5WKP: Human mitochondrial Cysteine Desulfurase

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. Determined by X-ray diffraction at 3.15 Å resolution. Released 15 Nov 2017.

Method: X-ray diffraction
Resolution: 3.15 Å
Organisms: Homo sapiens, Escherichia coli
Chains: 8
Atoms: 9,886
Mol. weight: 162.97 kDa
Ligands: PLP, 8Q1
Released: 15 Nov 2017

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

Secondary structure: helices and β-sheets

5WKP contains 75 α-helices and 57 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: 22 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	127-132	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	177-179	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	288-290	3
α-helix	298-334	37
β-strand	340-343	4	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	416-436	21
α-helix	438-444	7

Chains B and F: 5 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	1
α-helix	82-84	3

Chain C: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	7-14	8
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: 4 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	24	1	8
β-strand	34-40	7	8
β-strand	47-54	8	8
β-strand	59	1	9
β-strand	60-68	9	8
α-helix	71-83	13
β-strand	88	1	9
α-helix	89-93	5
α-helix	97-104	8
α-helix	112-131	20

Chain E: 23 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	56	1
β-strand	57	1	10
α-helix	58	1
β-strand	59-60	2	11
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	12
α-helix	127-141	15
β-strand	148-152	5	12
α-helix	157-168	12
β-strand	172-176	5	12
α-helix	177	1
β-strand	178	1	13
α-helix	179	1
α-helix	183	1
β-strand	184	1	13
α-helix	185	1
α-helix	186-192	7
β-strand	197-201	5	12
β-strand	205	1	14
β-strand	211	1	15
β-strand	212	1	14
α-helix	213	1
α-helix	215-224	10
β-strand	228-232	5	12
β-strand	251-255	5	12
α-helix	256-258	3
β-strand	266-270	5	12
α-helix	298-334	37
β-strand	340-342	3	16
α-helix	343	1
β-strand	349	1	15
β-strand	353-358	6	16
α-helix	363-369	7
β-strand	373-374	2	11
β-strand	376	1	16
α-helix	390-394	5
α-helix	399-402	4
β-strand	405-409	5	16
α-helix	416-436	21
α-helix	438-444	7
β-strand	455	1	17

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	18
α-helix	36-49	14
α-helix	56-59	4
β-strand	64	1	18
α-helix	65-72	8

Chain H: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	12-17	6
β-strand	24	1	17
β-strand	34-40	7	17
β-strand	47-54	8	17
β-strand	59	1	19
β-strand	60-68	9	17
α-helix	71-83	13
β-strand	88	1	19
α-helix	89-92	4
α-helix	97-104	8
α-helix	108-110	3
α-helix	112-131	20

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	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

>5WKP_1 Cysteine desulfurase, mitochondrial (chains A, E)
MGSSLRPLYMDVQATTPLDPRVLDAMLPYLINYYGNPHSRTHAYGWESEAAMERARQQVA
SLIGADPREIIFTSGATESNNIAIKGVARFYRSRKKHLITTQTEHKCVLDSCRSLEAEGF
QVTYLPVQKSGIIDLKELEAAIQPDTSLVSVMTVNNEIGVKQPIAEIGRICSSRKVYFHT
DAAQAVGKIPLDVNDMKIDLMSISGHKIYGPKGVGAIYIRRRPRVRVEALQSGGGQERGM
RSGTVPTPLVVGLGAACEVAQQEMEYDHKRISKLSERLIQNIMKSLPDVVMNGDPKHHYP
GCINLSFAYVEGESLLMALKDVALSSGSACTSASLEPSYVLRAIGTDEDLAHSSIRFGIG
RFTTEEEVDYTVEKCIQHVKRLREMSPLWEMVQDGIDLKSIKWTQH

Sequence of entity 2 (B, F), FASTA

>5WKP_2 LYR motif-containing protein 4 (chains B, F)
MAASSRAQVLALYRAMLRESKRFSAYNYRTYAVRRIRDAFRENKNVKDPVEIQTLVNKAK
RDLGVIRRQVHIGQLYSTDKLIIENRDMPRT

Sequence of entity 3 (C, G), FASTA

>5WKP_3 Acyl carrier protein (chains C, G)
STIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTVELVMALEEEFDTEIPDEEAE
KITTVQAAIDYINGHQA

Sequence of entity 4 (D, H), FASTA

>5WKP_4 Iron-sulfur cluster assembly enzyme ISCU, mitochondrial (chains D, H)
MVLIDMSVDLSTQVVDHYENPRNVGSLDKTSKNVGTGLVGAPACGDVMKLQIQVDEKGKI
VDARFKTFGCGSAIASSSLATEWVKGKTVEEALTIKNTDIAKELCLPPVKLHCSILAEDA
IKAALADYKLKQEPKKGEAEKKLEHHHHHH

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

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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