6o07

Structure and mechanism of acetylation by the N-terminal dual enzyme NatA/Naa50 complex

Method: X-RAY DIFFRACTION

▼

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

N-terminal acetyltransferase A complex subunit NAT5

Saccharomyces cerevisiae

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	Naa15 × 1 （G2WCC0） N-terminal acetyltransferase A complex catalytic subunit ARD1 × 1 （P07347） CHLORIDE ION × 18 GLYCEROL × 8 ACETYL COENZYME *A × 1 MALONATE ION × 4 INOSITOL HEXAKISPHOSPHATE × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NAT5_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain C； PDBConstruct 1–176； UniProt 1–176

Naa15

Saccharomyces cerevisiae

UniProt G2WCC0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	N-terminal acetyltransferase A complex subunit NAT5 × 1 （Q08689） N-terminal acetyltransferase A complex catalytic subunit ARD1 × 1 （P07347） CHLORIDE ION × 18 GLYCEROL × 8 ACETYL COENZYME *A × 1 MALONATE ION × 4 INOSITOL HEXAKISPHOSPHATE × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	G2WCC0_YEASK
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 1–854； UniProt 1–854

N-terminal acetyltransferase A complex catalytic subunit ARD1

Saccharomyces cerevisiae

UniProt P07347

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	N-terminal acetyltransferase A complex subunit NAT5 × 1 （Q08689） Naa15 × 1 （G2WCC0） CHLORIDE ION × 18 GLYCEROL × 8 ACETYL COENZYME *A × 1 MALONATE ION × 4 INOSITOL HEXAKISPHOSPHATE × 1 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ARD1_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain B； PDBConstruct 1–238； UniProt 1–238

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	6o07
Deposition date deposition_date	2019-02-15
Structure title title	Structure and mechanism of acetylation by the N-terminal dual enzyme NatA/Naa50 complex
Keywords keywords	N-terminal acetylation, protein complex, NatA, Naa50, NatE, 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.

6o07__assembly_1__model_1

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

Download this curve (.dat)

6o07__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6o07__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.01 Å
Rg (electron density)	33.14 Å
Total Rg	33.59 Å
Atom count	8848
Residues	1101
Excluded volume	157380 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6o07__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (10)

Entity 1 Entity 1 polymer

Description description	N-terminal acetyltransferase A complex subunit NAT5
Molecular weight formula_weight	19753.7 kDa
EC 编号 ec_number	2.3.1.258
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C
Atom count atom_count	9036

MGRDICTLDNVYANNLGMLTKLAHVTVPNLYQDAFFSALFAEDSLVAKNKKPSSKKDVHFTQMAYYSEIPVGGLVAKLVPKKQNELSLKGIQIEFLGVLPNYRHKSIGSKLLKFAEDKCSECHQHNVFVYLPAVDDLTKQWFIAHGFEQVGETVNNFIKGVNGDEQDAILLKKHIS

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Naa15
Molecular weight formula_weight	99067.2 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MSRKRSTKPKPAAKIALKKENDQFLEALKLYEGKQYKKSLKLLDAILKKDGSHVDSLALKGLDLYSVGEKDDAASYVANAIRKIEGASASPICCHVLGIYMRNTKEYKESIKWFTAALNNGSTNKQIYRDLATLQSQIGDFKSALVSRKKYWEAFLGYRANWTSLAVAQDVNGERQQAINTLSQFEKLAEGKISDSEKYEHSECLMYKNDVMYKAASDNQDKLQNVLKHLNDIEPCVFDKFGLLERKATIYMKLGQLKDASIVYRTLIKRNPDNFKYYKLLEVSLGIQGDNKLKKALYGKLEQFYPRCEPPKFIPLTFLQDKEELSKKLREYVLPQLKRGVPATFSNVKPLYQRRKSKVSPLLEKIVLDYLSGLDPTQDPIPFIWTNYYLSQHFLFLKDFPKAQEYIDAALDHTPTLVEFYILKARILKHLGLMDTAAGILEEGRQLDLQDRFINCKTVKYFLRANNIDKAVEVASLFTKNDDSVNGIKDLHLVEASWFIVEQAEAYYRLYLDRKKKLDDLESLKKEVESDKSEQIANDIKENQWLVRKYKGLALKRFNAIPKFYKQFEDDQLDFHSYCMRKGTPRAYLEMLEWGKALYTKPMYVRAMKEASKLYFQMHDDRLKRKSDSLDENSDEIQNNGQNSSSQKKKAKKEAAAMNKRKETEAKSVAAYPSDQDNDVFGEKLIETSTPMEDFATEFYNNYSMQVREDERDYILDFEFNYRIGKLALCFASLNKFAKRFGTTSGLFGSMAIVLLHATRNDTPFDPILKKVVTKSLEKEYSENFPLNEISNNSFDWLNFYQEKFGKNDINGLLFLYRYRDDVPIGSSNLKEMIISSLSPLEPHSQNEILQYYL

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	N-terminal acetyltransferase A complex catalytic subunit ARD1
Molecular weight formula_weight	27635.2 kDa
EC 编号 ec_number	2.3.1.255
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MPINIRRATINDIICMQNANLHNLPENYMMKYYMYHILSWPEASFVATTTTLDCEDSDEQDENDKLELTLDGTNDGRTIKLDPTYLAPGEKLVGYVLVKMNDDPDQQNEPPNGHITSLSVMRTYRRMGIAENLMRQALFALREVHQAEYVSLHVRQSNRAALHLYRDTLAFEVLSIEKSYYQDGEDAYAMKKVLKLEELQISNFTHRRLKENEEKLEDDLESDLLEDIIKQGVNDIIV

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	18

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 non-polymer

Description description	ACETYL COENZYME *A
Molecular weight formula_weight	809.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	MALONATE ION
Molecular weight formula_weight	102.0 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	INOSITOL HEXAKISPHOSPHATE
Molecular weight formula_weight	660.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	188

▼

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d6o07c_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamily	d.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family family	d.108.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	6o07B00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

Domain ID domain_id	6o07C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	630 — Aminopeptidase
Homologous superfamily homologous superfamily	30 — Gcn5-related N-acetyltransferase (GNAT)

▶

Unit-cell length a length_a	84.437 Å
Unit-cell length b length_b	125.726 Å
Unit-cell length c length_c	145.924 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	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.702 Å
Low-resolution limit resolution_low	47.658 Å
R factor r_factor	0.2235
R_work r_work	0.2221
R_free r_free	0.2503

Structure and mechanism of acetylation by the N-terminal dual enzyme NatA/Naa50 complex

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

N-terminal acetyltransferase A complex subunit NAT5

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Naa15

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

N-terminal acetyltransferase A complex catalytic subunit ARD1

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

6o07__assembly_1__model_1

6o07__assembly_1__model_1 | I(q)

6o07__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 (10)

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 non-polymer

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 water

6. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

CATH v4.4 (2 domains)

7. Citations (1)