6ygb

Crystal structure of the NatC complex bound to CoA

Method: X-RAY DIFFRACTION

▼

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

N-alpha-acetyltransferase 30

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	N-alpha-acetyltransferase 35, NatC auxiliary subunit × 1 （Q02197） N-alpha-acetyltransferase 38, NatC auxiliary subunit × 1 （P23059） COENZYME A × 1 CHLORIDE ION × 8 DI(HYDROXYETHYL)ETHER × 3 1,2-ETHANEDIOL × 9 IODIDE ION × 9 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NAA30_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–159； UniProt 1–159

N-alpha-acetyltransferase 35, NatC auxiliary subunit

Saccharomyces cerevisiae

UniProt Q02197

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	N-alpha-acetyltransferase 30 × 1 （Q03503） N-alpha-acetyltransferase 38, NatC auxiliary subunit × 1 （P23059） COENZYME A × 1 CHLORIDE ION × 8 DI(HYDROXYETHYL)ETHER × 3 1,2-ETHANEDIOL × 9 IODIDE ION × 9 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NAA35_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–735； UniProt 1–733

N-alpha-acetyltransferase 38, NatC auxiliary subunit

Saccharomyces cerevisiae

UniProt P23059

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 3	N-alpha-acetyltransferase 30 × 1 （Q03503） N-alpha-acetyltransferase 35, NatC auxiliary subunit × 1 （Q02197） COENZYME A × 1 CHLORIDE ION × 8 DI(HYDROXYETHYL)ETHER × 3 1,2-ETHANEDIOL × 9 IODIDE ION × 9 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NAA38_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–77； UniProt 1–77

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	6ygb
Deposition date deposition_date	2020-03-27
Structure title title	Crystal structure of the NatC complex bound to CoA
Keywords keywords	N-terminal acetylation, NAT, GNAT, acetyltransferase, Naa30, Naa35, Naa38, Mak3, Mak10, Mak31, 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.

6ygb__assembly_1__model_1

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

Download this curve (.dat)

6ygb__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ygb__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	34.03 Å
Rg (electron density)	33.44 Å
Total Rg	34.08 Å
Atom count	7886
Residues	961
Excluded volume	141940 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ygb__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 (9)

Entity 1 Entity 1 polymer

Description description	N-alpha-acetyltransferase 30
Molecular weight formula_weight	18559.6 kDa
EC 编号 ec_number	2.3.1.256
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	8118

MEIVYKPLDIRNEEQFASIKKLIDADLSEPYSIYVYRYFLNQWPELTYIAVDNKSGTPNIPIGCIVCKMDPHRNVRLRGYIGMLAVESTYRGHGIAKKLVEIAIDKMQREHCDEIMLETEVENSAALNLYEGMGFIRMKRMFRYYLNEGDAFKLILPLT

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	N-alpha-acetyltransferase 35, NatC auxiliary subunit
Molecular weight formula_weight	84549.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GPMEVDSILGSLSITDDFDQLVDVTSLFDELCSKLKPEAIVKDPRFDLFEGTHSLEVNNSKLDSSLIELTAEEIEFDVNVAYDPPLASVAAIADRLLRCVISWLNDYQTLPTTVLSCRYTESLLSSLVKGTTAGSSWCTGNILYDKVLGSCILGVCYLTKFVQKLLSAGIVFEEEDLNFNNMGFNTFDNLPGQDVVINSLTESLQILEAYSDDSLHLTMLKHILKIIICLVHLEDHLTDYSTKTSHLDELIENANSVNGIFPQLQLSPPKGAFSTYIQKHRSNQFPPRKITKLPTDYSGFITLANDVKTILLVDKAESALETYQFAKFFNKLEQRHVIARILFPLFFIRDDRTVLGKFSYTQFYLLHVKEFSAQTPSEFESSIGNELIQESSNMLLEWYQNCSQNTCRYRQGFNRQLILWDSLQAQFESVNSQVYCSWTYFMKLSSMIEFSLKGFDLDIYKPFEAYSMFWYVYYLSHHLETFLKDSQNDIESNINAIHSMNKKLKKLKAGEKKDQLRLKYRFAMDNEMEQLQATKQFLNYLLKEINITKSLCLIEVFQFAILKSFGLIDNKNSTPSKFSNERLIHNLRFKPFNSIGVPELPEYEVFQQTLKDFVIEEKGAAFDIKLERATNFIETEVRNVVSSIDEIMQGIKGGDNNGVLVTGTRLVQELSLEYYCKLKHTSKALSVNSKVIVNTLKKNIKNKDSHEYKVELVHTTEGWNYFPIQTLRIKQDRYK

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 BL21(DE3)

Entity 3 Entity 3 polymer

Description description	N-alpha-acetyltransferase 38, NatC auxiliary subunit
Molecular weight formula_weight	8550.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

MDILKLSDFIGNTLIVSLTEDRILVGSLVAVDAQMNLLLDHVEERMGSSSRMMGLVSVPRRSVKTIMIDKPVLQELT

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 BL21(DE3)

Entity 4 Entity 4 non-polymer

Description description	COENZYME A
Molecular weight formula_weight	767.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 6 Entity 6 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 8 Entity 8 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	9

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	190

▶

Unit-cell length a length_a	48.042 Å
Unit-cell length b length_b	139.789 Å
Unit-cell length c length_c	166.561 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	2.451 Å
Low-resolution limit resolution_low	45.434 Å
R factor r_factor	0.2047
R_work r_work	0.2031
R_free r_free	0.2357

Crystal structure of the NatC complex bound to CoA

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

N-alpha-acetyltransferase 30

State in the Current Structure

Other States of the Same Protein in the Database

N-alpha-acetyltransferase 35, NatC auxiliary subunit

State in the Current Structure

Other States of the Same Protein in the Database

N-alpha-acetyltransferase 38, NatC auxiliary subunit

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6ygb__assembly_1__model_1

6ygb__assembly_1__model_1 | I(q)

6ygb__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 (9)

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 water

7. Citations (1)

Crystal structure of the NatC complex bound to CoA

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

N-alpha-acetyltransferase 30

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-alpha-acetyltransferase 35, NatC auxiliary subunit

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-alpha-acetyltransferase 38, NatC auxiliary subunit

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

6ygb__assembly_1__model_1

6ygb__assembly_1__model_1 | I(q)

6ygb__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 (9)

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 water

7. Citations (1)