Dimerized human TOP3B-TDRD3 core complex with a DNA mismatch bubble
Resolution: 4.25 Å
EM Method: Single-particle
Fitted PDBs: 9c9w
Q-score: 0.198
Yang X, Chen X, Yang W, Pommier Y
Nat Commun (2025) 16 pp. 834-834 [ Pubmed: 39828754 DOI: doi:10.1038/s41467-025-55959-y ]
- Manganese (ii) ion (54 Da, Ligand)
- Dna topoisomerase 3-beta-1 (69 kDa, Protein from Homo sapiens)
- Dna (5'-d(p*cp*ap*gp*ap*tp*cp*ap*gp*ap*ap*tp*gp*ap*ap*tp*ap*tp*ap*cp*tp*ap*ap*a)-3') (7 kDa, DNA from Homo sapiens)
- Dna topoisomerase 3-beta-1 (69 kDa, Protein from Homo sapiens)
- Dna (5'-d(*ap*tp*tp*gp*gp*ap*gp*tp*tp*cp*ap*tp*gp*tp*gp*ap*tp*gp*c)-3') (5 kDa, DNA from Homo sapiens)
- Dna (38-mer) (12 kDa, DNA from Homo sapiens)
- Tudor domain-containing protein 3 (17 kDa, Protein from Homo sapiens)
- Dimerized human top3b-tdrd3 core complexes with a dna mismatch bubble (Complex from Homo sapiens)
Structure of the FDX2-bound core ISC complex (proximal conformation)
Resolution: 2.26 Å
EM Method: Single-particle
Fitted PDBs: 8rmc
Q-score: 0.702
Steinhilper R, Boss L, Freibert SA, Schulz V, Krapoth N, Kaltwasser S, Lill R, Murphy BJ
Nat Commun (2024) 15 pp. 10559-10559 [ DOI: doi:10.1038/s41467-024-54585-4 Pubmed: 39632806 ]
- Isoform 1 of iron-sulfur cluster assembly enzyme iscu (15 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Ferredoxin-2, mitochondrial (13 kDa, Protein from Homo sapiens)
- Isoform mitochondrial of cysteine desulfurase (45 kDa, Protein from Homo sapiens)
- Human fdx2-bound core isc complex (nfs1-isd11-acp1-iscu2-fdx2) (Complex from Homo sapiens)
- Fe (ii) ion (55 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Lyr motif-containing protein 4 (13 kDa, Protein from Homo sapiens)
- S-[2-({n-[(2r)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate (540 Da, Ligand)
- Acyl carrier protein (8 kDa, Protein from Escherichia coli BL21(DE3))
Structure of the FDX2-bound core ISC complex (distal conformation)
Resolution: 2.52 Å
EM Method: Single-particle
Fitted PDBs: 8rmd
Q-score: 0.642
Steinhilper R, Boss L, Freibert SA, Schulz V, Krapoth N, Kaltwasser S, Lill R, Murphy BJ
Nat Commun (2024) 15 pp. 10559-10559 [ DOI: doi:10.1038/s41467-024-54585-4 Pubmed: 39632806 ]
- Isoform 1 of iron-sulfur cluster assembly enzyme iscu (15 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Ferredoxin-2, mitochondrial (13 kDa, Protein from Homo sapiens)
- Isoform mitochondrial of cysteine desulfurase (45 kDa, Protein from Homo sapiens)
- Human fdx2-bound core isc complex (nfs1-isd11-acp1-iscu2-fdx2) (Complex from Homo sapiens)
- Fe (ii) ion (55 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Lyr motif-containing protein 4 (13 kDa, Protein from Homo sapiens)
- S-[2-({n-[(2r)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate (540 Da, Ligand)
- Acyl carrier protein (8 kDa, Protein from Escherichia coli BL21(DE3))
Structure of the core ISC complex under turnover conditions (frataxin-bound)
Resolution: 2.49 Å
EM Method: Single-particle
Fitted PDBs: 8rme
Q-score: 0.615
Steinhilper R, Boss L, Freibert SA, Schulz V, Krapoth N, Kaltwasser S, Lill R, Murphy BJ
Nat Commun (2024) 15 pp. 10559-10559 [ DOI: doi:10.1038/s41467-024-54585-4 Pubmed: 39632806 ]
- Isoform 1 of iron-sulfur cluster assembly enzyme iscu (15 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Isoform mitochondrial of cysteine desulfurase (45 kDa, Protein from Homo sapiens)
- Fe (ii) ion (55 Da, Ligand)
- Frataxin mature form (14 kDa, Protein from Homo sapiens)
- Lyr motif-containing protein 4 (13 kDa, Protein from Homo sapiens)
- S-[2-({n-[(2r)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate (540 Da, Ligand)
- Acyl carrier protein (8 kDa, Protein from Escherichia coli BL21(DE3))
- Human core isc complex (nfs1-isd11-acp1-iscu2-fxn/fdx2) under turnover conditions (Complex from Homo sapiens)
Structure of the core ISC complex under turnover conditions (FDX2-bound in proximal conformation)
Resolution: 2.33 Å
EM Method: Single-particle
Fitted PDBs: 8rmf
Q-score: 0.633
Steinhilper R, Boss L, Freibert SA, Schulz V, Krapoth N, Kaltwasser S, Lill R, Murphy BJ
Nat Commun (2024) 15 pp. 10559-10559 [ DOI: doi:10.1038/s41467-024-54585-4 Pubmed: 39632806 ]
- Isoform 1 of iron-sulfur cluster assembly enzyme iscu (15 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Ferredoxin-2, mitochondrial (13 kDa, Protein from Homo sapiens)
- Isoform mitochondrial of cysteine desulfurase (45 kDa, Protein from Homo sapiens)
- Fe (ii) ion (55 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Lyr motif-containing protein 4 (13 kDa, Protein from Homo sapiens)
- S-[2-({n-[(2r)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate (540 Da, Ligand)
- Acyl carrier protein (8 kDa, Protein from Escherichia coli BL21(DE3))
- Human core isc complex (nfs1-isd11-acp1-iscu2-fxn/fdx2) under turnover conditions (Complex from Homo sapiens)
Structure of the core ISC complex under turnover conditions (FDX2-bound in distal conformation)
Resolution: 2.46 Å
EM Method: Single-particle
Fitted PDBs: 8rmg
Q-score: 0.598
Steinhilper R, Boss L, Freibert SA, Schulz V, Krapoth N, Kaltwasser S, Lill R, Murphy BJ
Nat Commun (2024) 15 pp. 10559-10559 [ DOI: doi:10.1038/s41467-024-54585-4 Pubmed: 39632806 ]
- Isoform 1 of iron-sulfur cluster assembly enzyme iscu (15 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Ferredoxin-2, mitochondrial (13 kDa, Protein from Homo sapiens)
- Isoform mitochondrial of cysteine desulfurase (45 kDa, Protein from Homo sapiens)
- Fe (ii) ion (55 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Lyr motif-containing protein 4 (13 kDa, Protein from Homo sapiens)
- S-[2-({n-[(2r)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate (540 Da, Ligand)
- Acyl carrier protein (8 kDa, Protein from Escherichia coli BL21(DE3))
- Human core isc complex (nfs1-isd11-acp1-iscu2-fxn/fdx2) under turnover conditions (Complex from Homo sapiens)
cryoEM structure of the Drosophila melanogaster TOM core complex
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 9etm
Q-score: 0.416
Periasamy A, Ornelas P, Bausewein T, Mitchell N, Zhao J, Quinn LM, Kuehlbrandt W, Gulbis JM
IUCrJ (2025) 12 pp. 49-61 [ Pubmed: 39575538 DOI: doi:10.1107/S2052252524011011 ]
- Mitochondrial import receptor subunit tom5 (4 kDa, Protein from Drosophila melanogaster)
- Translocase of the outer mitochondrial membrane core complex of drosophila melanogaster (Complex from Drosophila melanogaster)
- Mitochondrial import receptor subunit tom6 (4 kDa, Protein from Drosophila melanogaster)
- Mitochondrial import receptor subunit tom7 (5 kDa, Protein from Drosophila melanogaster)
- Mitochondrial import receptor subunit tom22 (5 kDa, Protein from Drosophila melanogaster)
- Diundecyl phosphatidyl choline (622 Da, Ligand)
- Mitochondrial import receptor subunit tom40 (31 kDa, Protein from Drosophila melanogaster)
Cryo-EM structure of S. cerevisiae PolE-core-DNA
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 9b8r
Q-score: 0.332
Yuan Z, Georgescu R, Yao NY, Yurieva O, O'Donnell ME, Li H
Science (2024) 385 pp. eadk5901-eadk5901 [ Pubmed: 39088616 DOI: doi:10.1126/science.adk5901 ]
- Pole-core-dna complex (Complex from Saccharomyces cerevisiae)
- Primer dna (3 kDa, DNA from DNA molecule)
- Dna polymerase epsilon catalytic subunit (133 kDa, Protein from Saccharomyces cerevisiae)
- Iron/sulfur cluster (351 Da, Ligand)
- Template dna (3 kDa, DNA from DNA molecule)
Infectious bronchitis virus core polymerase complex
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 9cpo
Q-score: 0.477
Hoferle PJ, Anderson TK, Kirchdoerfer RN
bioRxiv (2024) [ DOI: doi:10.1101/2024.07.23.604833 Pubmed: 39091740 ]
- Non-structural protein 7 (8 kDa, Protein from Infectious bronchitis virus)
- Core polymerase complex of the infectious bronchitis virus composed of nsp12, nsp8, nsp7, and an dsrna substrate (194 kDa, Complex from Infectious bronchitis virus)
- Rna primer (9 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
- Non-structural protein 8 (21 kDa, Protein from Infectious bronchitis virus)
- Zinc ion (65 Da, Ligand)
- Rna-directed rna polymerase nsp12 (107 kDa, Protein from Infectious bronchitis virus)
- Rna template (10 kDa, RNA from Severe acute respiratory syndrome coronavirus 2)
Spo11 core complex with gapped DNA
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 8urq
Q-score: 0.442
Yu Y, Wang J, Liu K, Zheng Z, Arter M, Claeys Bouuaert C, Pu S, Patel DJ, Keeney S
Nat Struct Mol Biol (2025) 32 pp. 113-124 [ Pubmed: 39304764 DOI: doi:10.1038/s41594-024-01382-8 ]
- Magnesium ion (24 Da, Ligand)
- Gapped dna (21 kDa, DNA from Saccharomyces cerevisiae S288C)
- Spo11 core complex bound to gapped dna (140 kDa, Complex from Saccharomyces cerevisiae S288C)
- Meiosis-specific protein spo11 (50 kDa, Protein from Saccharomyces cerevisiae S288C)
- Meiotic recombination protein rec102 (30 kDa, Protein from Saccharomyces cerevisiae S288C)
- Antiviral protein ski8 (44 kDa, Protein from Saccharomyces cerevisiae S288C)
- Meiotic recombination protein rec104 (20 kDa, Protein from Saccharomyces cerevisiae S288C)