Cryo-EM structure of the SFV009 3G01 Fab in complex with A/California/04/2009
Resolution: 2.9 Å
EM Method: Single-particle
Fitted PDBs: 9dm0
Q-score: 0.511
Lin TH, Lee CD, Fernandez-Quintero ML, Ferguson JA, Han J, Zhu X, Yu W, Guthmiller JJ, Krammer F, Wilson PC, Ward AB, Wilson IA
Nat Commun (2025) 16 pp. 1268-1268 [ DOI: doi:10.1038/s41467-025-56496-4 Pubmed: 39894881 ]
- Hemagglutinin ca09 homotrimer bound to anchor fab (Complex from Homo sapiens)
- Hemagglutinin ha1/2 (Complex)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Fab heavy chain (13 kDa, Protein from Homo sapiens)
- Fab light chain (11 kDa, Protein from Homo sapiens)
- Hemagglutinin (26 kDa, Protein from Influenza A virus (A/California/04/2009(H1N1)))
- Fab (Complex)
- Hemagglutinin (35 kDa, Protein from Influenza A virus (A/California/04/2009(H1N1)))
Inactive Mu-Opioid Receptor with Nb6M, NabFab, and isoquinuclidine compound#020_E1
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 9mqi
Q-score: 0.352
Vigneron SF, Ohno S, Braz J, Kim JY, Kweon OS, Webb C, Billesbolle C, Bhardwaj K, Irwin J, Manglik A, Basbaum AI, Ellman JA, Shoichet BK
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.09.632033 Pubmed: 39868130 ]
- Nanobody 6m (14 kDa, Protein from synthetic construct)
- Mu-type opioid receptor (46 kDa, Protein from Homo sapiens)
- Nabfab light chain (23 kDa, Protein from synthetic construct)
- Nabfab heavy chain (25 kDa, Protein from synthetic construct)
- Methyl (1s,3r,4s,6s,8m)-2-[(1-ethyl-1h-pyrazol-4-yl)methyl]-8-(3-hydroxyphenyl)-3,4-dimethyl-2-azabicyclo[2.2.2]oct-7-ene-6-carboxylate (395 Da, Ligand)
- Human mu-opioid receptor (46 MDa, Complex from Homo sapiens)
Inactive Kappa-Opioid Receptor with Nb6M, NabFab, and isoquinuclidine compound #020_E1
Resolution: 3.18 Å
EM Method: Single-particle
Fitted PDBs: 9mqk
Q-score: 0.466
Vigneron SF, Ohno S, Braz J, Kim JY, Kweon OS, Webb C, Billesbolle C, Bhardwaj K, Irwin J, Manglik A, Basbaum AI, Ellman JA, Shoichet BK
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.09.632033 Pubmed: 39868130 ]
- Nanobody 6m (14 kDa, Protein from synthetic construct)
- Nabfab light chain (23 kDa, Protein from synthetic construct)
- Nabfab heavy chain (25 kDa, Protein from synthetic construct)
- Methyl (1s,3r,4s,6s,8m)-2-[(1-ethyl-1h-pyrazol-4-yl)methyl]-8-(3-hydroxyphenyl)-3,4-dimethyl-2-azabicyclo[2.2.2]oct-7-ene-6-carboxylate (395 Da, Ligand)
- Human kappa-opioid receptor (46 MDa, Complex from Homo sapiens)
- Kappa-opioid receptor (43 kDa, Protein from Homo sapiens)
Integrin alpha-5 beta-1 in complex with BIIG2 Fab
Resolution: 2.6 Å
EM Method: Single-particle
Fitted PDBs: 9b9j
Q-score: 0.589
Nguyen A, Heim JB, Cordara G, Chan MC, Johannesen H, Charlesworth C, Li M, Azumaya CM, Madden B, Krengel U, Meves A, Campbell MG
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.08.631572 Pubmed: 39829743 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Biig2 fab light chain (23 kDa, Protein from Rattus norvegicus)
- Calcium ion (40 Da, Ligand)
- Protein complex of integrin alpha-5 beta-1 with biig2 fab (Complex from Homo sapiens)
- Integrin alpha-5 light chain (108 kDa, Protein from Homo sapiens)
- Biig2 fab heavy chain (23 kDa, Protein from Rattus norvegicus)
- Integrin beta-1 (80 kDa, Protein from Homo sapiens)
Integrin alpha-5 beta-1 in complex with MINT1526A Fab
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 9b9k
Q-score: 0.547
Nguyen A, Heim JB, Cordara G, Chan MC, Johannesen H, Charlesworth C, Li M, Azumaya CM, Madden B, Krengel U, Meves A, Campbell MG
bioRxiv (2025) [ DOI: doi:10.1101/2025.01.08.631572 Pubmed: 39829743 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Protein complex of integrin alpha-5 beta-1 with mint1526a fab (Complex from Homo sapiens)
- Integrin alpha-5 light chain (108 kDa, Protein from Homo sapiens)
- Mint1526a fab heavy chain (13 kDa, Protein from unidentified)
- Mint1526a fab light chain (11 kDa, Protein from unidentified)
- Integrin beta-1 (80 kDa, Protein from Homo sapiens)
Cryo-EM structure of E. coli FimH lectin domain bound to Fabs 440-2 and 454-3
Resolution: 4.24 Å
EM Method: Single-particle
Fitted PDBs: 9d6f
Q-score: 0.412
Silmon de Monerri NC, Che Y, Lees JA, Jasti J, Wu H, Griffor MC, Kodali S, Hawkins JC, Lypowy J, Ponce C, Curley K, Esadze A, Carcamo J, Keeney D, Illenberger A, Matsuka YV, Shanker S, Chorro L, Gribenko AV, Han S, Anderson AS, Donald RGK
To Be Published
- Fimh-dsg tm (Complex from Escherichia coli)
- Fab 440-2 (Complex from Mus musculus)
- 440-2 fab light chain (24 kDa, Protein from Mus musculus)
- Fimh-dsg tm in complex with fabs 440-2 and 445-3 (Complex)
- 445-3 fab heavy chain (24 kDa, Protein from Mus musculus)
- Fab 445-3 (Complex from Mus musculus)
- 440-2 fab heavy chain (24 kDa, Protein from Mus musculus)
- 445-3 fab light chain (23 kDa, Protein from Mus musculus)
- Type 1 fimbrin d-mannose specific adhesin fimh, donor strand complemented with fimg peptide 'triple mutant' (32 kDa, Protein from Escherichia coli)
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 8znz
Q-score: 0.547
Xu JG, Chen S, He Y, Zhu X, Wang Y, Ye Z, Zhou JC, Wu X, Zhang L, Ren X, Jia H, Yu H, Wei X, Feng Y, Chen X, Cui X, Pan X, Wang S, Xia S, Shang H, Pu Y, Xu W, Li H, Chen Q, Chen Z, Wang M, Yan X, Shi H, Li M, Xia Y, Bellelli R, Dong S, He J, Huang J, Cai CL, Zhu X, Zhan Y, Wan L
Nat Commun (2024) 15 pp. 10872-10872 [ DOI: doi:10.1038/s41467-024-55207-9 Pubmed: 39738003 ]
- Zinc ion (65 Da, Ligand)
- Hb0038 fab light chain (11 kDa, Protein from Homo sapiens)
- Calcium ion (40 Da, Ligand)
- Hb0038 fab heavy chain (13 kDa, Protein from Homo sapiens)
- Hb0039 fab light chain (11 kDa, Protein from Homo sapiens)
- Sodium ion (22 Da, Ligand)
- Hb0039 fab heavy chain (13 kDa, Protein from Homo sapiens)
- Cd73 complexed with hb0017 antibody coaktail (630 kDa, Complex from Homo sapiens)
- 5'-nucleotidase (58 kDa, Protein from Homo sapiens)
Fibriansah G, Ng TS, Lim XN, Tan AWK, Shi J, Crowe JE, Lok SM
To Be Published
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Dengue serotype 2 strain d2y98p-pp1 n153q mutant (Complex from dengue virus type 2)
- Envelope protein (54 kDa, Protein from dengue virus type 2)
- Dengue virus serotype 2 strain y98p-pp1 n153q mutant in complex with human antibody 2d22 fab at 37 deg c (Complex)
- Human antibody 2d22 fab (heavy and light chains) (Complex from Homo sapiens)
- Membrane polyprotein (8 kDa, Protein from dengue virus type 2)
- Human antibody 2d22 fab heavy chain (13 kDa, Protein from Homo sapiens)
- Human antibody 2d22 fab light chain (12 kDa, Protein from Homo sapiens)
Fibriansah G, Ng TS, Lim XN, Tan AWK, Shi J, Crowe JE, Lok SM
To Be Published
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Membrane protein (8 kDa, Protein from dengue virus type 2)
- Dengue serotype 2 strain d2y98p-pp1 n153q mutant (Complex from dengue virus type 2)
- Envelope protein (54 kDa, Protein from dengue virus type 2)
- Human antibody c10 fab (light chain) (11 kDa, Protein from Homo sapiens)
- Human antibody c10 fab (heavy chain) (14 kDa, Protein from Homo sapiens)
- Human antibody c10 fab (heavy and light chains) (Complex from Homo sapiens)
- Dengue virus serotype 2 strain y98p-pp1 n153q mutant in complex with human antibody c10 fab at 37 deg c (Complex)
Fibriansah G, Ng TS, Lim XN, Tan AWK, Shi J, Crowe JE, Lok SM
To Be Published
- Human antibody 2d22 fab (heavy chain) (13 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Dengue virus serotype 2 strain d2y98p-pp1 in complex with human antibody 2d22 fab at 37 deg c (Complex)
- Envelope protein (54 kDa, Protein from dengue virus type 2)
- Human antibody 2d22 fab (light chain) (12 kDa, Protein from Homo sapiens)
- Human antibody 2d22 fab (heavy and light chains) (Complex from Homo sapiens)
- Dengue serotype 2 strain d2y98p-pp1 (Complex from dengue virus type 2)
- Membrane polyprotein (8 kDa, Protein from dengue virus type 2)