, Ren Y, Wang P, Li Y, Wang J, Mao X, Shao F, Wang Y, Gupta RK, Cao Y, Wang X
Natl Sci Rev (2024) 11 pp. nwae206-nwae206 [ Pubmed: 39071099 DOI: doi:10.1093/nsr/nwae206 ]
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Xbb.1.5 spike trimer in complex with heparan sulfate (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 2-o-sulfo-beta-l-altropyranuronic acid (274 Da, Ligand)
BA.2.86-T356K Spike Trimer in complex with heparan sulfate (Local refinement)
Resolution: 3.69 Å
EM Method: Single-particle
Fitted PDBs: 8xuu
Q-score: 0.329
Liu P, Yue C, Meng B, Xiao T, Yang S, Liu S, Jian F, Zhu Q, Yu Y, Ren Y, Wang P, Li Y, Wang J, Mao X, Shao F, Wang Y, Gupta RK, Cao Y, Wang X
Natl Sci Rev (2024) 11 pp. nwae206-nwae206 [ Pubmed: 39071099 DOI: doi:10.1093/nsr/nwae206 ]
- Ba.2.86-t356k spike trimer in complex with heparan sulfate (local refinement) (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 2-o-sulfo-beta-l-altropyranuronic acid (274 Da, Ligand)
- Spike glycoprotein (134 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
BA.2.86 RBD in complex with hACE2 (local refinement)
Resolution: 3.93 Å
EM Method: Single-particle
Fitted PDBs: 8whz
Q-score: 0.317
Liu P, Yue C, Meng B, Xiao T, Yang S, Liu S, Jian F, Zhu Q, Yu Y, Ren Y, Wang P, Li Y, Wang J, Mao X, Shao F, Wang Y, Gupta RK, Cao Y, Wang X
Natl Sci Rev (2024) 11 pp. nwae206-nwae206 [ Pubmed: 39071099 DOI: doi:10.1093/nsr/nwae206 ]
- Processed angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Spike protein s1 (22 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- Severe acute respiratory syndrome coronavirus 2 (Virus from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
CalA3 complex structure with amidation product
Resolution: 3.84 Å
EM Method: Single-particle
Fitted PDBs: 8i4y
Q-score: 0.416
Wang J, Wang X, Li X, Kong L, Du Z, Li D, Gou L, Wu H, Cao W, Wang X, Lin S, Shi T, Deng Z, Wang Z, Liang J
Nat Commun (2023) 14 pp. 1319-1319 [ DOI: doi:10.1038/s41467-023-36989-w Pubmed: 36899013 ]
- 3-hydroxyanthranilic acid (153 Da, Ligand)
- Beta-ketoacyl-acyl-carrier-protein synthase i (178 kDa, Protein from Streptomyces chartreusis NRRL 3882)
- 11-oxidanylidene-11-(1~{h}-pyrrol-2-yl)undecanoic acid (265 Da, Ligand)
- An assembly-line polyketide synthase module containing ks-at-dh-kr domains with amidation product (360 kDa, Cellular component from Streptomyces chartreusis NRRL 3882cha)
SARS-CoV-2 BA.2.75 S Trimer in complex with ACE2(state1)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7yr2
Q-score: 0.354
Cao Y, Song W, Wang L, Liu P, Yue C, Jian F, Yu Y, Yisimayi A, Wang P, Wang Y, Zhu Q, Deng J, Fu W, Yu L, Zhang N, Wang J, Xiao T, An R, Wang J, Liu L, Yang S, Niu X, Gu Q, Shao F, Hao X, Meng B, Gupta RK, Jin R, Wang Y, Xie XS, Wang X
Cell Host Microbe (2022) 30 pp. 1527- [ Pubmed: 36270286 DOI: doi:10.1016/j.chom.2022.09.018 ]
- Water (18 Da, Ligand)
- Spike glycoprotein (141 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Ace2 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Ba.2.75 s trimer (Complex)
- Zinc ion (65 Da, Ligand)
- Chloride ion (35 Da, Ligand)
- Ba.2.75 s trimer in complex with ace2 (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)