SARS-CoV-2 Omicron spike in complex with 5817 Fab
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8khc
Q-score: 0.351
Wang Y, Zhang Z, Yang M, Xiong X, Yan Q, Cao L, Wei P, Zhang Y, Zhang L, Lv K, Chen J, Liu X, Zhao X, Xiao J, Zhang S, Zhu A, Gan M, Zhang J, Cai R, Zhuo J, Zhang Y, Rao H, Qu B, Zhang Y, Chen L, Dai J, Cheng L, Hu Q, Chen Y, Lv H, So RTY, Peiris M, Zhao J, Liu X, Mok CKP, Wang X, Zhao J
Cell Rep (2024) 43 pp. 113653-113653 [ Pubmed: 38175758 DOI: doi:10.1016/j.celrep.2023.113653 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Light chain of 5817 fab (11 kDa, Protein from Homo sapiens)
- Heavy chain of 5817 fab (13 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Spike glycoprotein (124 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 omicron spike in complex with 5817 fab (Complex from Severe acute respiratory syndrome coronavirus 2)
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 8wgw
Q-score: 0.541
He X, Zhang X, Wu B, Deng J, Zhang Y, Zhu A, Yuan Y, Lin Y, Chen A, Feng J, Wang X, Wu S, Liu Y, Liu J, Wang Y, Li R, Liang C, Yuan Q, Liang Y, Fang Q, Xi Z, Li W, Liang L, Zhang Z, Tang H, Peng Y, Ke C, Ma X, Cai W, Pan T, Liu B, Deng K, Chen J, Zhao J, Wei X, Chen R, Zhang Y, Zhang H
Nat Immunol (2024) 25 pp. 622-632 [ DOI: doi:10.1038/s41590-024-01776-2 Pubmed: 38454157 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Angiotensin-converting enzyme 2 (70 kDa, Protein from Homo sapiens)
- Rbd complexed with human ace2 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of human ZDHHC9/GCP16 complex
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8hf3
Q-score: 0.496
Yang A, Liu S, Zhang Y, Chen J, Fan Y, Wang F, Zou Y, Feng S, Wu J, Hu Q
Nat Struct Mol Biol (2024) 31 pp. 436-446 [ Pubmed: 38182928 DOI: doi:10.1038/s41594-023-01183-5 ]
- Palmitic acid (256 Da, Ligand)
- Golgin subfamily a member 7 (16 kDa, Protein from Homo sapiens)
- Human zdhhc9/gcp16 complex (Complex from Homo sapiens)
- 1,2-dilauroyl-sn-glycero-3-phosphate (535 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Palmitoyltransferase zdhhc9 (41 kDa, Protein from Homo sapiens)
Cryo-EM structure of yeast Erf2/Erf4 complex
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8hfc
Q-score: 0.503
Yang A, Liu S, Zhang Y, Chen J, Fan Y, Wang F, Zou Y, Feng S, Wu J, Hu Q
Nat Struct Mol Biol (2024) 31 pp. 436-446 [ Pubmed: 38182928 DOI: doi:10.1038/s41594-023-01183-5 ]
- Palmitic acid (256 Da, Ligand)
- Palmitoyltransferase erf2 (43 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ras modification protein erf4 (29 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Erf2/erf4 complex (Complex from Saccharomyces cerevisiae)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of the linoleic acid bound GPR120-Gi complex
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8id4
Q-score: 0.547
Mao C, Xiao P, Tao XN, Qin J, He QT, Zhang C, Guo SC, Du YQ, Chen LN, Shen DD, Yang ZS, Zhang HQ, Huang SM, He YH, Cheng J, Zhong YN, Shang P, Chen J, Zhang DL, Wang QL, Liu MX, Li GY, Guo Y, Xu HE, Wang C, Zhang C, Feng S, Yu X, Zhang Y, Sun JP
Science (2023) 380 pp. eadd6220-eadd6220 [ DOI: doi:10.1126/science.add6220 Pubmed: 36862765 ]
- Free fatty acid receptor 4 (40 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Homo sapiens)
- Linoleic acid (280 Da, Ligand)
- Water (18 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Cryo-em structure of the linoleic acid bound gpr120-gi complex (Complex from Homo sapiens)
- Scfv16 (30 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein from Homo sapiens)
Cryo-EM structure of the eicosapentaenoic acid bound GPR120-Gi complex
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8id9
Q-score: 0.538
Mao C, Xiao P, Tao XN, Qin J, He QT, Zhang C, Guo SC, Du YQ, Chen LN, Shen DD, Yang ZS, Zhang HQ, Huang SM, He YH, Cheng J, Zhong YN, Shang P, Chen J, Zhang DL, Wang QL, Liu MX, Li GY, Guo Y, Xu HE, Wang C, Zhang C, Feng S, Yu X, Zhang Y, Sun JP
Science (2023) 380 pp. eadd6220-eadd6220 [ DOI: doi:10.1126/science.add6220 Pubmed: 36862765 ]
- Free fatty acid receptor 4 (40 kDa, Protein from Homo sapiens)
- 5,8,11,14,17-eicosapentaenoic acid (302 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Homo sapiens)
- Cryo-em structure of the eicosapentaenoic acid bound gpr120-gi complex (Complex from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Scfv16 (30 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i) subunit alpha-1 (40 kDa, Protein 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 [ DOI: doi:10.1038/s41564-022-01235-4 Pubmed: 36151403 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Processed angiotensin-converting enzyme 2 (69 kDa, Protein from Homo sapiens)
- Ace2 (Complex from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 s-gsas/6p spike trimer (Complex from Homo sapiens)
- Heavy chain of r1-32 (23 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)
- R1-32 fab (Complex)
- Zinc ion (65 Da, Ligand)
- Light chain of r1-32 (22 kDa, Protein from Homo sapiens)
- Spike protein s1 (21 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
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 ]
- Sars-cov-2 spike_gsas_6p (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Angiotensin-converting enzyme 2 (69 kDa, Protein 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)
- Zinc ion (65 Da, Ligand)
- Light chain of r1-32 fab (22 kDa, Protein from Homo sapiens)
- Spike glycoprotein (133 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Heavy chain of r1-32 fab (23 kDa, Protein from Homo sapiens)
- Fabs (Complex)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 6nbf
Q-score: 0.444
Zhao LH, Ma S, Sutkeviciute I, Shen DD, Zhou XE, de Waal PW, Li CY, Kang Y, Clark LJ, Jean-Alphonse FG, White AD, Yang D, Dai A, Cai X, Chen J, Li C, Jiang Y, Watanabe T, Gardella TJ, Melcher K, Wang MW, Vilardaga JP, Xu HE, Zhang Y
Science (2019) 364 pp. 148-153 [ DOI: doi:10.1126/science.aav7942 Pubmed: 30975883 ]
- Cholesterol (386 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Bos taurus)
- Palmitic acid (256 Da, Ligand)
- Long-acting parathyroid hormone analog (4 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Rattus norvegicus)
- Gs protein alpha subunit (43 kDa, Protein from Bos taurus)
- Nanobody-35 (13 kDa, Protein from synthetic construct)
- Cryo-em structure of parathyroid hormone receptor type 1 in complex with a long-acting parathyroid hormone analog and g protein (Complex from Homo sapiens)
- Parathyroid hormone/parathyroid hormone-related peptide receptor (54 kDa, Protein from Homo sapiens)
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 6nbh
Q-score: 0.347
Zhao LH, Ma S, Sutkeviciute I, Shen DD, Zhou XE, de Waal PW, Li CY, Kang Y, Clark LJ, Jean-Alphonse FG, White AD, Yang D, Dai A, Cai X, Chen J, Li C, Jiang Y, Watanabe T, Gardella TJ, Melcher K, Wang MW, Vilardaga JP, Xu HE, Zhang Y
Science (2019) 364 pp. 148-153 [ DOI: doi:10.1126/science.aav7942 Pubmed: 30975883 ]
- Cholesterol (386 Da, Ligand)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Bos taurus)
- Palmitic acid (256 Da, Ligand)
- Long-acting parathyroid hormone analog (4 kDa, Protein from Homo sapiens)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (37 kDa, Protein from Rattus norvegicus)
- Gs protein alpha subunit (43 kDa, Protein from Bos taurus)
- Nanobody-35 (13 kDa, Protein from synthetic construct)
- Cryo-em structure of parathyroid hormone receptor type 1 in complex with a long-acting parathyroid hormone analog and g protein (Complex from Homo sapiens)
- Parathyroid hormone/parathyroid hormone-related peptide receptor (54 kDa, Protein from Homo sapiens)