5KZ5: Cysteine desulfurase, mitochondrial

Architecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery: the Complex Formed by the Iron Donor, the Sulfur Donor, and the Scaffold. Determined by electron microscopy at 14.3 Å resolution. Released 31 Aug 2016.

Method: Electron microscopy
Resolution: 14.3 Å
Organism: Homo sapiens
Chains: 36
Atoms: 62,880
Mol. weight: 897.65 kDa
Released: 31 Aug 2016

Explore 5KZ5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5KZ5 contains 282 α-helices and 327 β-strands across 36 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 1: 15 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	72-77	6
α-helix	98-114	17
β-strand	124	1	1
α-helix	127-141	15
β-strand	148-150	3	2
α-helix	157-168	12
β-strand	172-174	3	2
β-strand	178	1	3
β-strand	184	1	3
α-helix	186-192	7
β-strand	199-201	3	1
β-strand	205	1	4
β-strand	212	1	4
α-helix	215-224	10
β-strand	228-232	5	1
β-strand	251-255	5	1
α-helix	256-258	3
β-strand	266-268	3	1
β-strand	287	1	5
β-strand	290	1	5
α-helix	299-308	10
α-helix	309-314	6
α-helix	315-336	22
β-strand	354-356	3	6
α-helix	363-369	7
α-helix	391-393	3
α-helix	399-403	5
β-strand	406-408	3	6
α-helix	416-434	19
α-helix	436-445	10

Chain 2: 13 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	72-82	11
α-helix	94-114	21
β-strand	123-124	2	9
α-helix	127-141	15
β-strand	148-150	3	10
α-helix	157-168	12
β-strand	172-174	3	10
β-strand	178	1	11
β-strand	184	1	11
α-helix	186-192	7
β-strand	199-201	3	9
β-strand	205	1	12
β-strand	212	1	12
α-helix	215-224	10
β-strand	228-232	5	9
β-strand	251-256	6	9
β-strand	265-270	6	9
α-helix	295-297	3
α-helix	299-310	12
α-helix	315-336	22
β-strand	342-343	2	13
β-strand	354-356	3	13
α-helix	363-369	7
α-helix	399-403	5
β-strand	406-408	3	13
α-helix	416-434	19
α-helix	436-444	9

Chain 3: 14 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	71-84	14
α-helix	97-114	18
α-helix	127-141	15
β-strand	148-152	5	16
α-helix	157-168	12
β-strand	172-176	5	16
β-strand	178	1	17
β-strand	184	1	17
α-helix	186-192	7
β-strand	201	1	18
β-strand	205	1	19
β-strand	211	1	20
β-strand	212	1	19
α-helix	215-224	10
α-helix	228-229	2
β-strand	230-232	3	18
β-strand	237	1	21
β-strand	240	1	21
β-strand	251-254	4	18
β-strand	267-270	4	18
α-helix	296-297	2
α-helix	298-313	16
α-helix	315-336	22
β-strand	342-343	2	22
β-strand	349	1	20
β-strand	350	1	23
β-strand	353	1	23
β-strand	355-356	2	22
α-helix	363-370	8
α-helix	399-403	5
β-strand	406-407	2	22
α-helix	416-434	19
α-helix	436-445	10

Chain 4: 16 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	74-76	3
α-helix	94-97	4
α-helix	102-113	12
β-strand	121-124	4	25
α-helix	127-141	15
β-strand	148-152	5	26
α-helix	157-168	12
β-strand	172-176	5	26
β-strand	178	1	27
β-strand	184	1	27
α-helix	186-192	7
β-strand	200-201	2	25
α-helix	215-224	10
α-helix	228	1
β-strand	229-232	4	25
β-strand	251-255	5	25
β-strand	266-269	4	25
α-helix	299-311	13
α-helix	312-314	3
α-helix	315-336	22
β-strand	341-342	2	28
β-strand	356-357	2	28
α-helix	363-369	7
β-strand	374	1	29
α-helix	399-402	4
α-helix	406	1
β-strand	407	1	29
α-helix	416-434	19
α-helix	436-445	10

Chain a: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	55	1	97
β-strand	60-63	4	100
β-strand	74-77	4	100
β-strand	78	1	101
β-strand	86	1	101
α-helix	96-109	14
α-helix	114-119	6
α-helix	122-129	8
α-helix	137-156	20
α-helix	160-163	4

Chain A: 8 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	52-58	7
α-helix	67-70	4
β-strand	74	1	97
β-strand	80	1	98
α-helix	91-93	3
α-helix	100-115	16
β-strand	146-147	2	99
α-helix	153	1
β-strand	154-158	5	99
β-strand	162-165	4	99
α-helix	166	1
α-helix	173-174	2
α-helix	182-194	13

Chain b: 4 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	52	1	104
β-strand	54	1	104
β-strand	60-63	4	105
β-strand	74-77	4	105
β-strand	84	1	106
β-strand	88-91	4	105
α-helix	96-109	14
β-strand	113	1	106
α-helix	114-118	5
α-helix	122-129	8
α-helix	137-156	20

Chain B: 3 helices, 6 β-strands

Element	Residues	Length	Sheet
α-helix	52-61	10
α-helix	98-115	18
β-strand	124-127	4	102
β-strand	131-135	5	102
β-strand	142-147	6	102
β-strand	154-155	2	102
β-strand	167-168	2	103
β-strand	173-174	2	103
α-helix	182-194	13

28 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cysteine desulfurase, mitochondrial	1, 2, 3, 4, M, N, O, P, Q, R, S, T	protein	391	Homo sapiens	Q9Y697 (AlphaFold model)
Frataxin, mitochondrial	A, B, C, D, E, F, G, H, I, J, K, L	protein	169	Homo sapiens	Q16595 (AlphaFold model)
Iron-sulfur cluster assembly enzyme ISCU, mitochondrial	a, b, c, d, e, f, g, h, i, j, k, l	protein	118	Homo sapiens	Q9H1K1 (AlphaFold model)

Sequence of entity 1 (1, 2, 3, 4, M, N, O, P, Q, R, S, T), FASTA

>5KZ5_1 Cysteine desulfurase, mitochondrial (chains 1, 2, 3, 4, M, N, O, P, Q, R, S, T)
TPLDPRVLDAMLPYLINYYGNPHSRTHAYGWESEAAMERARQQVASLIGADPREIIFTSG
ATESNNIAIKGVARFYRSRKKHLITTQTEHKCVLDSCRSLEAEGFQVTYLPVQKSGIIDL
KELEAAIQPDTSLVSVMTVNNEIGVKQPIAEIGRICSSRKVYFHTDAAQAVGKIPLDVND
MKIDLMSISGHKIYGPKGVGAIYIRRRPRVRVEALQSGGGQERGMRSGTVPTPLVVGLGA
ACEVAQQEMEYDHKRISKLSERLIQNIMKSLPDVVMNGDPKHHYPGCINLSFAYVEGESL
LMALKDVALSSGSACTSASLEPSYVLRAIGTDEDLAHSSIRFGIGRFTTEEEVDYTVEKC
IQHVKRLREMSPLWEMVQDGIDLKSIKWTQH

Sequence of entity 2 (A, B, C, D, E, F, G, H, I, J, K, L), FASTA

>5KZ5_2 Frataxin, mitochondrial (chains A, B, C, D, E, F, G, H, I, J, K, L)
LRTDIDATCTPRRASSNQRGLNQIWNVKKQSVYLMNLRKSGTLGHPGSLDETTYERLAEE
TLDSLAEFFEDLADKPYTFEDYDVSFGSGVLTVKLGGDLGTYVINKQTPNKQIWLSSPSS
GPKRYDWTGKNWVYSHDGVSLHELLAAELTKALKTKLDLSSLAYSGKDA

Sequence of entity 3 (a, b, c, d, e, f, g, h, i, j, k, l), FASTA

>5KZ5_3 Iron-sulfur cluster assembly enzyme ISCU, mitochondrial (chains a, b, c, d, e, f, g, h, i, j, k, l)
GSLDKTSKNVGTGLVGAPACGDVMKLQIQVDEKGKIVDARFKTFGCGSAIASSSLATEWV
KGKTVEEALTIKNTDIAKELCLPPVKLHCSMLAEDAIKAALADYKLKQEPKKGEAEKK

Primary citation

Architecture of the Human Mitochondrial Iron-Sulfur Cluster Assembly Machinery. Gakh, O., Ranatunga, W., Smith, D.Y. et al. J Biol Chem (2016) 291:21296-21321. DOI 10.1074/jbc.M116.738542 · 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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