6wi2

Structure of human mitochondrial complex Nfs1-ISCU2-ISD11 with E.coli ACP1 at 1.95 A resolution (NIAU)2. N-terminal mutation of ISCU2 (L35) traps Nfs1 Cys loop in the active site of ISCU2 without metal present.

Method: X-RAY DIFFRACTION

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cysteine desulfurase, mitochondrial

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	LYR motif-containing protein 4 × 1 （Q9HD34） Acyl carrier protein × 1 （B7MJ81） Iron-sulfur cluster assembly enzyme ISCU, mitochondrial × 1 （Q9H1K1） PYRIDOXAL-5'-PHOSPHATE × 1 1,2-ETHANEDIOL × 36 GLYCEROL × 3 DI(HYDROXYETHYL)ETHER × 10 TETRAETHYLENE GLYCOL × 2 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1 TRIETHYLENE GLYCOL × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID × 1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 1 PENTAETHYLENE GLYCOL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NFS1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–406； UniProt 56–457

LYR motif-containing protein 4

Homo sapiens

UniProt Q9HD34

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cysteine desulfurase, mitochondrial × 1 （Q9Y697） Acyl carrier protein × 1 （B7MJ81） Iron-sulfur cluster assembly enzyme ISCU, mitochondrial × 1 （Q9H1K1） PYRIDOXAL-5'-PHOSPHATE × 1 1,2-ETHANEDIOL × 36 GLYCEROL × 3 DI(HYDROXYETHYL)ETHER × 10 TETRAETHYLENE GLYCOL × 2 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1 TRIETHYLENE GLYCOL × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID × 1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 1 PENTAETHYLENE GLYCOL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LYRM4_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–91； UniProt 1–91

Acyl carrier protein

OrganismNot specified

UniProt B7MJ81

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cysteine desulfurase, mitochondrial × 1 （Q9Y697） LYR motif-containing protein 4 × 1 （Q9HD34） Iron-sulfur cluster assembly enzyme ISCU, mitochondrial × 1 （Q9H1K1） PYRIDOXAL-5'-PHOSPHATE × 1 1,2-ETHANEDIOL × 36 GLYCEROL × 3 DI(HYDROXYETHYL)ETHER × 10 TETRAETHYLENE GLYCOL × 2 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1 TRIETHYLENE GLYCOL × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID × 1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 1 PENTAETHYLENE GLYCOL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACP_ECO45
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–77； UniProt 2–78

Iron-sulfur cluster assembly enzyme ISCU, mitochondrial

Homo sapiens

UniProt Q9H1K1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Cysteine desulfurase, mitochondrial × 1 （Q9Y697） LYR motif-containing protein 4 × 1 （Q9HD34） Acyl carrier protein × 1 （B7MJ81） PYRIDOXAL-5'-PHOSPHATE × 1 1,2-ETHANEDIOL × 36 GLYCEROL × 3 DI(HYDROXYETHYL)ETHER × 10 TETRAETHYLENE GLYCOL × 2 2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL × 1 TRIETHYLENE GLYCOL × 1 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 1 {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID × 1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 1 PENTAETHYLENE GLYCOL × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ISCU_HUMAN
Isoform	Q9H1K1-2
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 3–135； UniProt 10–142

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6wi2
Deposition date deposition_date	2020-04-08
Structure title title	Structure of human mitochondrial complex Nfs1-ISCU2-ISD11 with E.coli ACP1 at 1.95 A resolution (NIAU)2. N-terminal mutation of ISCU2 (L35) traps Nfs1 Cys loop in the active site of ISCU2 without metal present.
Keywords keywords	complex, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6wi2__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6wi2__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6wi2__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	30.90 Å
Rg (electron density)	30.22 Å
Total Rg	30.68 Å
Atom count	5602
Residues	686
Excluded volume	100360 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6wi2__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (16)

Entity 1 Entity 1 polymer

Description description	Cysteine desulfurase, mitochondrial
Molecular weight formula_weight	45081.6 kDa
EC 编号 ec_number	2.8.1.7
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6127

MGSSLRPLYMDVQATTPLDPRVLDAMLPYLINYYGNPHSRTHAYGWESEAAMERARQQVASLIGADPREIIFTSGATESNNIAIKGVARFYRSRKKHLITTQTEHKCVLDSCRSLEAEGFQVTYLPVQKSGIIDLKELEAAIQPDTSLVSVMTVNNEIGVKQPIAEIGRICSSRKVYFHTDAAQAVGKIPLDVNDMKIDLMSISGHKIYGPKGVGAIYIRRRPRVRVEALQSGGGQERGMRSGTVPTPLVVGLGAACEVAQQEMEYDHKRISKLSERLIQNIMKSLPDVVMNGDPKHHYPGCINLSFAYVEGESLLMALKDVALSSGSACTSASLEPSYVLRAIGTDEDLAHSSIRFGIGRFTTEEEVDYTVEKCIQHVKRLREMSPLWEMVQDGIDLKSIKWTQH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	LYR motif-containing protein 4
Molecular weight formula_weight	10763.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MAASSRAQVLALYRAMLRESKRFSAYNYRTYAVRRIRDAFRENKNVKDPVEIQTLVNKAKRDLGVIRRQVHIGQLYSTDKLIIENRDMPRT

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Acyl carrier protein
Molecular weight formula_weight	8514.3 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

STIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTVELVMALEEEFDTEIPDEEAEKITTVQAAIDYINGHQA

Entity 4 Entity 4 polymer

Description description	Iron-sulfur cluster assembly enzyme ISCU, mitochondrial
Molecular weight formula_weight	15553.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MALSTQVVDHYENPRNVGSLDKTSKNVGTGLVGAPACGDVMKLQIQVDEKGKIVDARFKTFGCGSAIASSSLATEWVKGKTVEEALTIKNTDIAKELCLPPVKLHCSMLAEDAIKAALADYKLKQEPKKGEAEKKLEHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	Human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 non-polymer

Description description	PYRIDOXAL-5'-PHOSPHATE
Molecular weight formula_weight	247.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	36

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 9 Entity 9 non-polymer

Description description	TETRAETHYLENE GLYCOL
Molecular weight formula_weight	194.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	2-{2-[2-2-(METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
Molecular weight formula_weight	208.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 11 Entity 11 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 non-polymer

Description description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
Molecular weight formula_weight	195.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 13 Entity 13 non-polymer

Description description	{[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID
Molecular weight formula_weight	292.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 14 Entity 14 non-polymer

Description description	S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate
Molecular weight formula_weight	540.7 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 15 Entity 15 non-polymer

Description description	PENTAETHYLENE GLYCOL
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 16 Entity 16 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	403

▼

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d6wi2a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.67 — PLP-dependent transferase-like
Superfamily Superfamily superfamily	c.67.1 — PLP-dependent transferases
Family Family family	c.67.1.3 — Cystathionine synthase-like

Domain ID domain_id	d6wi2a2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d6wi2b_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.71 — LYR proteins from mammalian respiratory complex I
Superfamily Superfamily superfamily	f.71.1 — LYR protein-like
Family Family family	f.71.1.1 — LYR proteins

Domain ID domain_id	d6wi2c_
Class class	a — All alpha proteins
Fold Fold fold	a.28 — Acyl carrier protein-like
Superfamily Superfamily superfamily	a.28.1 — ACP-like
Family Family family	a.28.1.1 — Acyl-carrier protein (ACP)

Domain ID domain_id	d6wi2d1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.224 — SufE/NifU
Superfamily Superfamily superfamily	d.224.1 — SufE/NifU
Family Family family	d.224.1.2 — NifU/IscU domain

Domain ID domain_id	d6wi2d2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id	6wi2A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	640 — Aspartate Aminotransferase; domain 2
Homologous superfamily homologous superfamily	10 — Type I PLP-dependent aspartate aminotransferase-like (Major domain)

Domain ID domain_id	6wi2D01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1010 — Sufe protein. Chain: A
Homologous superfamily homologous superfamily	10 —

▶

Unit-cell length a length_a	86.430 Å
Unit-cell length b length_b	86.430 Å
Unit-cell length c length_c	246.120 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	49.011 Å
R factor r_factor	0.1521
R_work r_work	0.1504
R_free r_free	0.1849

Structure of human mitochondrial complex Nfs1-ISCU2-ISD11 with E.coli ACP1 at 1.95 A resolution (NIAU)2. N-terminal mutation of ISCU2 (L35) traps Nfs1 Cys loop in the active site of ISCU2 without metal present.

1. Protein Identity and Related Structures Protein Identity & Related Structures

Cysteine desulfurase, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

LYR motif-containing protein 4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Acyl carrier protein

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Iron-sulfur cluster assembly enzyme ISCU, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6wi2__assembly_1__model_1

6wi2__assembly_1__model_1 | I(q)

6wi2__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (16)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 non-polymer

Entity 12 Entity 12 non-polymer

Entity 13 Entity 13 non-polymer

Entity 14 Entity 14 non-polymer

Entity 15 Entity 15 non-polymer

Entity 16 Entity 16 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (6 domains)

CATH v4.4 (2 domains)

7. Citations (1)