8RMG: Core ISC complex under turnover conditions

Structure of the core ISC complex under turnover conditions (FDX2-bound in distal conformation). Determined by electron microscopy at 2.46 Å resolution. Released 18 Dec 2024.

Method: Electron microscopy
Resolution: 2.46 Å
Organisms: Homo sapiens, Escherichia coli BL21(DE3)
Chains: 9
Atoms: 11,755
Mol. weight: 180.71 kDa
Ligands: FES, FE2, 8Q1
Released: 18 Dec 2024

Explore 8RMG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8RMG contains 80 α-helices and 63 β-strands across 9 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
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	157-167	11
β-strand	172-176	5	3
α-helix	186-191	6
β-strand	197-201	5	3
β-strand	205	1	4
β-strand	211	1	5
β-strand	212	1	4
α-helix	215-224	10
β-strand	228-232	5	3
α-helix	244-247	4
β-strand	251-255	5	3
β-strand	266-270	5	3
β-strand	272	1	6
β-strand	275	1	6
α-helix	298-336	39
β-strand	340-342	3	7
β-strand	349	1	5
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	387-389	3
α-helix	390-394	5
α-helix	399-402	4
β-strand	405-409	5	7
α-helix	416-436	21
α-helix	438-444	7
α-helix	453-454	2

Chain B: 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	4-16	13
β-strand	28	1	8
α-helix	37-50	14
α-helix	54-56	3
α-helix	57-62	6
β-strand	65	1	8
α-helix	66-75	10

Chain D: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	37-44	8
β-strand	49	1	9
β-strand	59-66	8	9
β-strand	71-79	9	9
β-strand	85-93	9	9
α-helix	96-109	14
α-helix	114-117	4
α-helix	122-129	8
α-helix	133-135	3
α-helix	136-156	21

Chain E: 22 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	57	1	12
α-helix	58	1
β-strand	59-60	2	13
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	14
α-helix	127-132	6
α-helix	133-137	5
α-helix	138-141	4
β-strand	148-152	5	14
α-helix	157-168	12
β-strand	172-176	5	14
β-strand	178	1	15
β-strand	184	1	15
α-helix	186-192	7
β-strand	197-201	5	14
β-strand	205	1	16
β-strand	211	1	17
β-strand	212	1	16
α-helix	213	1
α-helix	215-225	11
β-strand	228-232	5	14
β-strand	251-255	5	14
α-helix	256-258	3
β-strand	266-270	5	14
β-strand	272	1	18
β-strand	275	1	18
α-helix	276	1
α-helix	288-290	3
α-helix	298-336	39
β-strand	340-342	3	19
α-helix	346-348	3
β-strand	349	1	17
β-strand	353-358	6	19
α-helix	363-369	7
β-strand	373-374	2	13
β-strand	376-377	2	19
α-helix	390-394	5
α-helix	399-402	4
β-strand	405-409	5	19
α-helix	416-436	21
α-helix	438-444	7

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	12

Chain G: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-16	13
β-strand	28	1	20
α-helix	37-50	14
α-helix	57-62	6
β-strand	65	1	20
α-helix	66-75	10

Chain H: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	37-44	8
β-strand	49	1	21
β-strand	59-65	7	21
β-strand	72-79	8	21
β-strand	85-93	9	21
α-helix	96-109	14
α-helix	114-117	4
α-helix	122-129	8
α-helix	133-135	3
α-helix	136-157	22

1 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
Isoform Mitochondrial of Cysteine desulfurase	A, E	protein	404	Homo sapiens	Q9Y697 (AlphaFold model)
LYR motif-containing protein 4	B, F	protein	115	Homo sapiens	Q9HD34 (AlphaFold model)
Acyl carrier protein	C, G	protein	78	Escherichia coli BL21(DE3)	P0A6A8 (AlphaFold model)
Isoform 1 of Iron-sulfur cluster assembly enzyme ISCU	D, H	protein	143	Homo sapiens	Q9H1K1 (AlphaFold model)
Ferredoxin-2, mitochondrial	I	protein	121	Homo sapiens	Q6P4F2

Sequence of entity 1 (A, E), FASTA

>8RMG_1 Isoform Mitochondrial of Cysteine desulfurase (chains A, E)
MSLRPLYMDVQATTPLDPRVLDAMLPYLINYYGNPHSRTHAYGWESEAAMERARQQVASL
IGADPREIIFTSGATESNNIAIKGVARFYRSRKKHLITTQTEHKCVLDSCRSLEAEGFQV
TYLPVQKSGIIDLKELEAAIQPDTSLVSVMTVNNEIGVKQPIAEIGRICSSRKVYFHTDA
AQAVGKIPLDVNDMKIDLMSISGHKIYGPKGVGAIYIRRRPRVRVEALQSGGGQERGMRS
GTVPTPLVVGLGAACEVAQQEMEYDHKRISKLSERLIQNIMKSLPDVVMNGDPKHHYPGC
INLSFAYVEGESLLMALKDVALSSGSACTSASLEPSYVLRAIGTDEDLAHSSIRFGIGRF
TTEEEVDYTVEKCIQHVKRLREMSPLWEMVQDGIDLKSIKWTQH

Sequence of entity 2 (B, F), FASTA

>8RMG_2 LYR motif-containing protein 4 (chains B, F)
MGSSHHHHHHGSPTTENLYFQGHNMAASSRAQVLALYRAMLRESKRFSAYNYRTYAVRRI
RDAFRENKNVKDPVEIQTLVNKAKRDLGVIRRQVHIGQLYSTDKLIIENRDMPRT

Sequence of entity 3 (C, G), FASTA

>8RMG_3 Acyl carrier protein (chains C, G)
MSTIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTVELVMALEEEFDTEIPDEEA
EKITTVQAAIDYINGHQA

Sequence of entity 4 (D, H), FASTA

>8RMG_4 Isoform 1 of Iron-sulfur cluster assembly enzyme ISCU (chains D, H)
MAYHKKVVDHYENPRNVGSLDKTSKNVGTGLVGAPACGDVMKLQIQVDEKGKIVDARFKT
FGCGSAIASSSLATEWVKGKTVEEALTIKNTDIAKELCLPPVKLHCSMLAEDAIKAALAD
YKLKQEPKKGEAEKKLEHHHHHH

Sequence of entity 5 (I), FASTA

>8RMG_5 Ferredoxin-2, mitochondrial (chains I)
MASDVVNVVFVDRSGQRIPVSGRVGDNVLHLAQRHGVDLEGACEASLACSTCHVYVSEDH
LDLLPPPEEREDDMLDMAPLLQENSRLGCQIVLTPELEGAEFTLPKITRNFYVDGHVPKP
H

Ligands and cofactors

ID	Name	Formula	Copies
FES	FE2/S2 (inorganic) cluster	Fe2 S2	1
FE2	FE (II) ion	Fe	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

Two-stage binding of mitochondrial ferredoxin-2 to the core iron-sulfur cluster assembly complex. Steinhilper, R., Boss, L., Freibert, S.A. et al. Nat Commun (2024) 15:10559-10559. DOI 10.1038/s41467-024-54585-4 · 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…
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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