Cryo-EM structure of human CD5L bound to IgM-Fc/J
Resolution: 3.39 Å
EM Method: Single-particle
Fitted PDBs: 8wyr
Q-score: 0.4
Nat Commun (2024) 15 pp. 8397-8397 [ Pubmed: 39333069 DOI: doi:10.1038/s41467-024-52175-y ]
- Ternary complex of igm-fc with the j chain and cd5l (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Interleukin-2,isoform 1 of immunoglobulin heavy constant mu (44 kDa, Protein from Homo sapiens)
- Immunoglobulin j chain (19 kDa, Protein from Homo sapiens)
- Interleukin-2,cd5 antigen-like (39 kDa, Protein from Homo sapiens)
Local map of human CD5L bound to IgM-Fc/J
Resolution: 3.41 Å
EM Method: Single-particle
Fitted PDBs: 8wys
Q-score: 0.422
Nat Commun (2024) 15 pp. 8397-8397 [ Pubmed: 39333069 DOI: doi:10.1038/s41467-024-52175-y ]
- Ternary complex of igm-fc with the j chain and cd5l (Complex from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Interleukin-2,isoform 1 of immunoglobulin heavy constant mu (44 kDa, Protein from Homo sapiens)
- Immunoglobulin j chain (19 kDa, Protein from Homo sapiens)
- Interleukin-2,cd5 antigen-like (39 kDa, Protein from Homo sapiens)
Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 1
Resolution: 3.23 Å
EM Method: Single-particle
Fitted PDBs: 9b55
Q-score: 0.524
Kochanczyk T, Hann ZS, Lux MC, Delos Reyes AMV, Ji C, Tan DS, Lima CD
Nature (2024) 633 pp. 216-223 [ DOI: doi:10.1038/s41586-024-07828-9 Pubmed: 39143218 ]
- Covalent e2-ub-e3 hect transthiolation intermediate mimic complex (Complex from Schizosaccharomyces pombe 972h-)
- E3 ubiquitin-protein ligase pub2 (44 kDa, Protein from Schizosaccharomyces pombe 972h-)
- 4-aminobutanenitrile (84 Da, Ligand)
- Ubiquitin-conjugating enzyme e2 4 (17 kDa, Protein from Schizosaccharomyces pombe 972h-)
- Ubiquitin (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 2
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 9b56
Q-score: 0.465
Kochanczyk T, Hann ZS, Lux MC, Delos Reyes AMV, Ji C, Tan DS, Lima CD
Nature (2024) 633 pp. 216-223 [ DOI: doi:10.1038/s41586-024-07828-9 Pubmed: 39143218 ]
- Covalent e2-ub-e3 hect transthiolation intermediate mimic complex (Complex from Schizosaccharomyces pombe 972h-)
- E3 ubiquitin-protein ligase pub2 (44 kDa, Protein from Schizosaccharomyces pombe 972h-)
- 4-aminobutanenitrile (84 Da, Ligand)
- Ubiquitin-conjugating enzyme e2 4 (17 kDa, Protein from Schizosaccharomyces pombe 972h-)
- Ubiquitin (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 3
Resolution: 3.37 Å
EM Method: Single-particle
Fitted PDBs: 9b57
Q-score: 0.465
Kochanczyk T, Hann ZS, Lux MC, Delos Reyes AMV, Ji C, Tan DS, Lima CD
Nature (2024) 633 pp. 216-223 [ DOI: doi:10.1038/s41586-024-07828-9 Pubmed: 39143218 ]
- Covalent e2-ub-e3 hect transthiolation intermediate mimic complex (Complex from Schizosaccharomyces pombe 972h-)
- E3 ubiquitin-protein ligase pub2 (44 kDa, Protein from Schizosaccharomyces pombe 972h-)
- 4-aminobutanenitrile (84 Da, Ligand)
- Ubiquitin-conjugating enzyme e2 4 (17 kDa, Protein from Schizosaccharomyces pombe 972h-)
- Ubiquitin (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 4
Resolution: 3.39 Å
EM Method: Single-particle
Fitted PDBs: 9b58
Q-score: 0.447
Kochanczyk T, Hann ZS, Lux MC, Delos Reyes AMV, Ji C, Tan DS, Lima CD
Nature (2024) 633 pp. 216-223 [ DOI: doi:10.1038/s41586-024-07828-9 Pubmed: 39143218 ]
- Covalent e2-ub-e3 hect transthiolation intermediate mimic complex (Complex from Schizosaccharomyces pombe 972h-)
- E3 ubiquitin-protein ligase pub2 (44 kDa, Protein from Schizosaccharomyces pombe 972h-)
- 4-aminobutanenitrile (84 Da, Ligand)
- Ubiquitin-conjugating enzyme e2 4 (17 kDa, Protein from Schizosaccharomyces pombe 972h-)
- Ubiquitin (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 5
Resolution: 3.49 Å
EM Method: Single-particle
Fitted PDBs: 9b59
Q-score: 0.444
Kochanczyk T, Hann ZS, Lux MC, Delos Reyes AMV, Ji C, Tan DS, Lima CD
Nature (2024) 633 pp. 216-223 [ DOI: doi:10.1038/s41586-024-07828-9 Pubmed: 39143218 ]
- Covalent e2-ub-e3 hect transthiolation intermediate mimic complex (Complex from Schizosaccharomyces pombe 972h-)
- E3 ubiquitin-protein ligase pub2 (44 kDa, Protein from Schizosaccharomyces pombe 972h-)
- 4-aminobutanenitrile (84 Da, Ligand)
- Ubiquitin-conjugating enzyme e2 4 (17 kDa, Protein from Schizosaccharomyces pombe 972h-)
- Ubiquitin (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 6
Resolution: 3.65 Å
EM Method: Single-particle
Fitted PDBs: 9b5a
Q-score: 0.4
Kochanczyk T, Hann ZS, Lux MC, Delos Reyes AMV, Ji C, Tan DS, Lima CD
Nature (2024) 633 pp. 216-223 [ DOI: doi:10.1038/s41586-024-07828-9 Pubmed: 39143218 ]
- Covalent e2-ub-e3 hect transthiolation intermediate mimic complex (Complex from Schizosaccharomyces pombe 972h-)
- E3 ubiquitin-protein ligase pub2 (44 kDa, Protein from Schizosaccharomyces pombe 972h-)
- 4-aminobutanenitrile (84 Da, Ligand)
- Ubiquitin-conjugating enzyme e2 4 (17 kDa, Protein from Schizosaccharomyces pombe 972h-)
- Ubiquitin (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
Ubiquitin E2-Ub-E3 HECT tetrahedral transthiolation intermediate mimic - state 7
Resolution: 3.31 Å
EM Method: Single-particle
Fitted PDBs: 9b5b
Q-score: 0.46
Kochanczyk T, Hann ZS, Lux MC, Delos Reyes AMV, Ji C, Tan DS, Lima CD
Nature (2024) 633 pp. 216-223 [ DOI: doi:10.1038/s41586-024-07828-9 Pubmed: 39143218 ]
- Covalent e2-ub-e3 hect transthiolation intermediate mimic complex (Complex from Schizosaccharomyces pombe 972h-)
- E3 ubiquitin-protein ligase pub2 (44 kDa, Protein from Schizosaccharomyces pombe 972h-)
- 4-aminobutanenitrile (84 Da, Ligand)
- Ubiquitin-conjugating enzyme e2 4 (17 kDa, Protein from Schizosaccharomyces pombe 972h-)
- Ubiquitin (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 9b5c
Q-score: 0.614
Kochanczyk T, Hann ZS, Lux MC, Delos Reyes AMV, Ji C, Tan DS, Lima CD
Nature (2024) 633 pp. 216-223 [ DOI: doi:10.1038/s41586-024-07828-9 Pubmed: 39143218 ]
- Covalent e1-ub-e2 transthiolation intermediate mimic complex with second ub bound to e1 (doubly ub-loaded e1-ub-e2 complex) (Complex from Schizosaccharomyces pombe 972h-)
- 4-aminobutanenitrile (84 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Ubiquitin-activating enzyme e1 1 (111 kDa, Protein from Schizosaccharomyces pombe 972h-)
- Large ribosomal subunit protein el40b (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
- Ubiquitin-conjugating enzyme e2 4 (17 kDa, Protein from Schizosaccharomyces pombe 972h-)
- Ubiquitin (8 kDa, Protein from Schizosaccharomyces pombe 972h-)