8RMD: FDX2-bound core ISC complex

Structure of the FDX2-bound core ISC complex (distal conformation). Determined by electron microscopy at 2.52 Å resolution. Released 18 Dec 2024.

Method: Electron microscopy
Resolution: 2.52 Å
Organisms: Homo sapiens, Escherichia coli BL21(DE3)
Chains: 9
Atoms: 11,857
Mol. weight: 180.71 kDa
Ligands: FES, FE2, 8Q1
Released: 18 Dec 2024

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

Secondary structure: helices and β-sheets

8RMD contains 79 α-helices and 61 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: 20 helices, 18 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	157-168	12
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
β-strand	251-255	5	3
α-helix	256-258	3
β-strand	266-270	5	3
α-helix	288-290	3
α-helix	298-336	39
β-strand	340-342	3	6
α-helix	346-348	3
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

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

Chains C and G: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-16	13
β-strand	28	1	7
α-helix	37-50	14
α-helix	57-62	6
β-strand	65	1	7
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	8
β-strand	59-66	8	8
β-strand	71-79	9	8
β-strand	85-93	9	8
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

Chain E: 24 helices, 22 β-strands

Element	Residues	Length	Sheet
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	215-225	11
β-strand	228-232	5	13
α-helix	244-247	4
β-strand	251-255	5	13
α-helix	256-258	3
β-strand	266-270	5	13
β-strand	272	1	17
β-strand	275	1	17
α-helix	288-290	3
α-helix	298-334	37
β-strand	340-342	3	18
α-helix	346-348	3
β-strand	349	1	16
β-strand	353-358	6	18
α-helix	363-369	7
β-strand	373-374	2	12
β-strand	376-377	2	18
α-helix	380-382	3
α-helix	390-394	5
α-helix	399-402	4
β-strand	405-409	5	18
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	11

Chain H: 6 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	37-44	8
β-strand	49	1	20
β-strand	59-65	7	20
β-strand	72-79	8	20
β-strand	85-93	9	20
α-helix	96-109	14
α-helix	114-118	5
α-helix	122-129	8
α-helix	133-135	3
α-helix	136-157	22

Chain I: 6 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	70-76	7	9
β-strand	82-88	7	9
β-strand	92	1	10
α-helix	93-99	7
β-strand	118-121	4	9
α-helix	122	1
α-helix	130-133	4
α-helix	134-140	7
β-strand	150-152	3	9
α-helix	153-155	3
β-strand	157	1	10
α-helix	160-162	3
β-strand	166-168	3	9

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

>8RMD_1 Isoform Mitochondrial of Cysteine desulfurase (chains A, E)
MSLRPLYMDVQATTPLDPRVLDAMLPYLINYYGNPHSRTHAYGWESEAAMERARQQVASL
IGADPREIIFTSGATESNNIAIKGVARFYRSRKKHLITTQTEHKCVLDSCRSLEAEGFQV
TYLPVQKSGIIDLKELEAAIQPDTSLVSVMTVNNEIGVKQPIAEIGRICSSRKVYFHTDA
AQAVGKIPLDVNDMKIDLMSISGHKIYGPKGVGAIYIRRRPRVRVEALQSGGGQERGMRS
GTVPTPLVVGLGAACEVAQQEMEYDHKRISKLSERLIQNIMKSLPDVVMNGDPKHHYPGC
INLSFAYVEGESLLMALKDVALSSGSACTSASLEPSYVLRAIGTDEDLAHSSIRFGIGRF
TTEEEVDYTVEKCIQHVKRLREMSPLWEMVQDGIDLKSIKWTQH

Sequence of entity 2 (B, F), FASTA

>8RMD_2 LYR motif-containing protein 4 (chains B, F)
MGSSHHHHHHGSPTTENLYFQGHNMAASSRAQVLALYRAMLRESKRFSAYNYRTYAVRRI
RDAFRENKNVKDPVEIQTLVNKAKRDLGVIRRQVHIGQLYSTDKLIIENRDMPRT

Sequence of entity 3 (C, G), FASTA

>8RMD_3 Acyl carrier protein (chains C, G)
MSTIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTVELVMALEEEFDTEIPDEEA
EKITTVQAAIDYINGHQA

Sequence of entity 4 (D, H), FASTA

>8RMD_4 Isoform 1 of Iron-sulfur cluster assembly enzyme ISCU (chains D, H)
MAYHKKVVDHYENPRNVGSLDKTSKNVGTGLVGAPACGDVMKLQIQVDEKGKIVDARFKT
FGCGSAIASSSLATEWVKGKTVEEALTIKNTDIAKELCLPPVKLHCSMLAEDAIKAALAD
YKLKQEPKKGEAEKKLEHHHHHH

Sequence of entity 5 (I), FASTA

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

Browse structure collections

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