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Liu B, Liu H, Han P, Wang X, Wang C, Yan X, Lei W, Xu K, Zhou J, Qi J, Fan R, Wu G, Tian WX, Gao GF, Wang Q
Signal Transduct Target Ther (2024) 9 pp. 131-131 [ Pubmed: 38740785 DOI: doi:10.1038/s41392-024-01847-8 ]
- Nanobody n235 (13 kDa, Protein from Vicugna pacos)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- The n-terminal domain of omicron ba.1 in complex with nanobody n235 and s2l20 fab (Complex from Vicugna pacos)
- Spike protein s2' (34 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- S2l20 light chain (26 kDa, Protein from Homo sapiens)
- S2l20 heavy chain (52 kDa, Protein from Homo sapiens)
Neisseria meningitidis Type IV pilus SB-GATDH variant bound to the C24 nanobody
Resolution: 2.9 Å
EM Method: Helical reconstruction
Fitted PDBs: 8pij
Q-score: 0.558
Fernandez-Martinez D, Kong Y, Goussard S, Zavala A, Gastineau P, Rey M, Ayme G, Chamot-Rooke J, Lafaye P, Vos M, Mechaly A, Dumenil G
Nat Commun (2024) 15 pp. 2414-2414 [ DOI: doi:10.1038/s41467-024-46677-y Pubmed: 38499587 ]
- (2~{r})-~{n}-[(2~{r},3~{s},4~{s},5~{r},6~{r})-5-acetamido-2-methyl-4,6-bis(oxidanyl)oxan-3-yl]-2,3-bis(oxidanyl)propanamide (292 Da, Ligand)
- Sn-glycerol-3-phosphate (172 Da, Ligand)
- Complex of neisseria meningitidis pile sb-gatdh and the c24 nanobody (Complex from Neisseria meningitidis 8013)
- Pilin (17 kDa, Protein from Neisseria meningitidis 8013)
- C24 nanobody (13 kDa, Protein from Vicugna pacos)
Neisseria meningitidis Type IV pilus SB-DATDH variant bound to the C24 nanobody
Resolution: 2.75 Å
EM Method: Helical reconstruction
Fitted PDBs: 8piz
Q-score: 0.547
Fernandez-Martinez D, Kong Y, Goussard S, Zavala A, Gastineau P, Rey M, Ayme G, Chamot-Rooke J, Lafaye P, Vos M, Mechaly A, Dumenil G
Nat Commun (2024) 15 pp. 2414-2414 [ DOI: doi:10.1038/s41467-024-46677-y Pubmed: 38499587 ]
- C24 nanobody (16 kDa, Protein from Vicugna pacos)
- Sn-glycerol-3-phosphate (172 Da, Ligand)
- Pilin (17 kDa, Protein from Neisseria meningitidis 8013)
- Neisseria meningitidis pile, sb-datdh variant, bound to the c24 nanobody (Complex from Neisseria meningitidis 8013)
- 2,4-bisacetamido-2,4,6-trideoxy-beta-d-glucopyranose (246 Da, Ligand)
Neisseria meningitidis PilE, SB-GATDH variant, bound to the F10 nanobody
Resolution: 2.92 Å
EM Method: Helical reconstruction
Fitted PDBs: 8pjp
Q-score: 0.556
Fernandez-Martinez D, Kong Y, Goussard S, Zavala A, Gastineau P, Rey M, Ayme G, Chamot-Rooke J, Lafaye P, Vos M, Mechaly A, Dumenil G
Nat Commun (2024) 15 pp. 2414-2414 [ DOI: doi:10.1038/s41467-024-46677-y Pubmed: 38499587 ]
- (2~{r})-~{n}-[(2~{r},3~{s},4~{s},5~{r},6~{r})-5-acetamido-2-methyl-4,6-bis(oxidanyl)oxan-3-yl]-2,3-bis(oxidanyl)propanamide (292 Da, Ligand)
- Sn-glycerol-3-phosphate (172 Da, Ligand)
- Nanobody f10 (15 kDa, Protein from Vicugna pacos)
- Pilin (17 kDa, Protein from Neisseria meningitidis 8013)
- Neisseria meningitidis pile, variant sa-gatdh complexed with the f10 nanobody (Complex from Neisseria meningitidis 8013)
Cryo-EM structure of styrene oxide isomerase bound to benzylamine inhibitor
Resolution: 2.12 Å
EM Method: Single-particle
Fitted PDBs: 8pnu
Q-score: 0.708
Khanppnavar B, Korkhov V, Li X
To Be Published
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Styrene oxide isomerase (19 kDa, Protein from Pseudomonas sp. VLB120)
- Nanobody (14 kDa, Protein from Vicugna pacos)
- Water (18 Da, Ligand)
- Benzylamine (107 Da, Ligand)
- Styrene oxide isomerase-nanobody-benzylamine complex (201 MDa, Complex from Pseudomonas sp. VLB120)
Cryo-EM structure of styrene oxide isomerase
Resolution: 2.048 Å
EM Method: Single-particle
Fitted PDBs: 8pnv
Q-score: 0.745
Khanppnavar B, Korkhov B, Li X
To Be Published
- Styrene oxide isomerase-nanobody complex (Complex from Pseudomonas sp. VLB120)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Styrene oxide isomerase (19 kDa, Protein from Pseudomonas sp. VLB120)
- Water (18 Da, Ligand)
- Nanobody (14 kDa, Protein from Vicugna pacos)
SARS-CoV-2 spike/nanobody mixture complex
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8g70
Q-score: 0.358
Ye G, Bu F, Pan R, Wen W, Mendoza A, Spiller B, Du L, Perlman S, Liu B, Li F
To Be Published
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Nanosota-5 (15 kDa, Protein from Vicugna pacos)
- Nanosota-6 (15 kDa, Protein from Vicugna pacos)
- Nanosota-4 (16 kDa, Protein from Vicugna pacos)
- Sars-cov-2 spike/nanobody mixture complex (547 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Spike glycoprotein (136 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Nanosota-3 (15 kDa, Protein from Vicugna pacos)
Resolution: 3.8 Å
EM Method: Single-particle
Fitted PDBs: 8g76
Q-score: 0.348
Ye G, Bu F, Pan R, Wen W, Mendoza A, Spiller B, Du L, Perlman S, Liu B, Li F
To Be Published
- Nanosota-5 (15 kDa, Protein from Vicugna pacos)
- Spike glycoprotein (136 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Sars-cov-2 spike/nb5 complex (425 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8g77
Q-score: 0.472
Ye G, Bu F, Pan R, Wen W, Mendoza A, Spiller B, Du L, Perlman S, Liu B, Li F
To Be Published
- Nanosota-6 (15 kDa, Protein from Vicugna pacos)
- Spike glycoprotein (136 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)
- Sars-cov-2 spike/nb6 complex (456 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Local refinement of SARS-CoV-2 spike/nanobody mixture complex around NTD
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 8g78
Q-score: 0.391
Ye G, Bu F, Pan R, Wen W, Mendoza A, Spiller B, Du L, Perlman S, Liu B, Li F
To Be Published
- Local refinement of sars-cov-2 spike/nanobody mixture complex (547 kDa, Complex from Severe acute respiratory syndrome coronavirus 2)
- Nanosota-6 (15 kDa, Protein from Vicugna pacos)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Nanosota-5 (14 kDa, Protein from Vicugna pacos)
- Spike glycoprotein (136 kDa, Protein from Severe acute respiratory syndrome coronavirus 2)