6NZU: Cysteine desulfurase, mitochondrial

Structure of the human frataxin-bound iron-sulfur cluster assembly complex. Determined by electron microscopy at 3.2 Å resolution. Released 22 May 2019.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 10
Atoms: 12,570
Mol. weight: 185.44 kDa
Ligands: ZN, 8Q1, PLP
Released: 22 May 2019

Explore 6NZU in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6NZU contains 78 α-helices and 72 β-strands across 10 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: 20 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	57	1	1
α-helix	68-70	3
α-helix	71-77	7
α-helix	79-82	4
α-helix	100-114	15
α-helix	118-120	3
β-strand	121-124	4	2
α-helix	127-133	7
α-helix	136-141	6
β-strand	148-152	5	2
α-helix	157-166	10
α-helix	167-169	3
β-strand	172-176	5	2
α-helix	186-192	7
β-strand	197-201	5	2
β-strand	205	1	3
β-strand	211	1	4
β-strand	212	1	3
α-helix	216-224	9
β-strand	229-232	4	2
β-strand	251-255	5	2
β-strand	266-270	5	2
β-strand	282	1	5
α-helix	288-290	3
β-strand	292	1	5
α-helix	298-308	11
α-helix	310-313	4
α-helix	315-336	22
β-strand	340-342	3	6
β-strand	349	1	4
β-strand	353-358	6	6
α-helix	364-367	4
β-strand	376	1	6
α-helix	390-394	5
α-helix	399-401	3
β-strand	405-409	5	6
α-helix	416-428	13
α-helix	453-454	2

Chains B and F: 3 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	7-20	14
α-helix	26-42	17
α-helix	49-75	27
β-strand	81	1	1

Chains C and G: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-10	4
α-helix	12-15	4
β-strand	28	1	7
α-helix	37-49	13
α-helix	58-61	4
β-strand	65	1	7
α-helix	67-73	7

Chains D and H: 7 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	37-44	8
β-strand	49	1	8
β-strand	59	1	8
β-strand	62-66	5	8
β-strand	71-79	9	8
β-strand	84	1	9
β-strand	85-91	7	8
α-helix	96-108	13
α-helix	109-111	3
β-strand	113	1	9
α-helix	116-119	4
α-helix	122-128	7
α-helix	133-136	4
α-helix	137-152	16

Chain E: 20 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	57	1	10
α-helix	68-70	3
α-helix	71-77	7
α-helix	79-82	4
α-helix	100-114	15
α-helix	118-120	3
β-strand	121-124	4	11
α-helix	127-133	7
α-helix	136-141	6
β-strand	148-152	5	11
α-helix	157-166	10
α-helix	167-169	3
β-strand	172-176	5	11
α-helix	186-192	7
β-strand	197-201	5	11
β-strand	205	1	12
β-strand	212	1	12
α-helix	216-224	9
β-strand	229-232	4	11
β-strand	251-255	5	11
β-strand	266-270	5	11
β-strand	282	1	13
α-helix	288-290	3
β-strand	292	1	13
α-helix	298-308	11
α-helix	310-313	4
α-helix	315-336	22
β-strand	340-342	3	14
β-strand	353-358	6	14
α-helix	364-367	4
β-strand	376	1	14
α-helix	390-394	5
α-helix	399-401	3
β-strand	405-409	5	14
α-helix	416-425	10
α-helix	453-454	2

Chain I: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	92-102	11
α-helix	104-110	7
α-helix	113-115	3
β-strand	124	1	18
β-strand	127	1	18
β-strand	131-135	5	18
β-strand	142-148	7	18
β-strand	153-157	5	18
β-strand	163-168	6	18
β-strand	173-174	2	18
β-strand	181	1	18
α-helix	182-194	13

Chain J: 4 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	92-102	11
α-helix	104-110	7
α-helix	113-115	3
β-strand	124	1	19
β-strand	127	1	20
β-strand	131-132	2	20
β-strand	135	1	19
β-strand	142	1	19
β-strand	144-148	5	20
β-strand	153-157	5	20
β-strand	163-168	6	20
β-strand	173-174	2	20
β-strand	181	1	20
α-helix	182-194	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cysteine desulfurase, mitochondrial	A, E	protein	403	Homo sapiens	Q9Y697 (AlphaFold model)
LYR motif-containing protein 4	B, F	protein	92	Homo sapiens	Q9HD34 (AlphaFold model)
Acyl carrier protein	C, G	protein	74	Escherichia coli	A0A437HBF4
Iron-sulfur cluster assembly enzyme ISCU, mitochondrial	D, H	protein	124	Homo sapiens	Q9H1K1 (AlphaFold model)
Frataxin, mitochondrial	I, J	protein	132	Homo sapiens	Q16595

Sequence of entity 1 (A, E), FASTA

>6NZU_1 Cysteine desulfurase, mitochondrial (chains A, E)
MLRPLYMDVQATTPLDPRVLDAMLPYLINYYGNPHSRTHAYGWESEAAMERARQQVASLI
GADPREIIFTSGATESNNIAIKGVARFYRSRKKHLITTQTEHKCVLDSCRSLEAEGFQVT
YLPVQKSGIIDLKELEAAIQPDTSLVSVMTVNNEIGVKQPIAEIGRICSSRKVYFHTDAA
QAVGKIPLDVNDMKIDLMSISGHKIYGPKGVGAIYIRRRPRVRVEALQSGGGQERGMRSG
TVPTPLVVGLGAACEVAQQEMEYDHKRISKLSERLIQNIMKSLPDVVMNGDPKHHYPGCI
NLSFAYVEGESLLMALKDVALSSGSACTSASLEPSYVLRAIGTDEDLAHSSIRFGIGRFT
TEEEVDYTVEKCIQHVKRLREMSPLWEMVQDGIDLKSIKWTQH

Sequence of entity 2 (B, F), FASTA

>6NZU_2 LYR motif-containing protein 4 (chains B, F)
SMAASSRAQVLALYRAMLRESKRFSAYNYRTYAVRRIRDAFRENKNVKDPVEIQTLVNKA
KRDLGVIRRQVHIGQLYSTDKLIIENRDMPRT

Sequence of entity 3 (C, G), FASTA

>6NZU_3 Acyl carrier protein (chains C, G)
MSTIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTVELVMALEEEFDTEIPDEEA
EKITTVQAAIDYIN

Sequence of entity 4 (D, H), FASTA

>6NZU_4 Iron-sulfur cluster assembly enzyme ISCU, mitochondrial (chains D, H)
MYHKKVVDHYENPRNVGSLDKTSKNVGTGLVGAPACGDVMKLQIQVDEKGKIVDARFKTF
GCGSAIASSSLATEWVKGKTVEEALTIKNTDIAKELCLPPVKLHCSMLAEDAIKAALADY
KLKQ

Sequence of entity 5 (I, J), FASTA

>6NZU_5 Frataxin, mitochondrial (chains I, J)
SMSGTLGHPGSLDETTYERLAEETLDSLAEFFEDLADKPYTFEDYDVSFGSGVLTVKLGG
DLGTYVINKQTPNKQIWLSSPSSGPKRYDWTGKNWVYSHDGVSLHELLAAELTKALKTKL
DLSSLAYSGKDA

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
8Q1	S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}ami…	C23 H45 N2 O8 P S	2
PLP	Pyridoxal-5'-phosphate	C8 H10 N O6 P	2

Primary citation

Structure of the human frataxin-bound iron-sulfur cluster assembly complex provides insight into its activation mechanism. Fox, N.G., Yu, X., Feng, X. et al. Nat Commun (2019) 10:2210-2210. DOI 10.1038/s41467-019-09989-y · 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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