Cryo-EM structure of BG505 Env mutant A517E in complex with antibody ACS202 Fab
Reveiz M, Xu K, Lee M, Wang S, Olia AS, Harris DR, Liu K, Liu T, Schaub AJ, Stephens T, Wang Y, Zhang B, Huang R, Tsybovsky Y, Kwong PD, Rawi R
Front Immunol (2024) 15 pp. 1484029-1484029 [ Pubmed: 39611147 DOI: doi:10.3389/fimmu.2024.1484029 ]
- Envelope glycoprotein gp41 (17 kDa, Protein from Human immunodeficiency virus 1)
- Hiv-1 env trimer complexed with antibody fab (Complex from Human immunodeficiency virus 1)
- Water (18 Da, Ligand)
- Antibody acs202 fab light chain (23 kDa, Protein from Homo sapiens)
- Envelope glycoprotein gp120 (53 kDa, Protein from Human immunodeficiency virus 1)
- Antibody acs202 fab heavy chain (25 kDa, Protein from Homo sapiens)
- Antibody fab (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
SARS-CoV-2 Omicron XBB.1.5 RBD complexed with human ACE2 and S304
Resolution: 2.91 Å
EM Method: Single-particle
Fitted PDBs: 8we4
Q-score: 0.462
Li W, Xu Z, Niu T, Xie Y, Zhao Z, Li D, He Q, Sun W, Shi K, Guo W, Chang Z, Liu K, Fan Z, Qi J, Gao GF
EMBO J (2024) 43 pp. 1484-1498 [ Pubmed: 38467833 DOI: doi:10.1038/s44318-024-00062-z ]
- Ace2 (Complex from Homo sapiens)
- Sars-cov-2 omicron xbb.1.5 rbd complexed with human ace2 and fab s304 (Complex)
- Spike protein s1 (25 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Fabs304 (Complex from Homo sapiens)
- S304 fab heavy chain (24 kDa, Protein from Homo sapiens)
- S304 fab light chain (23 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Sars-cov-2 omicron xbb.1.5 rbd (Complex from Severe acute respiratory syndrome coronavirus 2)
- Angiotensin-converting enzyme 2 (92 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
BA.4/5-5 FAB IN COMPLEX WITH SARS-COV-2 BA.4 SPIKE GLYCOPROTEIN
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 8cin
Q-score: 0.514
Zhou D, Supasa P, Liu C, Dijokaite-Guraliuc A, Duyvesteyn HME, Selvaraj M, Mentzer AJ, Das R, Dejnirattisai W, Temperton N, Klenerman P, Dunachie SJ, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR
Nat Commun (2024) 15 pp. 2734-2734 [ Pubmed: 38548763 DOI: doi:10.1038/s41467-024-46982-6 ]
- Ba.4/5-5 fab heavy and light chains. (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Spike glycoprotein (124 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-coronavirus-2 ba.4 spike glycoprotein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Ba.4/5-5 fab light chain (22 kDa, Protein from Homo sapiens)
- Sars-coronavirus-2 ba.4 spike glycoprotein in complex with ba.4/5-5 fab (Complex from Severe acute respiratory syndrome coronavirus 2)
- Ba.4/5-5 fab heavy chain (23 kDa, Protein from Homo sapiens)
Structure of human phagocyte NADPH oxidase in the activated state
Resolution: 2.79 Å
EM Method: Single-particle
Fitted PDBs: 8wej
Q-score: 0.535
Liu X, Shi Y, Liu R, Song K, Chen L
Nature (2024) 627 pp. 189-195 [ Pubmed: 38355798 DOI: doi:10.1038/s41586-024-07056-1 ]
- Neutrophil cytosolic factor 2 (65kda, chronic granulomatous disease, autosomal 2), isoform cra_a (34 kDa, Protein from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- 7d5 fab light chain (26 kDa, Protein from Mus musculus)
- Cytochrome b-245 light chain (21 kDa, Protein from Homo sapiens)
- Dihydroflavine-adenine dinucleotide (787 Da, Ligand)
- Neutrophil cytosol factor 1 (32 kDa, Protein from Homo sapiens)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- 7d5 fab heavy chain (27 kDa, Protein from Mus musculus)
- Cytochrome b-245 heavy chain (65 kDa, Protein from Homo sapiens)
- Rac family small gtpase 1 (21 kDa, Protein from Homo sapiens)
- Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate (745 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Activated nox2-p22 complex (Complex from Homo sapiens)
Structure of human phagocyte NADPH oxidase in the resting state in the presence of 2 mM NADPH
Resolution: 2.99 Å
EM Method: Single-particle
Fitted PDBs: 8x2l
Q-score: 0.487
Liu X, Shi Y, Liu R, Song K, Chen L
Nature (2024) 627 pp. 189-195 [ Pubmed: 38355798 DOI: doi:10.1038/s41586-024-07056-1 ]
- Magnesium ion (24 Da, Ligand)
- Water (18 Da, Ligand)
- 7d5 fab light chain (26 kDa, Protein from Mus musculus)
- Cytochrome b-245 light chain (21 kDa, Protein from Homo sapiens)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Resting nox2-p22 complex (Complex from Homo sapiens)
- 7d5 fab heavy chain (27 kDa, Protein from Mus musculus)
- Cytochrome b-245 heavy chain (65 kDa, Protein from Homo sapiens)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Cryo-EM structure of human NTCP-myr-preS1-YN9048Fab complex
Resolution: 2.89 Å
EM Method: Single-particle
Fitted PDBs: 8hrx
Q-score: 0.523
Asami J, Park JH, Nomura Y, Kobayashi C, Mifune J, Ishimoto N, Uemura T, Liu K, Sato Y, Zhang Z, Muramatsu M, Wakita T, Drew D, Iwata S, Shimizu T, Watashi K, Park SY, Nomura N, Ohto U
Nat Struct Mol Biol (2024) 31 pp. 447-454 [ Pubmed: 38233573 DOI: doi:10.1038/s41594-023-01191-5 ]
- Ntcp-myr-pres1-yn9048fab (Complex from Homo sapiens)
- Pres1 protein (fragment) (6 kDa, Protein from Hepatitis B virus)
- Fab heavy chain from antibody igg clone number yn9048 (26 kDa, Protein from Ondatra zibethicus)
- Sodium/bile acid cotransporter (38 kDa, Protein from Homo sapiens)
- Fab light chain from antibody igg clone number yn9048 (23 kDa, Protein from Ondatra zibethicus)
Structure of mouse Myomaker bound to Fab18G7 in detergent
Resolution: 2.72 Å
EM Method: Single-particle
Fitted PDBs: 8t03
Q-score: 0.574
Long T, Zhang Y, Donnelly L, Li H, Pien YC, Liu N, Olson EN, Li X
Nat Struct Mol Biol (2023) 30 pp. 1746-1754 [ Pubmed: 37770716 DOI: doi:10.1038/s41594-023-01110-8 ]
- 18g7 fab heavy chain (13 kDa, Protein from Mus musculus)
- Water (18 Da, Ligand)
- Fab18g7 (Complex from Mus musculus)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Complex of mouse myomaker and fab18g7 (Complex)
- 18g7 fab light chain (11 kDa, Protein from Mus musculus)
- Cholesterol (386 Da, Ligand)
- Mouse myomaker (Complex from Mus musculus)
- Protein myomaker (24 kDa, Protein from Mus musculus)
Structure of mouse Myomaker bound to Fab18G7 in nanodiscs
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 8t04
Q-score: 0.528
Long T, Zhang Y, Donnelly L, Li H, Pien YC, Liu N, Olson EN, Li X
Nat Struct Mol Biol (2023) 30 pp. 1746-1754 [ Pubmed: 37770716 DOI: doi:10.1038/s41594-023-01110-8 ]
- 18g7 fab heavy chain (13 kDa, Protein from Mus musculus)
- Fab18g7 (Complex from Mus musculus)
- 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (760 Da, Ligand)
- Complex of mouse myomaker with fab18g7 in nanodiscs (Complex)
- Zinc ion (65 Da, Ligand)
- 18g7 fab light chain (11 kDa, Protein from Mus musculus)
- Cholesterol (386 Da, Ligand)
- Mouse myomaker (Complex from Mus musculus)
- Protein myomaker (24 kDa, Protein from Mus musculus)
Cryo-EM Structure of SARS-CoV-2 BA.2 Spike protein in complex with BA7535
Resolution: 2.44 Å
EM Method: Single-particle
Fitted PDBs: 8h7l
Q-score: 0.377
Wang Y, Yan A, Song D, Duan M, Dong C, Chen J, Jiang Z, Gao Y, Rao M, Feng J, Zhang Z, Qi R, Ma X, Liu H, Yu B, Wang Q, Zong M, Jiao J, Xing P, Pan R, Li D, Xiao J, Sun J, Li Y, Zhang L, Shen Z, Sun B, Zhao Y, Zhang L, Dai J, Zhao J, Wang L, Dou C, Liu Z, Zhao J
Nat Commun (2024) 15 pp. 842-842 [ DOI: doi:10.1038/s41467-024-45050-3 Pubmed: 38287016 ]
- Sars-cov-2 ba.2 spike protein (Complex from Severe acute respiratory syndrome coronavirus 2)
- Ba7535 fab light chain (23 kDa, Protein from Homo sapiens)
- Ba7535 (Complex from Homo sapiens)
- Cryo-em structure of sars-cov-2 ba.2 spike protein in complex with ba7535 (Complex)
- Ba7535 fab heavt chain (49 kDa, Protein from Homo sapiens)
- Spike glycoprotein (124 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Cryo-EM structure of SARS-CoV-2 Omicron spike protein (S-6P-RRAR) in complex with S309 fab
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7xco
Q-score: 0.433
Zhao Z, Zhou J, Tian M, Huang M, Liu S, Xie Y, Han P, Bai C, Han P, Zheng A, Fu L, Gao Y, Peng Q, Li Y, Chai Y, Zhang Z, Zhao X, Song H, Qi J, Wang Q, Wang P, Gao GF
Nat Commun (2022) 13 pp. 4958- [ DOI: doi:10.1038/s41467-022-32665-7 ]
- S309 fab light chain (23 kDa, Protein from Homo sapiens)
- S309 fab heavy chain (24 kDa, Protein from Homo sapiens)
- Sars-cov-2 omicron spike protein (Complex from Homo sapiens)
- S309 fab (Complex)
- Spike glycoprotein (138 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Cryo-em structure of sars-cov-2 omicron spike protein in complex with s309 fab (Complex from Severe acute respiratory syndrome coronavirus 2)