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5kz5

Architecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery: the Complex Formed by the Iron Donor, the Sulfur Donor, and the Scaffold

Method: ELECTRON MICROSCOPY Dmax: 205.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cysteine desulfurase, mitochondrial

Homo sapiens

UniProt Q9Y697

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 36 PDB declaration: 36-meric（36） Consistent with protein copy count Chain 1； UniProt 67–457 Chain 2； UniProt 67–457 Chain 3； UniProt 67–457 Chain 4； UniProt 67–457 Chain M； UniProt 67–457 Chain N； UniProt 67–457 Chain O； UniProt 67–457 Chain P； UniProt 67–457 Chain Q； UniProt 67–457 Chain R； UniProt 67–457 Chain S； UniProt 67–457 Chain T； UniProt 67–457 Not recorded Frataxin, mitochondrial × 12 （Q16595） Iron-sulfur cluster assembly enzyme ISCU, mitochondrial × 12 （Q9H1K1） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 Resolution 14.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5KZ5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5USR Crystal structure of human NFS1-ISD11 in complex with E. coli acyl-carrier protein at 3.09 angstroms Deposited 2017-02-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 56–457（402 aa）
Chain G 56–457（402 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；295 K；450 uL 0.1 M CBTP (pH = 6.4), 0.3 M CsCl, 0.2 M D,L - allylglycine, 5 mM TCEP, 8 % (wt/vol) PEG 3350 mixed with 50 uL of 40 % (vol/vol) acetone
Resolution 3.09 Å R-free 0.259
5USR Crystal structure of human NFS1-ISD11 in complex with E. coli acyl-carrier protein at 3.09 angstroms Deposited 2017-02-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 56–457（402 aa）
Chain E 56–457（402 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；295 K；450 uL 0.1 M CBTP (pH = 6.4), 0.3 M CsCl, 0.2 M D,L - allylglycine, 5 mM TCEP, 8 % (wt/vol) PEG 3350 mixed with 50 uL of 40 % (vol/vol) acetone
Resolution 3.09 Å R-free 0.259
5WGB Crystal Structure of the Human mitochondrial Cysteine Desulfurase in complex with ISD11 and E. coli ACP1 protein at 2.75A Deposited 2017-07-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 56–457（402 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 1 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；285 K；0.1 M MES pH 6.5 0.3 M Ammonium Acetate 20 mM Calcium Acetate 20 mM CaCl2 19 % isopropanol
Resolution 2.75 Å R-free 0.255
5WKP Crystal Structure of the Human mitochondrial Cysteine Desulfurase in complex with ISD11 and Iron-Sulfur Cluster Scaffold Protein ISCU1, and E. coli ACP1 protein at 3.15A Deposited 2017-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 56–457（402 aa） Fragment：UNP residues 56-457
Chain E 56–457（402 aa） Fragment：UNP residues 56-457
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；285 K；0.1 M MES pH 7 15 % PEG 3350
Resolution 3.15 Å R-free 0.242
5WLW Crystal Structure of the Human Mitochondrial Cysteine Desulfurase with active Cysteine Loop within ISCU1 active site, coordinating Zn ion. Complexed with human ISD11 and E. coli ACP1 at 3.3A. Deposited 2017-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 56–457（402 aa） Fragment：UNP residues 56-457
Chain E 56–457（402 aa） Fragment：UNP residues 56-457
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；285 K；0.1 M MES pH 7.0 15 % PEG 3350
Resolution 3.32 Å R-free 0.255
6NZU Structure of the human frataxin-bound iron-sulfur cluster assembly complex Deposited 2019-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain A 56–457（402 aa） Fragment：UNP residues 56-457
Chain E 56–457（402 aa） Fragment：UNP residues 56-457
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6UXE Structure of the human mitochondrial desulfurase complex Nfs1-ISCU2(M140I)-ISD11 with E.coli ACP1 at 1.57 A resolution showing flexibility of N terminal end of ISCU2 Deposited 2019-11-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 56–457（402 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 GOL GLYCEROL × 12 EDO 1,2-ETHANEDIOL × 100 PEG DI(HYDROXYETHYL)ETHER × 22 PG4 TETRAETHYLENE GLYCOL × 4 P15 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL × 2 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 PGE TRIETHYLENE GLYCOL × 6 EDT {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID × 2 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 1PE PENTAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；288 K；0.1 M MES pH 6.0-6.5, 22% PEG400
Resolution 1.57 Å R-free 0.180
6W1D Structure of human mitochondrial complex Nfs1-ISCU2 (WT)-ISD11 with E.coli ACP1 at 1.8 A resolution (NIAU)2 Deposited 2020-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 56–457（402 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 GOL GLYCEROL × 12 EDO 1,2-ETHANEDIOL × 96 PEG DI(HYDROXYETHYL)ETHER × 22 PG4 TETRAETHYLENE GLYCOL × 4 P15 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL × 2 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 PGE TRIETHYLENE GLYCOL × 6 EDT {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID × 2 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 1PE PENTAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；288 K；0.1 M MES pH 6.0-6.5 22 % PEG 400
Resolution 1.79 Å R-free 0.189
6WI2 Structure of human mitochondrial complex Nfs1-ISCU2-ISD11 with E.coli ACP1 at 1.95 A resolution (NIAU)2. N-terminal mutation of ISCU2 (L35) traps Nfs1 Cys loop in the active site of ISCU2 without metal present. Deposited 2020-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 56–457（402 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 36 GOL GLYCEROL × 3 PEG DI(HYDROXYETHYL)ETHER × 10 PG4 TETRAETHYLENE GLYCOL × 2 ETE 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1 PGE TRIETHYLENE GLYCOL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 EDT {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID × 1 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 1 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；288 K；0.1 M MES pH 5.5 22.5 % PEG 400
Resolution 1.95 Å R-free 0.185
6WIH N-terminal mutation of ISCU2 (L35H36) traps Nfs1 Cys loop in the active site of ISCU2 without metal present. Structure of human mitochondrial complex Nfs1-ISCU2(L35H36)-ISD11 with E.coli ACP1 at 1.9 A resolution (NIAU)2. Deposited 2020-04-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 56–457（402 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 1 PEG DI(HYDROXYETHYL)ETHER × 9 GOL GLYCEROL × 5 EDO 1,2-ETHANEDIOL × 38 PG4 TETRAETHYLENE GLYCOL × 2 P15 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL × 1 PGE TRIETHYLENE GLYCOL × 3 EDT {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID × 1 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 1 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；288 K；0.1 M MES pH 5.5 22.5 % PEG 400
Resolution 1.90 Å R-free 0.186
7RTK Structure of the (NIAU)2 complex with N-terminal mutation of ISCU2 Y35D at 2.5 A resolution Deposited 2021-08-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 56–457（402 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 EDO 1,2-ETHANEDIOL × 58 GOL GLYCEROL × 6 PG4 TETRAETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 16 P15 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL × 2 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 PGE TRIETHYLENE GLYCOL × 6 EDT {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID × 2 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 1PE PENTAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；288 K；0.1 M MES pH 5.5 22.5 % PEG 400
Resolution 2.50 Å R-free 0.214
8PK8 Structure of the human mitochondrial iron-sulfur cluster biosynthesis complex during persulfide transfer (persulfide on ISCU2) Deposited 2023-06-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 56–457（402 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 1 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 1 FE2 FE (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.49 Å
8PK9 Structure of the human mitochondrial iron-sulfur cluster biosynthesis complex during persulfide transfer (persulfide on NFS1 and ISCU2) Deposited 2023-06-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 56–457（402 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) PLP PYRIDOXAL-5'-PHOSPHATE × 1 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 1 FE2 FE (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.58 Å
8PKA Structure of the human mitochondrial iron-sulfur cluster biosynthesis complex during persulfide transfer (without frataxin) Deposited 2023-06-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 56–457（402 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 1 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 1 FE2 FE (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.75 Å
8RMC Structure of the FDX2-bound core ISC complex (proximal conformation) Deposited 2024-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 56–457（402 aa）
Chain E 56–457（402 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) FE2 FE (II) ION × 2 FES FE2/S2 (INORGANIC) CLUSTER × 1 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.26 Å
8RMD Structure of the FDX2-bound core ISC complex (distal conformation) Deposited 2024-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 56–457（402 aa）
Chain E 56–457（402 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 FE2 FE (II) ION × 2 FES FE2/S2 (INORGANIC) CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.52 Å
8RME Structure of the core ISC complex under turnover conditions (frataxin-bound) Deposited 2024-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 56–457（402 aa）
Chain E 56–457（402 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) FE2 FE (II) ION × 2 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.49 Å
8RMF Structure of the core ISC complex under turnover conditions (FDX2-bound in proximal conformation) Deposited 2024-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 56–457（402 aa）
Chain E 56–457（402 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 FE2 FE (II) ION × 2 FES FE2/S2 (INORGANIC) CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.33 Å
8RMG Structure of the core ISC complex under turnover conditions (FDX2-bound in distal conformation) Deposited 2024-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 56–457（402 aa）
Chain E 56–457（402 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 FE2 FE (II) ION × 2 FES FE2/S2 (INORGANIC) CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.46 Å
8TVT Structure of human Cysteine desulfurase Nfs1 with L-propargylglycine bound to active site PLP in complex with ISD11, Acp1 and ISCU2 Deposited 2023-08-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 56–454（399 aa）
Not recorded EDO 1,2-ETHANEDIOL × 30 PLP PYRIDOXAL-5'-PHOSPHATE × 1 LPH L-Propargylglycine × 1 GOL GLYCEROL × 3 PEG DI(HYDROXYETHYL)ETHER × 8 PG4 TETRAETHYLENE GLYCOL × 2 P15 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 PGE TRIETHYLENE GLYCOL × 1 EDT {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID × 1 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；288 K；0.1 M MES pH 6.5 22.5 % PEG 400
Resolution 2.00 Å R-free 0.186

19 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NFS1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain 1； PDBConstruct 1–391； UniProt 67–457 Author chain 2； PDBConstruct 1–391； UniProt 67–457 Author chain 3； PDBConstruct 1–391； UniProt 67–457 Author chain 4； PDBConstruct 1–391； UniProt 67–457 Author chain M； PDBConstruct 1–391； UniProt 67–457 Author chain N； PDBConstruct 1–391； UniProt 67–457 Author chain O； PDBConstruct 1–391； UniProt 67–457 Author chain P； PDBConstruct 1–391； UniProt 67–457 Author chain Q； PDBConstruct 1–391； UniProt 67–457 Author chain R； PDBConstruct 1–391； UniProt 67–457 Author chain S； PDBConstruct 1–391； UniProt 67–457 Author chain T； PDBConstruct 1–391； UniProt 67–457

Frataxin, mitochondrial

Homo sapiens

UniProt Q16595

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 36 PDB declaration: 36-meric（36） Consistent with protein copy count Chain A； UniProt 42–210 Chain B； UniProt 42–210 Chain C； UniProt 42–210 Chain D； UniProt 42–210 Chain E； UniProt 42–210 Chain F； UniProt 42–210 Chain G； UniProt 42–210 Chain H； UniProt 42–210 Chain I； UniProt 42–210 Chain J； UniProt 42–210 Chain K； UniProt 42–210 Chain L； UniProt 42–210 Not recorded Cysteine desulfurase, mitochondrial × 12 （Q9Y697） Iron-sulfur cluster assembly enzyme ISCU, mitochondrial × 12 （Q9H1K1） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 Resolution 14.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5KZ5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1EKG MATURE HUMAN FRATAXIN Deposited 2000-03-08 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 84–210（127 aa） Fragment：RESIDUES 88-210
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；2.5 M ammonium sulfate, 0.1 sodium citrate, 2% sucrose, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 18K
Resolution 1.80 Å R-free 0.220
1LY7 The solution structure of the the c-terminal domain of frataxin, the protein responsible for friedreich ataxia Deposited 2002-06-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 91–210（120 aa） Fragment：C-TERMINAL DOMAIN (91-210)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；300 K；Ionic strength (raw mmCIF value) 10 mM phosphate；Pressure ambient
NMR sample composition 1 MM FRATAXIN. U-15N 10 MM PHOSPHATE BUFFER (PH 6.8)90% H2O, 10% D2O | h2o
Resolution not provided
3S4M Crystal structure of wild-type human frataxin Deposited 2011-05-19 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；30% MPD, 0.1 M sodium citrate, 0.2 M ammonium acetate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.30 Å R-free 0.187
3S5D Crystal structure of human frataxin variant W155A Deposited 2011-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：W155A SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；295 K；1.8 M ammonium sulfate, 0.2 M potassium sodium tartrate tetrahydrate, 0.1 M sodium citrate tribasic dihydrate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.50 Å R-free 0.192
3S5E Crystal structure of human frataxin variant W155R, one of the Friedreich's ataxia point mutations Deposited 2011-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：W155R MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；295 K；16% PEG2000 MME, 0.1 M MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.31 Å R-free 0.197
3S5F Crystal structure of human frataxin variant W155F Deposited 2011-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：W155F MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.2 M sodium acetate trihydrate, 0.1 M Tris hydrochloride, 30% PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.50 Å R-free 0.213
3S5F Crystal structure of human frataxin variant W155F Deposited 2011-05-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：W155F MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.2 M sodium acetate trihydrate, 0.1 M Tris hydrochloride, 30% PEG4000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.50 Å R-free 0.213
3T3J 1.70 A structure of Friedreich's ataxia frataxin variant N146K Deposited 2011-07-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：N146K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；28% PEG2000 MME, 0.1 M Tris, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.70 Å R-free 0.245
3T3K 1.24 A Structure of Friedreich's ataxia frataxin variant Q148R Deposited 2011-07-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：Q148R No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；20% PEG3000, 0.1 M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.24 Å R-free 0.197
3T3L 1.15 A structure of human frataxin variant Q153A Deposited 2011-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：Q153A SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；295 K；2.0 M ammonium sulfate, 0.1 M sodium citrate tribasic dihydrate, 0.2 M potassium sodium tartrate tetrahydrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.15 Å R-free 0.179
3T3T 1.38 A structure of human frataxin variant Q148G Deposited 2011-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：Q148G SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；2.0 M ammonium sulfate, 0.1 M citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.38 Å R-free 0.227
3T3T 1.38 A structure of human frataxin variant Q148G Deposited 2011-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：Q148G SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；2.0 M ammonium sulfate, 0.1 M citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.38 Å R-free 0.227
3T3T 1.38 A structure of human frataxin variant Q148G Deposited 2011-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：Q148G SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；2.0 M ammonium sulfate, 0.1 M citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.38 Å R-free 0.227
3T3T 1.38 A structure of human frataxin variant Q148G Deposited 2011-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：Q148G SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；2.0 M ammonium sulfate, 0.1 M citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.38 Å R-free 0.227
3T3X 1.57 A structure of Friedreich's ataxia frataxin variant R165C Deposited 2011-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：R165C SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；1.9 M ammonium sulfate, 0.1 M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.57 Å R-free 0.251
3T3X 1.57 A structure of Friedreich's ataxia frataxin variant R165C Deposited 2011-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 82–210（129 aa） Fragment：mature form (UNP residues 82-210)
Mutation：R165C SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；1.9 M ammonium sulfate, 0.1 M sodium citrate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.57 Å R-free 0.251
6NZU Structure of the human frataxin-bound iron-sulfur cluster assembly complex Deposited 2019-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain I 81–210（130 aa） Fragment：UNP residues 81-210
Chain J 81–210（130 aa） Fragment：UNP residues 81-210
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8PK8 Structure of the human mitochondrial iron-sulfur cluster biosynthesis complex during persulfide transfer (persulfide on ISCU2) Deposited 2023-06-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 81–210（130 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 1 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 1 FE2 FE (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.49 Å
8PK9 Structure of the human mitochondrial iron-sulfur cluster biosynthesis complex during persulfide transfer (persulfide on NFS1 and ISCU2) Deposited 2023-06-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 81–210（130 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 1 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 1 FE2 FE (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.58 Å
8RME Structure of the core ISC complex under turnover conditions (frataxin-bound) Deposited 2024-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain I 81–210（130 aa）
Not recorded FE2 FE (II) ION × 2 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.49 Å
9HO4 Crystal Structure of the Human Frataxin protein in complex with a tailored Camelid Nanobody 6B1 Deposited 2024-12-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 93–206（114 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M HEPES pH 7.0 0.8M Potassium Sodium Tartrate
Resolution 1.76 Å R-free 0.175
9HO5 Crystal Structure of the Human Frataxin protein in complex with a tailored Camelid Nanobody 4A7 Deposited 2024-12-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 90–210（121 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium Thiocyanate pH 6.9 20% PEG 3350
Resolution 1.50 Å R-free 0.210
9HO6 Crystal Structure of the Human Frataxin protein in complex with a tailored Camelid Nanobody 16C10 Deposited 2024-12-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 90–210（121 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；15% PEG 10K 0.1M Ammonium acetate 0.1M Bis-Tris pH 5.5
Resolution 2.00 Å R-free 0.227
9HO6 Crystal Structure of the Human Frataxin protein in complex with a tailored Camelid Nanobody 16C10 Deposited 2024-12-11 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 90–210（121 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；15% PEG 10K 0.1M Ammonium acetate 0.1M Bis-Tris pH 5.5
Resolution 2.00 Å R-free 0.227

18 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FRDA_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 1–169； UniProt 42–210 Author chain B； PDBConstruct 1–169； UniProt 42–210 Author chain C； PDBConstruct 1–169； UniProt 42–210 Author chain D； PDBConstruct 1–169； UniProt 42–210 Author chain E； PDBConstruct 1–169； UniProt 42–210 Author chain F； PDBConstruct 1–169； UniProt 42–210 Author chain G； PDBConstruct 1–169； UniProt 42–210 Author chain H； PDBConstruct 1–169； UniProt 42–210 Author chain I； PDBConstruct 1–169； UniProt 42–210 Author chain J； PDBConstruct 1–169； UniProt 42–210 Author chain K； PDBConstruct 1–169； UniProt 42–210 Author chain L； PDBConstruct 1–169； UniProt 42–210

Iron-sulfur cluster assembly enzyme ISCU, mitochondrial

Homo sapiens

UniProt Q9H1K1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 36 PDB declaration: 36-meric（36） Consistent with protein copy count Chain a； UniProt 25–142 Chain b； UniProt 25–142 Chain c； UniProt 25–142 Chain d； UniProt 25–142 Chain e； UniProt 25–142 Chain f； UniProt 25–142 Chain g； UniProt 25–142 Chain h； UniProt 25–142 Chain i； UniProt 25–142 Chain j； UniProt 25–142 Chain k； UniProt 25–142 Chain l； UniProt 25–142 Not recorded Cysteine desulfurase, mitochondrial × 12 （Q9Y697） Frataxin, mitochondrial × 12 （Q16595） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 Resolution 14.30 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 5KZ5 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5WKP Crystal Structure of the Human mitochondrial Cysteine Desulfurase in complex with ISD11 and Iron-Sulfur Cluster Scaffold Protein ISCU1, and E. coli ACP1 protein at 3.15A Deposited 2017-07-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 1–142（142 aa）
Chain H 1–142（142 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；285 K；0.1 M MES pH 7 15 % PEG 3350
Resolution 3.15 Å R-free 0.242
5WLW Crystal Structure of the Human Mitochondrial Cysteine Desulfurase with active Cysteine Loop within ISCU1 active site, coordinating Zn ion. Complexed with human ISD11 and E. coli ACP1 at 3.3A. Deposited 2017-07-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 1–142（142 aa）
Chain H 1–142（142 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；285 K；0.1 M MES pH 7.0 15 % PEG 3350
Resolution 3.32 Å R-free 0.255
6NZU Structure of the human frataxin-bound iron-sulfur cluster assembly complex Deposited 2019-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain D 35–157（123 aa） Fragment：UNP residues 35-157
Chain H 35–157（123 aa） Fragment：UNP residues 35-157
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6UXE Structure of the human mitochondrial desulfurase complex Nfs1-ISCU2(M140I)-ISD11 with E.coli ACP1 at 1.57 A resolution showing flexibility of N terminal end of ISCU2 Deposited 2019-11-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 35–167（133 aa）
Mutation：M140I PLP PYRIDOXAL-5'-PHOSPHATE × 2 GOL GLYCEROL × 12 EDO 1,2-ETHANEDIOL × 100 PEG DI(HYDROXYETHYL)ETHER × 22 PG4 TETRAETHYLENE GLYCOL × 4 P15 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL × 2 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 PGE TRIETHYLENE GLYCOL × 6 EDT {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID × 2 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 1PE PENTAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；288 K；0.1 M MES pH 6.0-6.5, 22% PEG400
Resolution 1.57 Å R-free 0.180
6W1D Structure of human mitochondrial complex Nfs1-ISCU2 (WT)-ISD11 with E.coli ACP1 at 1.8 A resolution (NIAU)2 Deposited 2020-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 35–167（133 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 2 GOL GLYCEROL × 12 EDO 1,2-ETHANEDIOL × 96 PEG DI(HYDROXYETHYL)ETHER × 22 PG4 TETRAETHYLENE GLYCOL × 4 P15 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL × 2 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 PGE TRIETHYLENE GLYCOL × 6 EDT {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID × 2 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 1PE PENTAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 6；288 K；0.1 M MES pH 6.0-6.5 22 % PEG 400
Resolution 1.79 Å R-free 0.189
6WI2 Structure of human mitochondrial complex Nfs1-ISCU2-ISD11 with E.coli ACP1 at 1.95 A resolution (NIAU)2. N-terminal mutation of ISCU2 (L35) traps Nfs1 Cys loop in the active site of ISCU2 without metal present. Deposited 2020-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 10–142（133 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 1 EDO 1,2-ETHANEDIOL × 36 GOL GLYCEROL × 3 PEG DI(HYDROXYETHYL)ETHER × 10 PG4 TETRAETHYLENE GLYCOL × 2 ETE 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1 PGE TRIETHYLENE GLYCOL × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 EDT {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID × 1 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 1 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；288 K；0.1 M MES pH 5.5 22.5 % PEG 400
Resolution 1.95 Å R-free 0.185
6WIH N-terminal mutation of ISCU2 (L35H36) traps Nfs1 Cys loop in the active site of ISCU2 without metal present. Structure of human mitochondrial complex Nfs1-ISCU2(L35H36)-ISD11 with E.coli ACP1 at 1.9 A resolution (NIAU)2. Deposited 2020-04-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 10–142（133 aa）
Mutation：S11H PLP PYRIDOXAL-5'-PHOSPHATE × 1 PEG DI(HYDROXYETHYL)ETHER × 9 GOL GLYCEROL × 5 EDO 1,2-ETHANEDIOL × 38 PG4 TETRAETHYLENE GLYCOL × 2 P15 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL × 1 PGE TRIETHYLENE GLYCOL × 3 EDT {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID × 1 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 1 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；288 K；0.1 M MES pH 5.5 22.5 % PEG 400
Resolution 1.90 Å R-free 0.186
7RTK Structure of the (NIAU)2 complex with N-terminal mutation of ISCU2 Y35D at 2.5 A resolution Deposited 2021-08-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 35–167（133 aa）
Mutation：Y35D PLP PYRIDOXAL-5'-PHOSPHATE × 2 EDO 1,2-ETHANEDIOL × 58 GOL GLYCEROL × 6 PG4 TETRAETHYLENE GLYCOL × 2 PEG DI(HYDROXYETHYL)ETHER × 16 P15 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL × 2 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 PGE TRIETHYLENE GLYCOL × 6 EDT {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID × 2 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 1PE PENTAETHYLENE GLYCOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；288 K；0.1 M MES pH 5.5 22.5 % PEG 400
Resolution 2.50 Å R-free 0.214
8PK8 Structure of the human mitochondrial iron-sulfur cluster biosynthesis complex during persulfide transfer (persulfide on ISCU2) Deposited 2023-06-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 35–167（133 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) PLP PYRIDOXAL-5'-PHOSPHATE × 1 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 1 FE2 FE (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.49 Å
8PK9 Structure of the human mitochondrial iron-sulfur cluster biosynthesis complex during persulfide transfer (persulfide on NFS1 and ISCU2) Deposited 2023-06-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 35–167（133 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) PLP PYRIDOXAL-5'-PHOSPHATE × 1 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 1 FE2 FE (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.58 Å
8PKA Structure of the human mitochondrial iron-sulfur cluster biosynthesis complex during persulfide transfer (without frataxin) Deposited 2023-06-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 35–167（133 aa）
Not recorded PLP PYRIDOXAL-5'-PHOSPHATE × 1 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 1 FE2 FE (II) ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.75 Å
8RMC Structure of the FDX2-bound core ISC complex (proximal conformation) Deposited 2024-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain D 35–167（133 aa）
Chain H 35–167（133 aa）
Not recorded FE2 FE (II) ION × 2 FES FE2/S2 (INORGANIC) CLUSTER × 1 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.26 Å
8RMD Structure of the FDX2-bound core ISC complex (distal conformation) Deposited 2024-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain D 35–167（133 aa）
Chain H 35–167（133 aa）
Not recorded 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 FE2 FE (II) ION × 2 FES FE2/S2 (INORGANIC) CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.52 Å
8RME Structure of the core ISC complex under turnover conditions (frataxin-bound) Deposited 2024-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain D 35–167（133 aa）
Chain H 35–167（133 aa）
Not recorded FE2 FE (II) ION × 2 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.49 Å
8RMF Structure of the core ISC complex under turnover conditions (FDX2-bound in proximal conformation) Deposited 2024-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain D 35–167（133 aa）
Chain H 35–167（133 aa）
Not recorded 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 FE2 FE (II) ION × 2 FES FE2/S2 (INORGANIC) CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.33 Å
8RMG Structure of the core ISC complex under turnover conditions (FDX2-bound in distal conformation) Deposited 2024-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain D 35–167（133 aa）
Chain H 35–167（133 aa）
Not recorded 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 2 FE2 FE (II) ION × 2 FES FE2/S2 (INORGANIC) CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.46 Å
8TVT Structure of human Cysteine desulfurase Nfs1 with L-propargylglycine bound to active site PLP in complex with ISD11, Acp1 and ISCU2 Deposited 2023-08-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 35–167（133 aa）
Not recorded EDO 1,2-ETHANEDIOL × 30 PLP PYRIDOXAL-5'-PHOSPHATE × 1 LPH L-Propargylglycine × 1 GOL GLYCEROL × 3 PEG DI(HYDROXYETHYL)ETHER × 8 PG4 TETRAETHYLENE GLYCOL × 2 P15 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 PGE TRIETHYLENE GLYCOL × 1 EDT {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID × 1 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 1 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 1PE PENTAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；288 K；0.1 M MES pH 6.5 22.5 % PEG 400
Resolution 2.00 Å R-free 0.186

17 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ISCU_HUMAN
Isoform Q9H1K1-2
PDB entities 3
Chains and sequence ranges Author chain a； PDBConstruct 1–118； UniProt 25–142 Author chain b； PDBConstruct 1–118； UniProt 25–142 Author chain c； PDBConstruct 1–118； UniProt 25–142 Author chain d； PDBConstruct 1–118； UniProt 25–142 Author chain e； PDBConstruct 1–118； UniProt 25–142 Author chain f； PDBConstruct 1–118； UniProt 25–142 Author chain g； PDBConstruct 1–118； UniProt 25–142 Author chain h； PDBConstruct 1–118； UniProt 25–142 Author chain i； PDBConstruct 1–118； UniProt 25–142 Author chain j； PDBConstruct 1–118； UniProt 25–142 Author chain k； PDBConstruct 1–118； UniProt 25–142 Author chain l； PDBConstruct 1–118； UniProt 25–142

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 5kz5

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5kz5
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5kz5
Deposition date deposition_date2016-07-22
Structure title titleArchitecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery: the Complex Formed by the Iron Donor, the Sulfur Donor, and the Scaffold
Keywords keywordsfrataxin, iron-sulfur protein, mitochondria, protein complex, TRANSFERASE-OXIDOREDUCTASE complex; TRANSFERASE/OXIDOREDUCTASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier62.13 Å
Radius of gyration Rg (electron density) rg_electron61.59 Å
Forward intensity I(0) i011225900000.00
Molecular weight molecular_weight895830.0 kDa
Excluded volume excluded_volume1120700 ų
Envelope volume envelope_volume1431800 ų
Hydration-shell volume shell_volume176430 ų
Envelope diameter envelope_diameter192.4 Å
Shell Rg shell_rg75.11 Å
Envelope Rg envelope_rg61.29 Å
Shape Rg shape_rg61.54 Å
Total Rg total_rg61.94 Å
Total atoms total_atoms62880
Residues n_residues8136
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax205.2 Å
Rg (real space) rg_real61.77 Å
Rg uncertainty (real space) rg_real_error1.45 Å
I(0) (real space) i0_real1.1230e+10
I(0) uncertainty (real space) i0_real_error2.2940e+08
Rg (reciprocal space) rg_reciprocal62.40 Å
I(0) (reciprocal space) i0_reciprocal11240000000.0000
Solution quality estimate total_estimate0.8836
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary82.1 Å
Skewness Skewness skewness0.114
Kurtosis Kurtosis kurtosis-0.627
Angular range angular_range— – 0.1250 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha4853000000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.873; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.906
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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8. Citations (1)

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9. Files and Curves (10)