SAXSdb — 5j9q

▼

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

Histone acetyltransferase ESA1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Chromatin modification-related protein EAF6 × 1 （P47128） Enhancer of polycomb-like protein 1 × 1 （P43572） Chromatin modification-related protein YNG2 × 1 （P38806） Htz1 × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Chromatin modification-related protein EAF6 × 1 （P47128） Enhancer of polycomb-like protein 1 × 1 （P43572） Chromatin modification-related protein YNG2 × 1 （P38806） Htz1 × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 5	Chromatin modification-related protein EAF6 × 1 （P47128） Enhancer of polycomb-like protein 1 × 1 （P43572） Chromatin modification-related protein YNG2 × 1 （P38806） Htz1 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ESA1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–305； UniProt 141–445 Author chain E； PDBConstruct 1–305； UniProt 141–445 Author chain I； PDBConstruct 1–305； UniProt 141–445

Chromatin modification-related protein EAF6

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P47128

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Histone acetyltransferase ESA1 × 1 （Q08649） Enhancer of polycomb-like protein 1 × 1 （P43572） Chromatin modification-related protein YNG2 × 1 （P38806） Htz1 × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Histone acetyltransferase ESA1 × 1 （Q08649） Enhancer of polycomb-like protein 1 × 1 （P43572） Chromatin modification-related protein YNG2 × 1 （P38806） Htz1 × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 5	Histone acetyltransferase ESA1 × 1 （Q08649） Enhancer of polycomb-like protein 1 × 1 （P43572） Chromatin modification-related protein YNG2 × 1 （P38806） Htz1 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EAF6_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–113； UniProt 1–113 Author chain F； PDBConstruct 1–113； UniProt 1–113 Author chain J； PDBConstruct 1–113； UniProt 1–113

Enhancer of polycomb-like protein 1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P43572

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Histone acetyltransferase ESA1 × 1 （Q08649） Chromatin modification-related protein EAF6 × 1 （P47128） Chromatin modification-related protein YNG2 × 1 （P38806） Htz1 × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Histone acetyltransferase ESA1 × 1 （Q08649） Chromatin modification-related protein EAF6 × 1 （P47128） Chromatin modification-related protein YNG2 × 1 （P38806） Htz1 × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 5	Histone acetyltransferase ESA1 × 1 （Q08649） Chromatin modification-related protein EAF6 × 1 （P47128） Chromatin modification-related protein YNG2 × 1 （P38806） Htz1 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	EPL1_YEAST
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 1–351； UniProt 50–400 Author chain G； PDBConstruct 1–351； UniProt 50–400 Author chain N； PDBConstruct 1–351； UniProt 50–400

Chromatin modification-related protein YNG2

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P38806

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 5	Histone acetyltransferase ESA1 × 1 （Q08649） Chromatin modification-related protein EAF6 × 1 （P47128） Enhancer of polycomb-like protein 1 × 1 （P43572） Htz1 × 1	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 5	Histone acetyltransferase ESA1 × 1 （Q08649） Chromatin modification-related protein EAF6 × 1 （P47128） Enhancer of polycomb-like protein 1 × 1 （P43572） Htz1 × 1	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 5	Histone acetyltransferase ESA1 × 1 （Q08649） Chromatin modification-related protein EAF6 × 1 （P47128） Enhancer of polycomb-like protein 1 × 1 （P43572） Htz1 × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YNG2_YEAST
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain D； PDBConstruct 1–120； UniProt 1–120 Author chain H； PDBConstruct 1–120； UniProt 1–120 Author chain K； PDBConstruct 1–120； UniProt 1–120

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	5j9q
Deposition date deposition_date	2016-04-11
Structure title title	Crystal structure of the NuA4 core complex
Keywords keywords	NuA4, nucleosome, histone, acetylation, 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.

5j9q__assembly_1__model_1

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

Download this curve (.dat)

5j9q__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5j9q__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	32.53 Å
Rg (electron density)	32.01 Å
Total Rg	32.65 Å
Atom count	6578
Residues	787
Excluded volume	116960 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5j9q__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5j9q__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`5j9q__assembly_3__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Histone acetyltransferase ESA1
Molecular weight formula_weight	36556.9 kDa
EC 编号 ec_number	2.3.1.48
Mutation mutation	E338Q
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,A,I
Atom count atom_count	19671

HEDEIKKLRTSGSMTQNPHEVARVRNLNRIIMGKYEIEPWYFSPYPIELTDEDFIYIDDFTLQYFGSKKQYERYRKKCTLRHPPGNEIYRDDYVSFFEIDGRKQRTWCRNLCLLSKLFLDHKTLYYDVDPFLFYCMTRRDELGHHLVGYFSKEKESADGYNVACILTLPQYQRMGYGKLLIEFSYELSKKENKVGSPQKPLSDLGLLSYRAYWSDTLITLLVEHQKEITIDEISSMTSMTTTDILHTAKTLNILRYYKGQHIIFLNEDILDRYNRLKAKKRRTIDPNRLIWKPPVFTASQLRFAW

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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	Chromatin modification-related protein EAF6
Molecular weight formula_weight	12915.7 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	F,B,J

MTDELKSYEALKAELKKSLQDRREQEDTFDNLQQEIYDKETEYFSHNSNNNHSGHGGAHGSKSHYSGNIIKGFDTFSKSHHSHADSAFNNNDRIFSLSSATYVKQQHGQSQND

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Enhancer of polycomb-like protein 1
Molecular weight formula_weight	41835.2 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,N,C

SSNSRFRHRKISVKQHLKIYLPNDLKHLDKDELQQREVVEIETGVEKNEEKEVHLHRILQMGSGHTKHKDYIPTPDASMTWNEYDKFYTGSFQETTSYIKFSATVEDCCGTNYNMDERDETFLNEQVNKGSSDILTEDEFEILCSSFEHAIHERQPFLSMDPESILSFEELKPTLIKSDMADFNLRNQLNHEINSHKTHFITQFDPVSQMNTRPLIQLIEKFGSKIYDYWRERKIEVNGYEIFPQLKFERPGEKEEIDPYVCFRRREVRHPRKTRRIDILNSQRLRALHQELKNAKDLALLVAKRENVSLNWINDELKIFDQRVKIKNLKRSLNISGEDDDLINHKRKRPT

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
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	Chromatin modification-related protein YNG2
Molecular weight formula_weight	13828.9 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,H,K

MDPSLVLEQTIQDVSNLPSEFRYLLEEIGSNDLKLIEEKKKYEQKESQIHKFIRQQGSIPKHPQEDGLDKEIKESLLKCQSLQREKCVLANTALFLIARHLNKLEKNIALLEEDGVLAPV

Source Source

Source organism organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Common name common_name	;Baker's yeast ;
NCBI taxonomy ID ncbi_taxonomy_id	559292
Host organism host_organism	Escherichia coli

Entity 5 Entity 5 polymer

Description description	Htz1
Molecular weight formula_weight	979.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	L,M,O

SGAKDSGSLR

Source Source

Source organism organism	Saccharomyces cerevisiae
NCBI taxonomy ID ncbi_taxonomy_id	4932
Host organism host_organism	Escherichia coli

▼

6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

Domain ID domain_id	5j9qA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	60 — N-acetyl transferase-like

Domain ID domain_id	5j9qA02
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	5j9qA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	5j9qE01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	60 — N-acetyl transferase-like

Domain ID domain_id	5j9qE02
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	5j9qE03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Domain ID domain_id	5j9qI01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	60 — N-acetyl transferase-like

Domain ID domain_id	5j9qI02
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	5j9qI03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily	10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

▶

Unit-cell length a length_a	217.857 Å
Unit-cell length b length_b	190.990 Å
Unit-cell length c length_c	172.346 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	113.56 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.250 Å
Low-resolution limit resolution_low	29.996 Å
R factor r_factor	0.2508
R_work r_work	0.2502
R_free r_free	0.2731

Crystal structure of the NuA4 core complex

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

Histone acetyltransferase ESA1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Chromatin modification-related protein EAF6

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Enhancer of polycomb-like protein 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Chromatin modification-related protein YNG2

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

5j9q__assembly_1__model_1

5j9q__assembly_1__model_1 | I(q)

5j9q__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 (5)

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 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

7. Citations (1)