6W1D: Cysteine desulfurase, mitochondrial

Structure of human mitochondrial complex Nfs1-ISCU2 (WT)-ISD11 with E.coli ACP1 at 1.8 A resolution (NIAU)2. Determined by X-ray diffraction at 1.79 Å resolution. Released 18 Mar 2020.

Method: X-ray diffraction
Resolution: 1.79 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 4
Atoms: 6,266
Mol. weight: 87.55 kDa
Ligands: PLP, 8Q1, EDT, DTT
Released: 18 Mar 2020

Explore 6W1D in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6W1D contains 38 α-helices and 27 β-strands across 4 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: 21 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	56	1
β-strand	57	1	1
α-helix	58	1
β-strand	59-60	2	2
α-helix	68-70	3
α-helix	71-82	12
α-helix	94-114	21
α-helix	118-120	3
β-strand	121-124	4	3
α-helix	127-141	15
β-strand	148-152	5	3
α-helix	157-168	12
β-strand	172-176	5	3
α-helix	186-192	7
β-strand	197-201	5	3
β-strand	205	1	4
β-strand	211	1	5
β-strand	212	1	4
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
α-helix	276	1
α-helix	288-290	3
α-helix	298-336	39
β-strand	340-342	3	6
β-strand	349	1	5
β-strand	353-358	6	6
α-helix	363-369	7
β-strand	373-374	2	2
β-strand	376-377	2	6
α-helix	390-394	5
α-helix	399-402	4
β-strand	405-409	5	6
α-helix	416-435	20
α-helix	438-444	7
α-helix	449-451	3

Chain B: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	5-20	16
α-helix	26-42	17
α-helix	49-75	27
α-helix	79-80	2
β-strand	81	1	1
α-helix	82-84	3

Chain C: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	6-15	10
α-helix	19-21	3
β-strand	27	1	7
α-helix	36-50	15
α-helix	56-59	4
β-strand	64	1	7
α-helix	65-73	9

Chain D: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	37-44	8
β-strand	49	1	8
β-strand	59-66	8	8
α-helix	67-69	3
β-strand	71-79	9	8
β-strand	84	1	9
β-strand	85-93	9	8
α-helix	96-109	14
β-strand	113	1	9
α-helix	114-117	4
α-helix	122-129	8
α-helix	133-135	3
α-helix	136-157	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cysteine desulfurase, mitochondrial	A	protein	406	Homo sapiens	Q9Y697 (AlphaFold model)
LYR motif-containing protein 4	B	protein	91	Homo sapiens	Q9HD34 (AlphaFold model)
Acyl carrier protein	C	protein	77	Escherichia coli	P0A6A8 (AlphaFold model)
Iron-sulfur cluster assembly enzyme ISCU, mitochondrial	D	protein	143	Homo sapiens	Q9H1K1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6W1D_1 Cysteine desulfurase, mitochondrial (chains A)
MGSSLRPLYMDVQATTPLDPRVLDAMLPYLINYYGNPHSRTHAYGWESEAAMERARQQVA
SLIGADPREIIFTSGATESNNIAIKGVARFYRSRKKHLITTQTEHKCVLDSCRSLEAEGF
QVTYLPVQKSGIIDLKELEAAIQPDTSLVSVMTVNNEIGVKQPIAEIGRICSSRKVYFHT
DAAQAVGKIPLDVNDMKIDLMSISGHKIYGPKGVGAIYIRRRPRVRVEALQSGGGQERGM
RSGTVPTPLVVGLGAACEVAQQEMEYDHKRISKLSERLIQNIMKSLPDVVMNGDPKHHYP
GCINLSFAYVEGESLLMALKDVALSSGSACTSASLEPSYVLRAIGTDEDLAHSSIRFGIG
RFTTEEEVDYTVEKCIQHVKRLREMSPLWEMVQDGIDLKSIKWTQH

Sequence of entity 2 (B), FASTA

>6W1D_2 LYR motif-containing protein 4 (chains B)
MAASSRAQVLALYRAMLRESKRFSAYNYRTYAVRRIRDAFRENKNVKDPVEIQTLVNKAK
RDLGVIRRQVHIGQLYSTDKLIIENRDMPRT

Sequence of entity 3 (C), FASTA

>6W1D_3 Acyl carrier protein (chains C)
STIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTVELVMALEEEFDTEIPDEEAE
KITTVQAAIDYINGHQA

Sequence of entity 4 (D), FASTA

>6W1D_4 Iron-sulfur cluster assembly enzyme ISCU, mitochondrial (chains D)
MAYHKKVVDHYENPRNVGSLDKTSKNVGTGLVGAPACGDVMKLQIQVDEKGKIVDARFKT
FGCGSAIASSSLATEWVKGKTVEEALTIKNTDIAKELCLPPVKLHCSMLAEDAIKAALAD
YKLKQEPKKGEAEKKLEHHHHHH

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
EDT	{[-(bis-carboxymethyl-amino)-ethyl]-carboxymethyl-amino}-acetic acid	C10 H16 N2 O8	1
DTT	2,3-dihydroxy-1,4-dithiobutane	C4 H10 O2 S2	1
P15	2,5,8,11,14,17-hexaoxanonadecan-19-ol	C13 H28 O7	1

Water and common crystallization additives (PG4, PEG, EDO, GOL, 1PE, MES, PGE) are not listed.

Primary citation

The essential function of ISCU2 and its conserved N-terminus in Fe/S cluster biogenesis. Freibert, S.A., Boniecki, M.T., Shulz, V. et al. To be published.

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…
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)
8PK9 2.58 Å, Structure of the human mitochondrial iron-sulfur cluster biosynthesis complex during…

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