4psx

Crystal structure of histone acetyltransferase complex

Method: X-RAY DIFFRACTION

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

Histone acetyltransferase type B catalytic subunit

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	Histone acetyltransferase type B subunit 2 × 1 （P39984） Histone H4 × 1 （P02309） Histone H3 × 1 （P61830） COENZYME A × 1 SULFATE ION × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Histone acetyltransferase type B subunit 2 × 1 （P39984） Histone H4 × 1 （P02309） Histone H3 × 1 （P61830） COENZYME A × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HAT1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 7–319； UniProt 7–319 Author chain D； PDBConstruct 7–319； UniProt 7–319

Histone acetyltransferase type B subunit 2

Saccharomyces cerevisiae

UniProt P39984

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Histone acetyltransferase type B catalytic subunit × 1 （Q12341） Histone H4 × 1 （P02309） Histone H3 × 1 （P61830） COENZYME A × 1 SULFATE ION × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Histone acetyltransferase type B catalytic subunit × 1 （Q12341） Histone H4 × 1 （P02309） Histone H3 × 1 （P61830） COENZYME A × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	HAT2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 8–389； UniProt 8–389 Author chain E； PDBConstruct 8–389； UniProt 8–389

Histone H4

Saccharomyces cerevisiae

UniProt P02309

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Histone acetyltransferase type B catalytic subunit × 1 （Q12341） Histone acetyltransferase type B subunit 2 × 1 （P39984） Histone H3 × 1 （P61830） COENZYME A × 1 SULFATE ION × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Histone acetyltransferase type B catalytic subunit × 1 （Q12341） Histone acetyltransferase type B subunit 2 × 1 （P39984） Histone H3 × 1 （P61830） COENZYME A × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H4_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–48； UniProt 2–49 Author chain F； PDBConstruct 1–48； UniProt 2–49

Histone H3

Saccharomyces cerevisiae S288c

UniProt P61830

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Histone acetyltransferase type B catalytic subunit × 1 （Q12341） Histone acetyltransferase type B subunit 2 × 1 （P39984） Histone H4 × 1 （P02309） COENZYME A × 1 SULFATE ION × 1 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Histone acetyltransferase type B catalytic subunit × 1 （Q12341） Histone acetyltransferase type B subunit 2 × 1 （P39984） Histone H4 × 1 （P02309） COENZYME A × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H3_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain P； PDBConstruct 1–15； UniProt 2–16 Author chain Y； PDBConstruct 1–15； UniProt 2–16

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	4psx
Deposition date deposition_date	2014-03-08
Structure title title	Crystal structure of histone acetyltransferase complex
Keywords keywords	HAT WD40, acetyltransferase, AcCoA, Phosphorylation, HISTONE-TRANSFERASE complex; HISTONE/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.

4psx__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4psx__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4psx__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	31.02 Å
Rg (electron density)	30.49 Å
Total Rg	31.11 Å
Atom count	5878
Residues	721
Excluded volume	104050 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4psx__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4psx__assembly_2__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 (7)

Entity 1 Entity 1 polymer

Description description	Histone acetyltransferase type B catalytic subunit
Molecular weight formula_weight	37566.3 kDa
EC 编号 ec_number	2.3.1.48
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	12392

MSANDFKPETWTSSANEALRVSIVGENAVQFSPLFTYPIYGDSEKIYGYKDLIIHLAFDSVTFKPYVNVKYSAKLGDDNIVDVEKKLLSFLPKDDVIVRDEAKWVDCFAEERKTHNLSDVFEKVSEYSLNGEEFVVYKSSLVDDFARRMHRRVQIFSLLFIEAANYIDETDPSWQIYWLLNKKTKELIGFVTTYKYWHYLGAKSFDEDIDKKFRAKISQFLIFPPYQNKGHGSCLYEAIIQSWLEDKSITEITVEDPNEAFDDLRDRNDIQRLRKLGYDAVFQKHSDLSDEFLESSRKSLKLEERQFNRLVEMLLLLNNS

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Histone acetyltransferase type B subunit 2
Molecular weight formula_weight	45107.9 kDa
Mutation mutation	V143T
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

MENQEKPLSVDEEYDLWKSNVPLMYDFVSETRLTWPSLTVQWLPTPVQELDGGFIKQELIIGTHTSGEEENYLKFAEINLPKEILSNEDPQEEAGEEYQSSLPAPRSNIRITAKYEHEEEITRARYMPQDPNIVATINGQGTTFLYSRSEGLQSTLKFHKDNGYALSFSTLVKGRLLSGSDDHTVALWEVGSGGDPTKPVRTWNDLHSDIINDNKWHNFNKDLFGTVSEDSLLKINDVRANNTTIDTVKCPQPFNTLAFSHHSSNLLAAAGMDSYVYLYDLRNMKEPLHHMSGHEDAVNNLEFSTHVDGVVVSSGSDNRLMMWDLKQIGAEQTPDDAEDGVPELIMVHAGHRSSVNDFDLNPQIPWLVASAEEENILQVWKCSHSLPIVGGPPKVNKDIIS

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	Histone H4
Molecular weight formula_weight	5093.1 kDa
Mutation mutation	I21V
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISG

Source Source

Source organism organism	Saccharomyces cerevisiae
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 polymer

Description description	Histone H3
Molecular weight formula_weight	1565.8 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y,P

ARTKQTARKSTGGKA

Source Source

Source organism organism	Saccharomyces cerevisiae S288c
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Spodoptera frugiperda

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	2

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	606

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d4psxa_
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.108.1.1 — N-acetyl transferase, NAT

Domain ID domain_id	d4psxb_
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.4 — WD40 repeat-like
Family Family family	b.69.4.0 — automated matches

Domain ID domain_id	d4psxd_
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.108.1.1 — N-acetyl transferase, NAT

Domain ID domain_id	d4psxe_
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.4 — WD40 repeat-like
Family Family family	b.69.4.0 — automated matches

CATH v4.4 (8 domains)

Domain ID domain_id	4psxA01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	360 — Histone Acetyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Histone acetyl transferase 1 (HAT1), N-terminal domain

Domain ID domain_id	4psxA02
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	4psxA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	390 —

Domain ID domain_id	4psxB00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

Domain ID domain_id	4psxD01
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	360 — Histone Acetyltransferase; domain 1
Homologous superfamily homologous superfamily	10 — Histone acetyl transferase 1 (HAT1), N-terminal domain

Domain ID domain_id	4psxD02
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	4psxD03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	390 —

Domain ID domain_id	4psxE00
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	10 — YVTN repeat-like/Quinoprotein amine dehydrogenase

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Unit-cell length a length_a	78.548 Å
Unit-cell length b length_b	85.331 Å
Unit-cell length c length_c	114.510 Å
Unit-cell angle α angle_alpha	75.97 °
Unit-cell angle β angle_beta	72.40 °
Unit-cell angle γ angle_gamma	66.06 °
Molecules per unit cell Z z_pdb	2

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	2.509 Å
Low-resolution limit resolution_low	38.600 Å
R factor r_factor	0.1829
R_work r_work	0.1807
R_free r_free	0.2228

Crystal structure of histone acetyltransferase complex

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

Histone acetyltransferase type B catalytic 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

Histone acetyltransferase type B subunit 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H4

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Histone H3

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

4psx__assembly_2__model_1

4psx__assembly_2__model_1 | I(q)

4psx__assembly_2__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 (7)

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 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)