8tvt

Structure of human Cysteine desulfurase Nfs1 with L-propargylglycine bound to active site PLP in complex with ISD11, Acp1 and ISCU2

Method: X-RAY DIFFRACTION

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

Cysteine desulfurase

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 （A7ZKJ7） Iron-sulfur cluster assembly enzyme ISCU × 1 （Q9H1K1） 1,2-ETHANEDIOL × 30 PYRIDOXAL-5'-PHOSPHATE × 1 L-Propargylglycine × 1 GLYCEROL × 3 DI(HYDROXYETHYL)ETHER × 8 TETRAETHYLENE GLYCOL × 2 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL × 1 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 TRIETHYLENE GLYCOL × 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 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 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 5–403； UniProt 56–454

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 × 1 （Q9Y697） Acyl carrier protein × 1 （A7ZKJ7） Iron-sulfur cluster assembly enzyme ISCU × 1 （Q9H1K1） 1,2-ETHANEDIOL × 30 PYRIDOXAL-5'-PHOSPHATE × 1 L-Propargylglycine × 1 GLYCEROL × 3 DI(HYDROXYETHYL)ETHER × 8 TETRAETHYLENE GLYCOL × 2 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL × 1 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 TRIETHYLENE GLYCOL × 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 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 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

Escherichia coli

UniProt A7ZKJ7

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 × 1 （Q9Y697） LYR motif-containing protein 4 × 1 （Q9HD34） Iron-sulfur cluster assembly enzyme ISCU × 1 （Q9H1K1） 1,2-ETHANEDIOL × 30 PYRIDOXAL-5'-PHOSPHATE × 1 L-Propargylglycine × 1 GLYCEROL × 3 DI(HYDROXYETHYL)ETHER × 8 TETRAETHYLENE GLYCOL × 2 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL × 1 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 TRIETHYLENE GLYCOL × 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 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 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_ECO24
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–76； UniProt 2–77

Iron-sulfur cluster assembly enzyme ISCU

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 × 1 （Q9Y697） LYR motif-containing protein 4 × 1 （Q9HD34） Acyl carrier protein × 1 （A7ZKJ7） 1,2-ETHANEDIOL × 30 PYRIDOXAL-5'-PHOSPHATE × 1 L-Propargylglycine × 1 GLYCEROL × 3 DI(HYDROXYETHYL)ETHER × 8 TETRAETHYLENE GLYCOL × 2 2,5,8,11,14,17-HEXAOXANONADECAN-19-OL × 1 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 TRIETHYLENE GLYCOL × 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 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 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	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 3–135； UniProt 35–167

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8tvt
Deposition date deposition_date	2023-08-18
Structure title title	Structure of human Cysteine desulfurase Nfs1 with L-propargylglycine bound to active site PLP in complex with ISD11, Acp1 and ISCU2
Keywords keywords	Nfs1, PG-PLP bound, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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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.

8tvt__assembly_1__model_1

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

Download this curve (.dat)

8tvt__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8tvt__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	30.74 Å
Rg (electron density)	30.15 Å
Total Rg	30.61 Å
Atom count	5552
Residues	684
Excluded volume	99584 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8tvt__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (18)

Entity 1 Entity 1 polymer

Description description	Cysteine desulfurase
Molecular weight formula_weight	44714.2 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	6126

MGSSLRPLYMDVQATTPLDPRVLDAMLPYLINYYGNPHSRTHAYGWESEAAMERARQQVASLIGADPREIIFTSGATESNNIAIKGVARFYRSRKKHLITTQTEHKCVLDSCRSLEAEGFQVTYLPVQKSGIIDLKELEAAIQPDTSLVSVMTVNNEIGVKQPIAEIGRICSSRKVYFHTDAAQAVGKIPLDVNDMKIDLMSISGHKIYGPKGVGAIYIRRRPRVRVEALQSGGGQERGMRSGTVPTPLVVGLGAACEVAQQEMEYDHKRISKLSERLIQNIMKSLPDVVMNGDPKHHYPGCINLSFAYVEGESLLMALKDVALSSGSACTSASLEPSYVLRAIGTDEDLAHSSIRFGIGRFTTEEEVDYTVEKCIQHVKRLREMSPLWEMVQDGIDLKSIKW

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	8443.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

STIEERVKKIIGEQLGVKQEEVTNNASFVEDLGADSLDTVELVMALEEEFDTEIPDEEAEKITTVQAAIDYINGHQ

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Iron-sulfur cluster assembly enzyme ISCU
Molecular weight formula_weight	14613.0 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MAYHKKVVDHYENPRNVGSLDKTSKNVGTGLVGAPACGDVMKLQIQVDEKGKIVDARFKTFGCGSAIASSSLATEWVKGKTVEEALTIKNTDIAKELCLPPVKLHCSMLAEDAIKAALADYKLKQEPKKGEAEKK

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	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	30

Entity 6 Entity 6 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 7 Entity 7 non-polymer

Description description	L-Propargylglycine
Molecular weight formula_weight	113.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

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

Entity 9 Entity 9 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 10 Entity 10 non-polymer

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

Entity 11 Entity 11 non-polymer

Description description	2,5,8,11,14,17-HEXAOXANONADECAN-19-OL
Molecular weight formula_weight	296.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 12 Entity 12 non-polymer

Description description	2,3-DIHYDROXY-1,4-DITHIOBUTANE
Molecular weight formula_weight	154.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 13 Entity 13 non-polymer

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

Entity 14 Entity 14 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 15 Entity 15 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 16 Entity 16 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 17 Entity 17 non-polymer

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

Entity 18 Entity 18 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	414

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Unit-cell length a length_a	86.270 Å
Unit-cell length b length_b	86.270 Å
Unit-cell length c length_c	246.030 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	2.000 Å
Low-resolution limit resolution_low	48.950 Å
R factor r_factor	0.1519
R_work r_work	0.1501
R_free r_free	0.1863

Structure of human Cysteine desulfurase Nfs1 with L-propargylglycine bound to active site PLP in complex with ISD11, Acp1 and ISCU2

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

Cysteine desulfurase

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

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

8tvt__assembly_1__model_1

8tvt__assembly_1__model_1 | I(q)

8tvt__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 (18)

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

Source Source

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 non-polymer

Entity 17 Entity 17 non-polymer

Entity 18 Entity 18 water

7. Citations (1)