6ygd

Crystal structure of the NatC complex bound to Gag peptide and CoA

Method: X-RAY DIFFRACTION

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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 4	N-alpha-acetyltransferase 35, NatC auxiliary subunit × 1 （Q02197） N-alpha-acetyltransferase 38, NatC auxiliary subunit × 1 （P23059） Major capsid protein × 1 （P32503） COENZYME A × 1 CHLORIDE ION × 6 IODIDE ION × 10 1,2-ETHANEDIOL × 5 water × 3	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 4	N-alpha-acetyltransferase 30 × 1 （Q03503） N-alpha-acetyltransferase 38, NatC auxiliary subunit × 1 （P23059） Major capsid protein × 1 （P32503） COENZYME A × 1 CHLORIDE ION × 6 IODIDE ION × 10 1,2-ETHANEDIOL × 5 water × 3	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 4	N-alpha-acetyltransferase 30 × 1 （Q03503） N-alpha-acetyltransferase 35, NatC auxiliary subunit × 1 （Q02197） Major capsid protein × 1 （P32503） COENZYME A × 1 CHLORIDE ION × 6 IODIDE ION × 10 1,2-ETHANEDIOL × 5 water × 3	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

Major capsid protein

OrganismNot specified

UniProt P32503

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	N-alpha-acetyltransferase 30 × 1 （Q03503） N-alpha-acetyltransferase 35, NatC auxiliary subunit × 1 （Q02197） N-alpha-acetyltransferase 38, NatC auxiliary subunit × 1 （P23059） COENZYME A × 1 CHLORIDE ION × 6 IODIDE ION × 10 1,2-ETHANEDIOL × 5 water × 3	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GAG_SCVLA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–5； UniProt 1–5

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

6ygd__assembly_1__model_1

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

Download this curve (.dat)

6ygd__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6ygd__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	33.62 Å
Rg (electron density)	33.03 Å
Total Rg	33.67 Å
Atom count	7818
Residues	956
Excluded volume	140630 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6ygd__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 (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	7911

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 polymer

Description description	Major capsid protein
Molecular weight formula_weight	1281.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MLRFVGSRRR

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 7 Entity 7 non-polymer

Description description	IODIDE ION
Molecular weight formula_weight	126.9 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 8 Entity 8 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	93

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Unit-cell length a length_a	48.136 Å
Unit-cell length b length_b	134.927 Å
Unit-cell length c length_c	165.740 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	2.752 Å
Low-resolution limit resolution_low	45.337 Å
R factor r_factor	0.2061
R_work r_work	0.2039
R_free r_free	0.2480

Crystal structure of the NatC complex bound to Gag peptide and 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

Major capsid 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6ygd__assembly_1__model_1

6ygd__assembly_1__model_1 | I(q)

6ygd__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 polymer

Polymer 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)