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 ]
- Ferredoxin-2, mitochondrial (13 kDa, Protein from Homo sapiens)
- Isoform 1 of iron-sulfur cluster assembly enzyme iscu (15 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)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- 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)
- Lyr motif-containing protein 4 (13 kDa, Protein from Homo sapiens)
- Water (18 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 ]
- Ferredoxin-2, mitochondrial (13 kDa, Protein from Homo sapiens)
- Isoform 1 of iron-sulfur cluster assembly enzyme iscu (15 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)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- 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)
- Lyr motif-containing protein 4 (13 kDa, Protein from Homo sapiens)
- Water (18 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 ]
- S-[2-({n-[(2r)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate (540 Da, Ligand)
- Isoform 1 of iron-sulfur cluster assembly enzyme iscu (15 kDa, Protein from Homo sapiens)
- Human core isc complex (nfs1-isd11-acp1-iscu2-fxn/fdx2) under turnover conditions (Complex from Homo sapiens)
- Fe (ii) ion (55 Da, Ligand)
- Frataxin mature form (14 kDa, Protein from Homo sapiens)
- Isoform mitochondrial of cysteine desulfurase (45 kDa, Protein from Homo sapiens)
- Lyr motif-containing protein 4 (13 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Acyl carrier protein (8 kDa, Protein from Escherichia coli BL21(DE3))
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 ]
- Ferredoxin-2, mitochondrial (13 kDa, Protein from Homo sapiens)
- Isoform 1 of iron-sulfur cluster assembly enzyme iscu (15 kDa, Protein from Homo sapiens)
- Human core isc complex (nfs1-isd11-acp1-iscu2-fxn/fdx2) under turnover conditions (Complex from Homo sapiens)
- S-[2-({n-[(2r)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate (540 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- Isoform mitochondrial of cysteine desulfurase (45 kDa, Protein from Homo sapiens)
- Lyr motif-containing protein 4 (13 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Acyl carrier protein (8 kDa, Protein from Escherichia coli BL21(DE3))
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 ]
- Ferredoxin-2, mitochondrial (13 kDa, Protein from Homo sapiens)
- Isoform 1 of iron-sulfur cluster assembly enzyme iscu (15 kDa, Protein from Homo sapiens)
- Human core isc complex (nfs1-isd11-acp1-iscu2-fxn/fdx2) under turnover conditions (Complex from Homo sapiens)
- S-[2-({n-[(2r)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate (540 Da, Ligand)
- Fe2/s2 (inorganic) cluster (175 Da, Ligand)
- Fe (ii) ion (55 Da, Ligand)
- Isoform mitochondrial of cysteine desulfurase (45 kDa, Protein from Homo sapiens)
- Lyr motif-containing protein 4 (13 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Acyl carrier protein (8 kDa, Protein from Escherichia coli BL21(DE3))
Cryo-EM structure of Streptococcus pneumoniae NADPH oxidase
Resolution: 2.29 Å
EM Method: Single-particle
Fitted PDBs: 8qt6
Q-score: 0.678
Dubach VRA, San Segundo-Acosta P, Murphy BJ
Nat Struct Mol Biol (2024) 31 pp. 1769-1777 [ DOI: doi:10.1038/s41594-024-01348-w Pubmed: 39039317 ]
- Water (18 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Streptococcus pneumoniae nadph oxidase with fad and heme cofactors (46 kDa, Complex from Streptococcus pneumoniae)
- Fad-binding fr-type domain-containing protein (46 kDa, Protein from Streptococcus pneumoniae)
- Streptococcus pneumoniae nadph oxidase (Complex from Streptococcus pneumoniae)
- Flavin-adenine dinucleotide (785 Da, Ligand)
Cryo-EM structure of Streptococcus pneumoniae NADPH oxidase in complex with NADPH
Resolution: 2.2 Å
EM Method: Single-particle
Fitted PDBs: 8qt7
Q-score: 0.691
Dubach VRA, San Segundo-Acosta P, Murphy BJ
Nat Struct Mol Biol (2024) 31 pp. 1769-1777 [ DOI: doi:10.1038/s41594-024-01348-w Pubmed: 39039317 ]
- Water (18 Da, Ligand)
- Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate (745 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Streptococcus pneumoniae nadph oxidase with fad and heme cofactors (46 kDa, Complex from Streptococcus pneumoniae)
- Fad-binding fr-type domain-containing protein (46 kDa, Protein from Streptococcus pneumoniae)
- Flavin-adenine dinucleotide (785 Da, Ligand)
Cryo-EM structure of stably reduced Streptococcus pneumoniae NADPH oxidase in complex with NADH
Resolution: 2.36 Å
EM Method: Single-particle
Fitted PDBs: 8qt9
Q-score: 0.675
Dubach VRA, San Segundo-Acosta P, Murphy BJ
Nat Struct Mol Biol (2024) 31 pp. 1769-1777 [ DOI: doi:10.1038/s41594-024-01348-w Pubmed: 39039317 ]
- Water (18 Da, Ligand)
- 1,4-dihydronicotinamide adenine dinucleotide (665 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Fad-binding fr-type domain-containing protein (46 kDa, Protein from Streptococcus pneumoniae)
- Flavin-adenine dinucleotide (785 Da, Ligand)
- Streptococcus pneumoniae nadph oxidase with fad and heme cofactors and nadh bound (Complex from Streptococcus pneumoniae)
Cryo-EM structure of Streptococcus pneumoniae NADPH oxidase F397A mutant in complex with NADPH
Resolution: 2.64 Å
EM Method: Single-particle
Fitted PDBs: 8qta
Q-score: 0.621
Dubach VRA, San Segundo-Acosta P, Murphy BJ
Nat Struct Mol Biol (2024) 31 pp. 1769-1777 [ DOI: doi:10.1038/s41594-024-01348-w Pubmed: 39039317 ]
- Water (18 Da, Ligand)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Protein-substrate complex of nadph oxidase with nadph (46 kDa, Complex from Streptococcus pneumoniae)
- Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate (745 Da, Ligand)
- Fad-binding fr-type domain-containing protein (45 kDa, Protein from Streptococcus pneumoniae)
- Flavin-adenine dinucleotide (785 Da, Ligand)
Resolution: 2.08 Å
EM Method: Single-particle
Fitted PDBs: 8q3v
Q-score: 0.686
Aziz I, Kayastha K, Kaltwasser S, Vonck J, Welsch S, Murphy BJ, Kahnt J, Wu D, Wagner T, Shima S, Ermler U
PNAS (2024) 121 pp. e2315568121-e2315568121 [ Pubmed: 38530900 DOI: doi:10.1073/pnas.2315568121 ]
- Tetrahydromethanopterin s-methyltransferase subunit b (10 kDa, Protein from Methanothermobacter marburgensis)
- Tetrahydromethanopterin s-methyltransferase subunit e (31 kDa, Protein from Methanothermobacter marburgensis)
- Tetrahydromethanopterin s-methyltransferase subunit a 1 (25 kDa, Protein from Methanothermobacter marburgensis)
- Sodium ion (22 Da, Ligand)
- Methyl-h4mpt:com methyltransferase (430 MDa, Complex from Methanothermobacter marburgensis)
- Tetrahydromethanopterin s-methyltransferase subunit c (27 kDa, Protein from Methanothermobacter marburgensis)
- Tetrahydromethanopterin s-methyltransferase subunit f (7 kDa, Protein from Methanothermobacter marburgensis)
- Tetrahydromethanopterin s-methyltransferase subunit d (22 kDa, Protein from Methanothermobacter marburgensis)
- Magnesium ion (24 Da, Ligand)
- Tetrahydromethanopterin s-methyltransferase subunit g (9 kDa, Protein from Methanothermobacter marburgensis)
- Water (18 Da, Ligand)
- [(2~{s},7~{r},11~{r},15~{s},19~{s},22~{s},26~{s},30~{r},34~{r},39~{s},43~{r},47~{r},51~{s},55~{s},58~{s},62~{s},66~{r},70~{r})-39-[[(2~{r},3~{r},4~{s},5~{s},6~{r})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxymethyl]-7,11,15,19,22,26,30,34,43,47,51,55,58,62,66,70-hexadecamethyl-1,4,37,40-tetraoxacyclodoheptacont-2-yl]methyl [(2~{r},3~{s},5~{r},6~{r})-2,3,4,5,6-pentakis(oxidanyl)cyclohexyl] hydrogen phosphate (1 kDa, Ligand)