Qian Y, Ma Z, Xu Z, Duan Y, Xiong Y, Xia R, Zhu X, Zhang Z, Tian X, Yin H, Liu J, Song J, Lu Y, Zhang A, Guo C, Jin L, Kim WJ, Ke J, Xu F, Huang Z, He Y
Nat Commun (2024) 15 pp. 7644-7644 [ Pubmed: 39223191 DOI: doi:10.1038/s41467-024-52174-z ]
- Cholesterol hemisuccinate (486 Da, Ligand)
- Frizzled-4 (60 kDa, Protein from Homo sapiens)
- Segment polarity protein dishevelled homolog dvl-2 (79 kDa, Protein from Homo sapiens)
- Gpcr complex (450 kDa, Complex from Homo sapiens)
Fzd4/DEP complex (local refined)
Qian Y, Ma Z, Xu Z, Duan Y, Xiong Y, Xia R, Zhu X, Zhang Z, Tian X, Yin H, Liu J, Song J, Lu Y, Zhang A, Guo C, Jin L, Kim WJ, Ke J, Xu F, Huang Z, He Y
Nat Commun (2024) 15 pp. 7644-7644 [ Pubmed: 39223191 DOI: doi:10.1038/s41467-024-52174-z ]
- Frizzled-4 (60 kDa, Protein from Homo sapiens)
- Segment polarity protein dishevelled homolog dvl-2 (79 kDa, Protein from Homo sapiens)
- Gpcr complex (450 kDa, Complex from Homo sapiens)
Spike_GSAS_6P protomer RBD domain bound with R1-32 Fab and ACE2 with 3:3:3 ratio
Resolution: 3.98 Å
EM Method: Single-particle
Fitted PDBs: 7ydi
Q-score: 0.296
He P, Liu B, Gao X, Yan Q, Pei R, Sun J, Chen Q, Hou R, Li Z, Zhang Y, Zhao J, Sun H, Feng B, Wang Q, Yi H, Hu P, Li P, Zhang Y, Chen Z, Niu X, Zhong X, Jin L, Liu X, Qu K, Ciazynska KA, Carter AP, Briggs JAG, Chen J, Liu J, Chen X, He J, Chen L, Xiong X
Nat Microbiol (2022) 7 pp. 1635-1649 [ Pubmed: 36151403 DOI: doi:10.1038/s41564-022-01235-4 ]
- Zinc ion (65 Da, Ligand)
- Ace2 (Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- R1-32 fab (Complex)
- Sars-cov-2 s-gsas/6p spike trimer (Complex from Homo sapiens)
- Light chain of r1-32 (22 kDa, Protein from Homo sapiens)
- Spike protein s1 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Heavy chain of r1-32 (23 kDa, Protein from Homo sapiens)
- Processed angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Sars-cov-2 s-gsas/6p spike trimer bound to r1-32 fab with 3:1 ratio (Complex from Homo sapiens)
Spike_GSAS_6P and R1-32 Fab with 3to1 ratio
Resolution: 4.75 Å
EM Method: Single-particle
Fitted PDBs: 7ydy
Q-score: 0.151
He P, Liu B, Gao X, Yan Q, Pei R, Sun J, Chen Q, Hou R, Li Z, Zhang Y, Zhao J, Sun H, Feng B, Wang Q, Yi H, Hu P, Li P, Zhang Y, Chen Z, Niu X, Zhong X, Jin L, Liu X, Qu K, Ciazynska KA, Carter AP, Briggs JAG, Chen J, Liu J, Chen X, He J, Chen L, Xiong X
Nat Microbiol (2022) 7 pp. 1635-1649 [ Pubmed: 36151403 DOI: doi:10.1038/s41564-022-01235-4 ]
- Sars-cov-2 s-gsas/6p spike trimer bound to r1-32 fab with 3:1 ratio (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (133 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- R1-32 fab (Complex)
- Sars-cov-2 s-gsas/6p spike trimer (Complex from Homo sapiens)
- Light chain of r1-32 fab (22 kDa, Protein from Homo sapiens)
- Heavy chain of r1-32 fab (23 kDa, Protein from Homo sapiens)
SARS-COV-2 Spike_GSAS_6P bound with two R1-32 Fabs
Resolution: 6.75 Å
EM Method: Single-particle
Fitted PDBs: 7ye5
Q-score: 0.029
He P, Liu B, Gao X, Yan Q, Pei R, Sun J, Chen Q, Hou R, Li Z, Zhang Y, Zhao J, Sun H, Feng B, Wang Q, Yi H, Hu P, Li P, Zhang Y, Chen Z, Niu X, Zhong X, Jin L, Liu X, Qu K, Ciazynska KA, Carter AP, Briggs JAG, Chen J, Liu J, Chen X, He J, Chen L, Xiong X
Nat Microbiol (2022) 7 pp. 1635-1649 [ Pubmed: 36151403 DOI: doi:10.1038/s41564-022-01235-4 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (133 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 s-gsas/6p spike trimer (Complex from Homo sapiens)
- Sars-cov-2 s-gsas/6p spike trimer bound with r1-32 fab with 3:2 ratio (Complex from Severe acute respiratory syndrome coronavirus 2)
- Light chain of r1-32 fab (22 kDa, Protein from Homo sapiens)
- Fab (Complex)
- Heavy chain of r1-32 fab (23 kDa, Protein from Homo sapiens)
SARS-COV-2 Spike_GSAS_6P bound with three R1-32 Fabs
Resolution: 4.17 Å
EM Method: Single-particle
Fitted PDBs: 7ye9
Q-score: 0.17
He P, Liu B, Gao X, Yan Q, Pei R, Sun J, Chen Q, Hou R, Li Z, Zhang Y, Zhao J, Sun H, Feng B, Wang Q, Yi H, Hu P, Li P, Zhang Y, Chen Z, Niu X, Zhong X, Jin L, Liu X, Qu K, Ciazynska KA, Carter AP, Briggs JAG, Chen J, Liu J, Chen X, He J, Chen L, Xiong X
Nat Microbiol (2022) 7 pp. 1635-1649 [ Pubmed: 36151403 DOI: doi:10.1038/s41564-022-01235-4 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (133 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Light chain of r1-32 fab (22 kDa, Protein from Homo sapiens)
- Sars-cov-2 spike_gsas_6p bound with three r1-32 fabs (Complex from Severe acute respiratory syndrome coronavirus 2)
- Fab (Complex)
- Sars-cov-2 spike_gsas_6p (Complex from Homo sapiens)
- Heavy chain of r1-32 fab (23 kDa, Protein from Homo sapiens)
SARS-CoV-2 Spike (6P) in complex with 3 R1-32 Fabs and 3 ACE2
Resolution: 3.73 Å
EM Method: Single-particle
Fitted PDBs: 7yeg
Q-score: 0.149
He P, Liu B, Gao X, Yan Q, Pei R, Sun J, Chen Q, Hou R, Li Z, Zhang Y, Zhao J, Sun H, Feng B, Wang Q, Yi H, Hu P, Li P, Zhang Y, Chen Z, Niu X, Zhong X, Jin L, Liu X, Qu K, Ciazynska KA, Carter AP, Briggs JAG, Chen J, Liu J, Chen X, He J, Chen L, Xiong X
Nat Microbiol (2022) 7 pp. 1635-1649 [ Pubmed: 36151403 DOI: doi:10.1038/s41564-022-01235-4 ]
- Zinc ion (65 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (133 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Fabs (Complex)
- Angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Light chain of r1-32 fab (22 kDa, Protein from Homo sapiens)
- Heavy chain of r1-32 fab (23 kDa, Protein from Homo sapiens)
- Sars-cov-2 spike_gsas_6p (Complex from Homo sapiens)
- Ace2 (Complex from Homo sapiens)
- Sars-cov-2 spike_gsas_6p bound with three r1-32 fabs and three ace2 (Complex from Severe acute respiratory syndrome coronavirus 2)
Mechanism of eIF6 release from the nascent 60S ribosomal subunit
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 5an9
Q-score: 0.423
Weis F, Giudice E, Churcher M, Jin L, Hilcenko C, Wong CC, Traynor D, Kay RR, Warren AJ
Nat Struct Mol Biol (2015) 22 pp. 914-919 [ Pubmed: 26479198 DOI: doi:10.1038/NSMB.3112 ]
- Dictyostelium 60s carrying endogenous eif6 with recombinant human sbds (Sample)
- Shwachman-bodian-diamond syndrome protein (29 kDa, Protein from Homo sapiens)
- 60s ribosomal subunit (3 MDa, Complex from Dictyostelium discoideum)
- Eukaryotic translation initiation factor 6 (26 kDa, Protein from Dictyostelium discoideum)
Mechanism of eIF6 release from the nascent 60S ribosomal subunit
Resolution: 4.1 Å
EM Method: Single-particle
Fitted PDBs: 5anb
Q-score: 0.298
Weis F, Giudice E, Churcher M, Jin L, Hilcenko C, Wong CC, Traynor D, Kay RR, Warren AJ
Nat Struct Mol Biol (2015) 22 pp. 914-919 [ Pubmed: 26479198 DOI: doi:10.1038/NSMB.3112 ]
- Shwachman-bodian-diamond syndrome protein (29 kDa, Protein from Homo sapiens)
- Elongation factor-like 1 (125 kDa, Protein from Homo sapiens)
- 60s ribosomal subunit (3 MDa, Complex from Dictyostelium discoideum)
- Dictyostelium 60s carrying endogenous eif6 with recombinant human sbds and human efl1 (Sample)
- Eukaryotic translation initiation factor 6 (26 kDa, Protein from Dictyostelium discoideum)
Mechanism of eIF6 release from the nascent 60S ribosomal subunit
Resolution: 4.2 Å
EM Method: Single-particle
Fitted PDBs: 5anc
Q-score: 0.287
Weis F, Giudice E, Churcher M, Jin L, Hilcenko C, Wong CC, Traynor D, Kay RR, Warren AJ
Nat Struct Mol Biol (2015) 22 pp. 914-919 [ Pubmed: 26479198 DOI: doi:10.1038/NSMB.3112 ]
- Elongation factor-like 1 (125 kDa, Protein from Homo sapiens)
- 60s ribosomal subunit (3 MDa, Complex from Dictyostelium discoideum)
- Shwachman-bodian-diamond syndrome protein (29 kDa, Protein from Homo sapiens)
- Dictyostelium 60s with recombinant human sbds and human efl1 (Sample)