5WLW: Cysteine desulfurase, mitochondrial

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. Determined by X-ray diffraction at 3.32 Å resolution. Released 15 Nov 2017.

Method: X-ray diffraction
Resolution: 3.32 Å
Organisms: Homo sapiens, Escherichia coli O45:K1 (strain S88 / ExPEC)
Chains: 8
Atoms: 9,865
Mol. weight: 163.1 kDa
Ligands: PLP, 8Q1, ZN
Released: 15 Nov 2017

Explore 5WLW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5WLW contains 75 α-helices and 59 β-strands across 8 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, 20 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	127-132	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
β-strand	178	1	4
β-strand	184	1	4
α-helix	186-192	7
β-strand	197-201	5	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
α-helix	298-334	37
β-strand	340-342	3	7
β-strand	349	1	6
β-strand	353-358	6	7
α-helix	363-369	7
β-strand	373-374	2	2
β-strand	376-377	2	7
α-helix	380-382	3
α-helix	390-394	5
α-helix	399-402	4
β-strand	405-409	5	7
α-helix	416-435	20
α-helix	438-445	8

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: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-15	9
α-helix	19-21	3
β-strand	27	1	8
α-helix	28-32	5
α-helix	36-50	15
α-helix	56-59	4
β-strand	64	1	8
α-helix	65-71	7

Chain D: 7 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	12-19	8
β-strand	24	1	9
α-helix	29-31	3
β-strand	34-40	7	9
β-strand	47-54	8	9
β-strand	59	1	10
β-strand	60-68	9	9
α-helix	71-83	13
β-strand	88	1	10
α-helix	91-94	4
α-helix	97-104	8
α-helix	108-110	3
α-helix	111-130	20

Chain E: 22 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	56	1
β-strand	57	1	11
α-helix	58	1
β-strand	59-60	2	12
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	13
α-helix	127-132	6
α-helix	133-137	5
α-helix	138-141	4
β-strand	148-152	5	13
α-helix	157-168	12
β-strand	172-176	5	13
β-strand	178	1	14
α-helix	183	1
β-strand	184	1	14
α-helix	185	1
α-helix	186-192	7
β-strand	197-201	5	13
β-strand	205	1	15
β-strand	211	1	16
β-strand	212	1	15
α-helix	213	1
α-helix	215-224	10
β-strand	228-232	5	13
β-strand	251-255	5	13
α-helix	256-258	3
β-strand	266-270	5	13
α-helix	298-334	37
β-strand	340-343	4	17
β-strand	349	1	16
β-strand	353-358	6	17
α-helix	363-369	7
β-strand	373-374	2	12
β-strand	376-377	2	17
α-helix	390-394	5
α-helix	399-402	4
β-strand	405-409	5	17
α-helix	416-435	20
α-helix	438-445	8
β-strand	452	1	18

Chain F: 4 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	6-20	15
α-helix	26-42	17
α-helix	49-75	27
α-helix	79-80	2
β-strand	81	1	11

Chain G: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-15	9
α-helix	19-21	3
β-strand	27	1	19
α-helix	36-49	14
α-helix	56-59	4
β-strand	64	1	19
α-helix	65-71	7

Chain H: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	12-16	5
β-strand	24	1	18
β-strand	34-40	7	18
β-strand	47-54	8	18
β-strand	59	1	20
β-strand	60-68	9	18
α-helix	71-83	13
β-strand	88	1	20
α-helix	91-94	4
α-helix	97-104	8
α-helix	108-110	3
α-helix	111-131	21

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cysteine desulfurase, mitochondrial	A, E	protein	406	Homo sapiens	Q9Y697 (AlphaFold model)
LYR motif-containing protein 4	B, F	protein	91	Homo sapiens	Q9HD34 (AlphaFold model)
Acyl carrier protein	C, G	protein	77	Escherichia coli O45:K1 (strain S88 / ExPEC)	P0A6A8 (AlphaFold model)
Iron-sulfur cluster assembly enzyme ISCU, mitochondrial	D, H	protein	150	Homo sapiens	Q9H1K1 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>5WLW_1 Cysteine desulfurase, mitochondrial (chains A, E)
MGSSLRPLYMDVQATTPLDPRVLDAMLPYLINYYGNPHSRTHAYGWESEAAMERARQQVA
SLIGADPREIIFTSGATESNNIAIKGVARFYRSRKKHLITTQTEHKCVLDSCRSLEAEGF
QVTYLPVQKSGIIDLKELEAAIQPDTSLVSVMTVNNEIGVKQPIAEIGRICSSRKVYFHT
DAAQAVGKIPLDVNDMKIDLMSISGHKIYGPKGVGAIYIRRRPRVRVEALQSGGGQERGM
RSGTVPTPLVVGLGAACEVAQQEMEYDHKRISKLSERLIQNIMKSLPDVVMNGDPKHHYP
GCINLSFAYVEGESLLMALKDVALSSGSACTSASLEPSYVLRAIGTDEDLAHSSIRFGIG
RFTTEEEVDYTVEKCIQHVKRLREMSPLWEMVQDGIDLKSIKWTQH

Sequence of entity 2 (B, F), FASTA

>5WLW_2 LYR motif-containing protein 4 (chains B, F)
MAASSRAQVLALYRAMLRESKRFSAYNYRTYAVRRIRDAFRENKNVKDPVEIQTLVNKAK
RDLGVIRRQVHIGQLYSTDKLIIENRDMPRT

Sequence of entity 3 (C, G), FASTA

>5WLW_3 Acyl carrier protein (chains C, G)
STIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTVELVMALEEEFDTEIPDEEAE
KITTVQAAIDYINGHQA

Sequence of entity 4 (D, H), FASTA

>5WLW_4 Iron-sulfur cluster assembly enzyme ISCU, mitochondrial (chains D, H)
MVLIDMSVDLSTQVVDHYENPRNVGSLDKTSKNVGTGLVGAPACGDVMKLQIQVDEKGKI
VDARFKTFGCGSAIASSSLATEWVKGKTVEEALTIKNTDIAKELCLPPVKLHCSILAEDA
IKAALADYKLKQEPKKGEAEKKELHHHHHH

Ligands and cofactors

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

Primary citation

Structure and functional dynamics of the mitochondrial Fe/S cluster synthesis complex. Boniecki, M.T., Freibert, S.A., Muhlenhoff, U. et al. Nat Commun (2017) 8:1287-1287. DOI 10.1038/s41467-017-01497-1 · 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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