Electron Microscopy Data Bank

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Cryo-EM structure of human CD5L bound to IgM-Fc/J

Release date: Oct. 9, 2024
Resolution: 3.39 Å
EM Method: Single-particle
Fitted PDBs: 8wyr
Q-score: 0.4

Wang Y, Su C, Ji C, Xiao J

Nat Commun (2024) 15 pp. 8397-8397 [ Pubmed: 39333069 DOI: doi:10.1038/s41467-024-52175-y ]

Sample:

Calcium ion (40 Da, Ligand)
Interleukin-2,cd5 antigen-like (39 kDa, Protein from Homo sapiens)
Interleukin-2,isoform 1 of immunoglobulin heavy constant mu (44 kDa, Protein from Homo sapiens)
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)
Immunoglobulin j chain (19 kDa, Protein from Homo sapiens)

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EMD-37937

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Local map of human CD5L bound to IgM-Fc/J

Release date: Oct. 9, 2024
Resolution: 3.41 Å
EM Method: Single-particle
Fitted PDBs: 8wys
Q-score: 0.422

Wang Y, Su C, Ji C, Xiao J

Nat Commun (2024) 15 pp. 8397-8397 [ Pubmed: 39333069 DOI: doi:10.1038/s41467-024-52175-y ]

Sample:

Calcium ion (40 Da, Ligand)
Interleukin-2,cd5 antigen-like (39 kDa, Protein from Homo sapiens)
Interleukin-2,isoform 1 of immunoglobulin heavy constant mu (44 kDa, Protein from Homo sapiens)
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)
Immunoglobulin j chain (19 kDa, Protein from Homo sapiens)

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EMD-44207

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Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - consensus map and model

Release date: June 5, 2024
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 ]

Sample:

Large ribosomal subunit protein el40b (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
Magnesium ion (24 Da, Ligand)
Adenosine-5'-triphosphate (507 Da, Ligand)
Ubiquitin-activating enzyme e1 1 (111 kDa, Protein from Schizosaccharomyces pombe 972h-)
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-)
Ubiquitin-conjugating enzyme e2 4 (17 kDa, Protein from Schizosaccharomyces pombe 972h-)
Ubiquitin (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
4-aminobutanenitrile (84 Da, Ligand)

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EMD-44208

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Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 1 map and model from consensus

Release date: June 5, 2024
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 9b5d
Q-score: 0.552

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 ]

Sample:

Large ribosomal subunit protein el40b (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
Magnesium ion (24 Da, Ligand)
Adenosine-5'-triphosphate (507 Da, Ligand)
Ubiquitin-activating enzyme e1 1 (111 kDa, Protein from Schizosaccharomyces pombe 972h-)
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-)
Ubiquitin-conjugating enzyme e2 4 (17 kDa, Protein from Schizosaccharomyces pombe 972h-)
Ubiquitin (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
4-aminobutanenitrile (84 Da, Ligand)

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EMD-44209

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Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - Ub(T) class 10 map and model from consensus

Release date: June 5, 2024
Resolution: 2.81 Å
EM Method: Single-particle
Fitted PDBs: 9b5e
Q-score: 0.558

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 ]

Sample:

Large ribosomal subunit protein el40b (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
Magnesium ion (24 Da, Ligand)
Adenosine-5'-triphosphate (507 Da, Ligand)
Ubiquitin-activating enzyme e1 1 (111 kDa, Protein from Schizosaccharomyces pombe 972h-)
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-)
Ubiquitin-conjugating enzyme e2 4 (17 kDa, Protein from Schizosaccharomyces pombe 972h-)
Ubiquitin (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
4-aminobutanenitrile (84 Da, Ligand)

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EMD-44210

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Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - cluster 1 map and model (Ub(A)/ATP/Mg)

Release date: June 5, 2024
Resolution: 2.78 Å
EM Method: Single-particle
Fitted PDBs: 9b5f
Q-score: 0.585

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 ]

Sample:

Magnesium ion (24 Da, Ligand)
Adenosine-5'-triphosphate (507 Da, Ligand)
Ubiquitin-activating enzyme e1 1 (111 kDa, Protein from Schizosaccharomyces pombe 972h-)
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-)
Ubiquitin-conjugating enzyme e2 4 (17 kDa, Protein from Schizosaccharomyces pombe 972h-)
Polyubiquitin (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
Ubiquitin (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
4-aminobutanenitrile (84 Da, Ligand)

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EMD-44211

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Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - cluster 2 map and model (Ub(A)/ATP/Mg)

Release date: June 5, 2024
Resolution: 2.67 Å
EM Method: Single-particle
Fitted PDBs: 9b5g
Q-score: 0.601

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 ]

Sample:

Large ribosomal subunit protein el40b (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
Magnesium ion (24 Da, Ligand)
Adenosine-5'-triphosphate (507 Da, Ligand)
Ubiquitin-activating enzyme e1 1 (111 kDa, Protein from Schizosaccharomyces pombe 972h-)
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-)
Ubiquitin-conjugating enzyme e2 4 (17 kDa, Protein from Schizosaccharomyces pombe 972h-)
Ubiquitin (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
4-aminobutanenitrile (84 Da, Ligand)

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EMD-44212

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Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - cluster 3 map and model (Ub(A)-AMP/PPi/Mg)

Release date: June 5, 2024
Resolution: 2.69 Å
EM Method: Single-particle
Fitted PDBs: 9b5h
Q-score: 0.601

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 ]

Sample:

Large ribosomal subunit protein el40b (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
Magnesium ion (24 Da, Ligand)
Pyrophosphate 2- (175 Da, Ligand)
Adenosine monophosphate (347 Da, Ligand)
Ubiquitin-activating enzyme e1 1 (111 kDa, Protein from Schizosaccharomyces pombe 972h-)
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-)
Ubiquitin-conjugating enzyme e2 4 (17 kDa, Protein from Schizosaccharomyces pombe 972h-)
Ubiquitin (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
4-aminobutanenitrile (84 Da, Ligand)

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EMD-44213

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Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - cluster 4 map and model (Ub(A)-AMP/PPi/Mg)

Release date: June 5, 2024
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 9b5i
Q-score: 0.587

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 ]

Sample:

Magnesium ion (24 Da, Ligand)
Pyrophosphate 2- (175 Da, Ligand)
Adenosine monophosphate (347 Da, Ligand)
Ubiquitin-activating enzyme e1 1 (111 kDa, Protein from Schizosaccharomyces pombe 972h-)
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-)
Ubiquitin-conjugating enzyme e2 4 (17 kDa, Protein from Schizosaccharomyces pombe 972h-)
Polyubiquitin (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
Ubiquitin (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
4-aminobutanenitrile (84 Da, Ligand)

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EMD-44214

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Ubiquitin E1-Ub-E2 tetrahedral transthiolation intermediate mimic (doubly Ub-loaded) - cluster 5 map and model (Ub(A)-AMP)

Release date: June 5, 2024
Resolution: 2.86 Å
EM Method: Single-particle
Fitted PDBs: 9b5j
Q-score: 0.559

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 ]

Sample:

Large ribosomal subunit protein el40b (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
Adenosine monophosphate (347 Da, Ligand)
Ubiquitin-activating enzyme e1 1 (111 kDa, Protein from Schizosaccharomyces pombe 972h-)
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-)
Ubiquitin-conjugating enzyme e2 4 (17 kDa, Protein from Schizosaccharomyces pombe 972h-)
Ubiquitin (8 kDa, Protein from Schizosaccharomyces pombe 972h-)
4-aminobutanenitrile (84 Da, Ligand)

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