8PK9: Cysteine desulfurase
Structure of the human mitochondrial iron-sulfur cluster biosynthesis complex during persulfide transfer (persulfide on NFS1 and ISCU2). Determined by electron microscopy at 2.58 Å resolution. Released 1 May 2024.
- Method
- Electron microscopy
- Resolution
- 2.58 Å
- Organisms
- Homo sapiens, Escherichia coli BL21(DE3)
- Chains
- 5
- Atoms
- 6,409
- Mol. weight
- 98.23 kDa
- Ligands
- PLP, 8Q1, FE2
- Released
- 1 May 2024
Explore 8PK9 in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
8PK9 contains 45 α-helices and 38 β-strands across 5 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
Chain A: 28 helices, 22 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 57 | 1 | 1 |
| β-strand | 59-60 | 2 | 2 |
| α-helix | 68-70 | 3 | |
| α-helix | 71-77 | 7 | |
| α-helix | 79-82 | 4 | |
| α-helix | 94-114 | 21 | |
| α-helix | 118-120 | 3 | |
| β-strand | 121-124 | 4 | 3 |
| α-helix | 127-132 | 6 | |
| α-helix | 133-137 | 5 | |
| α-helix | 138-141 | 4 | |
| β-strand | 148-152 | 5 | 3 |
| α-helix | 157-168 | 12 | |
| β-strand | 172-176 | 5 | 3 |
| α-helix | 177 | 1 | |
| β-strand | 178 | 1 | 4 |
| α-helix | 179 | 1 | |
| α-helix | 183 | 1 | |
| β-strand | 184 | 1 | 4 |
| α-helix | 185 | 1 | |
| α-helix | 186-192 | 7 | |
| β-strand | 197-203 | 7 | 3 |
| β-strand | 205 | 1 | 5 |
| β-strand | 211 | 1 | 6 |
| β-strand | 212 | 1 | 5 |
| α-helix | 213 | 1 | |
| α-helix | 215-224 | 10 | |
| β-strand | 228-232 | 5 | 3 |
| β-strand | 251-255 | 5 | 3 |
| α-helix | 256-258 | 3 | |
| β-strand | 266-270 | 5 | 3 |
| β-strand | 272 | 1 | 7 |
| β-strand | 275 | 1 | 7 |
| α-helix | 276-277 | 2 | |
| α-helix | 288-290 | 3 | |
| α-helix | 298-336 | 39 | |
| β-strand | 340-342 | 3 | 8 |
| α-helix | 346-348 | 3 | |
| β-strand | 349 | 1 | 6 |
| β-strand | 353-358 | 6 | 8 |
| α-helix | 363-369 | 7 | |
| β-strand | 373-374 | 2 | 2 |
| β-strand | 376-377 | 2 | 8 |
| α-helix | 380-382 | 3 | |
| α-helix | 390-394 | 5 | |
| α-helix | 402-404 | 3 | |
| β-strand | 405-409 | 5 | 8 |
| α-helix | 416-436 | 21 | |
| α-helix | 438-444 | 7 | |
| α-helix | 449-451 | 3 | |
Chain B: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 7-20 | 14 | |
| α-helix | 26-42 | 17 | |
| α-helix | 49-75 | 27 | |
| α-helix | 79-80 | 2 | |
| β-strand | 81 | 1 | 1 |
Chain C: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 4-16 | 13 | |
| β-strand | 28 | 1 | 9 |
| α-helix | 37-51 | 15 | |
| α-helix | 54-56 | 3 | |
| α-helix | 57-62 | 6 | |
| β-strand | 65 | 1 | 9 |
| α-helix | 66-75 | 10 | |
Chain D: 6 helices, 6 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 37-44 | 8 | |
| β-strand | 49 | 1 | 10 |
| β-strand | 59-66 | 8 | 10 |
| β-strand | 71-79 | 9 | 10 |
| β-strand | 84 | 1 | 11 |
| β-strand | 85-93 | 9 | 10 |
| α-helix | 96-108 | 13 | |
| β-strand | 113 | 1 | 11 |
| α-helix | 114-117 | 4 | |
| α-helix | 122-129 | 8 | |
| α-helix | 133-135 | 3 | |
| α-helix | 136-156 | 21 | |
Chain E: 2 helices, 7 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 92-111 | 20 | |
| β-strand | 124-128 | 5 | 12 |
| β-strand | 131-137 | 7 | 12 |
| β-strand | 141-148 | 8 | 12 |
| β-strand | 153-158 | 6 | 12 |
| β-strand | 162-168 | 7 | 12 |
| β-strand | 173-175 | 3 | 12 |
| β-strand | 181 | 1 | 12 |
| α-helix | 182-194 | 13 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Cysteine desulfurase | A | protein | 404 | Homo sapiens | Q9Y697 (AlphaFold model) |
| LYR motif-containing protein 4 | B | protein | 115 | Homo sapiens | Q9HD34 (AlphaFold model) |
| Acyl carrier protein | C | protein | 78 | Escherichia coli BL21(DE3) | P0A6A8 (AlphaFold model) |
| Iron-sulfur cluster assembly enzyme ISCU | D | protein | 143 | Homo sapiens | Q9H1K1 (AlphaFold model) |
| Frataxin mature form | E | protein | 133 | Homo sapiens | Q16595 |
Sequence of entity 1 (A), FASTA
>8PK9_1 Cysteine desulfurase (chains A)
MSLRPLYMDVQATTPLDPRVLDAMLPYLINYYGNPHSRTHAYGWESEAAMERARQQVASL
IGADPREIIFTSGATESNNIAIKGVARFYRSRKKHLITTQTEHKCVLDSCRSLEAEGFQV
TYLPVQKSGIIDLKELEAAIQPDTSLVSVMTVNNEIGVKQPIAEIGRICSSRKVYFHTDA
AQAVGKIPLDVNDMKIDLMSISGHKIYGPKGVGAIYIRRRPRVRVEALQSGGGQERGMRS
GTVPTPLVVGLGAACEVAQQEMEYDHKRISKLSERLIQNIMKSLPDVVMNGDPKHHYPGC
INLSFAYVEGESLLMALKDVALSSGSACTSASLEPSYVLRAIGTDEDLAHSSIRFGIGRF
TTEEEVDYTVEKCIQHVKRLREMSPLWEMVQDGIDLKSIKWTQH
Sequence of entity 2 (B), FASTA
>8PK9_2 LYR motif-containing protein 4 (chains B)
MGSSHHHHHHGSPTTENLYFQGHNMAASSRAQVLALYRAMLRESKRFSAYNYRTYAVRRI
RDAFRENKNVKDPVEIQTLVNKAKRDLGVIRRQVHIGQLYSTDKLIIENRDMPRT
Sequence of entity 3 (C), FASTA
>8PK9_3 Acyl carrier protein (chains C)
MSTIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTVELVMALEEEFDTEIPDEEA
EKITTVQAAIDYINGHQA
Sequence of entity 4 (D), FASTA
>8PK9_4 Iron-sulfur cluster assembly enzyme ISCU (chains D)
MAYHKKVVDHYENPRNVGSLDKTSKNVGTGLVGAPACGDVMKLQIQVDEKGKIVDARFKT
FGCGSAIASSSLATEWVKGKTVEEALTIKNTDIAKELCLPPVKLHCSMLAEDAIKAALAD
YKLKQEPKKGEAEKKLEHHHHHH
Sequence of entity 5 (E), FASTA
>8PK9_5 Frataxin mature form (chains E)
SNASGTLGHPGSLDETTYERLAEETLDSLAEFFEDLADKPYTFEDYDVSFGSGVLTVKLG
GDLGTYVINKQTPNKQIWLSSPSSGPKRYDWTGKNWVYSHDGVSLHELLAAELTKALKTK
LDLSSLAYSGKDA
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| PLP | Pyridoxal-5'-phosphate | C8 H10 N O6 P | 1 |
| 8Q1 | S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}ami… | C23 H45 N2 O8 P S | 1 |
| FE2 | FE (II) ion | Fe | 1 |
Primary citation
Mechanism and structural dynamics of sulfur transfer during de novo [2Fe-2S] cluster assembly on ISCU2. Schulz, V., Steinhilper, R., Oltmanns, J. et al. Nat Commun (2024) 15:3269-3269. DOI 10.1038/s41467-024-47310-8 · PubMed
Other PDB entries of the same protein (UniProt Q9Y697 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 6UXE 1.57 Å, Structure of the human mitochondrial desulfurase complex Nfs1-ISCU2(M140I)-ISD11 with…
- 6W1D 1.79 Å, Structure of human mitochondrial complex Nfs1-ISCU2 (WT)-ISD11 with E.coli ACP1 at 1.8 A…
- 6WIH 1.9 Å, N-terminal mutation of ISCU2 (L35H36) traps Nfs1 Cys loop in the active site of ISCU2…
- 6WI2 1.95 Å, Structure of human mitochondrial complex Nfs1-ISCU2-ISD11 with E.coli ACP1 at 1.95 A…
- 8TVT 2.0 Å, Structure of human Cysteine desulfurase Nfs1 with L-propargylglycine bound to active…
- 8RMC 2.26 Å, Structure of the FDX2-bound core ISC complex (proximal conformation)
- 8RMF 2.33 Å, Structure of the core ISC complex under turnover conditions (FDX2-bound in proximal…
- 8RMG 2.46 Å, Structure of the core ISC complex under turnover conditions (FDX2-bound in distal…
- 8PK8 2.49 Å, Structure of the human mitochondrial iron-sulfur cluster biosynthesis complex during…
- 8RME 2.49 Å, Structure of the core ISC complex under turnover conditions (frataxin-bound)
- 7RTK 2.5 Å, Structure of the (NIAU)2 complex with N-terminal mutation of ISCU2 Y35D at 2.5 A…
- 8RMD 2.52 Å, Structure of the FDX2-bound core ISC complex (distal conformation)
Browse structure collections
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