7vvu

NuA4 HAT module bound to the nucleosome

Method: ELECTRON MICROSCOPY

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

Chromatin modification-related protein EAF6

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 13 DNA 2	Chromatin modification-related protein YNG2 × 1 （P38806） Enhancer of polycomb-like protein 1 × 2 （P43572） Histone H3 × 2 （A0A310TTQ1） H4 × 2 Histone H2A × 2 （Q6AZJ8） Histone H2B 1.1 × 2 （P02281） Histone acetyltransferase ESA1 × 1 （A0A6A5Q414） DNA (207-mer) × 1 DNA (207-mer) × 1 CARBOXYMETHYL COENZYME *A × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6A5PYU5_YEASX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain Y； PDBConstruct 1–113； UniProt 1–113

Chromatin modification-related protein YNG2

OrganismNot specified

UniProt P38806

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 13 DNA 2	Chromatin modification-related protein EAF6 × 1 （A0A6A5PYU5） Enhancer of polycomb-like protein 1 × 2 （P43572） Histone H3 × 2 （A0A310TTQ1） H4 × 2 Histone H2A × 2 （Q6AZJ8） Histone H2B 1.1 × 2 （P02281） Histone acetyltransferase ESA1 × 1 （A0A6A5Q414） DNA (207-mer) × 1 DNA (207-mer) × 1 CARBOXYMETHYL COENZYME *A × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	YNG2_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain V； PDBConstruct 1–282； UniProt 1–282

Enhancer of polycomb-like protein 1

OrganismNot specified

UniProt P43572

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 13 DNA 2	Chromatin modification-related protein EAF6 × 1 （A0A6A5PYU5） Chromatin modification-related protein YNG2 × 1 （P38806） Histone H3 × 2 （A0A310TTQ1） H4 × 2 Histone H2A × 2 （Q6AZJ8） Histone H2B 1.1 × 2 （P02281） Histone acetyltransferase ESA1 × 1 （A0A6A5Q414） DNA (207-mer) × 1 DNA (207-mer) × 1 CARBOXYMETHYL COENZYME *A × 1	Consistent with all polymers

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 T； PDBConstruct 1–832； UniProt 1–832 Author chain X； PDBConstruct 1–832； UniProt 1–832

Histone H3

Xenopus laevis

UniProt A0A310TTQ1

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 13 DNA 2	Chromatin modification-related protein EAF6 × 1 （A0A6A5PYU5） Chromatin modification-related protein YNG2 × 1 （P38806） Enhancer of polycomb-like protein 1 × 2 （P43572） H4 × 2 Histone H2A × 2 （Q6AZJ8） Histone H2B 1.1 × 2 （P02281） Histone acetyltransferase ESA1 × 1 （A0A6A5Q414） DNA (207-mer) × 1 DNA (207-mer) × 1 CARBOXYMETHYL COENZYME *A × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A310TTQ1_XENLA
Isoform	—
PDB entities	4
Chains and sequence ranges	Author chain A； PDBConstruct 1–136； UniProt 1–136 Author chain O； PDBConstruct 1–136； UniProt 1–136

Histone H2A

Xenopus laevis

UniProt Q6AZJ8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 13 DNA 2	Chromatin modification-related protein EAF6 × 1 （A0A6A5PYU5） Chromatin modification-related protein YNG2 × 1 （P38806） Enhancer of polycomb-like protein 1 × 2 （P43572） Histone H3 × 2 （A0A310TTQ1） H4 × 2 Histone H2B 1.1 × 2 （P02281） Histone acetyltransferase ESA1 × 1 （A0A6A5Q414） DNA (207-mer) × 1 DNA (207-mer) × 1 CARBOXYMETHYL COENZYME *A × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q6AZJ8_XENLA
Isoform	—
PDB entities	6
Chains and sequence ranges	Author chain N； PDBConstruct 1–130； UniProt 1–130 Author chain S； PDBConstruct 1–130； UniProt 1–130

Histone H2B 1.1

Xenopus laevis

UniProt P02281

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 13 DNA 2	Chromatin modification-related protein EAF6 × 1 （A0A6A5PYU5） Chromatin modification-related protein YNG2 × 1 （P38806） Enhancer of polycomb-like protein 1 × 2 （P43572） Histone H3 × 2 （A0A310TTQ1） H4 × 2 Histone H2A × 2 （Q6AZJ8） Histone acetyltransferase ESA1 × 1 （A0A6A5Q414） DNA (207-mer) × 1 DNA (207-mer) × 1 CARBOXYMETHYL COENZYME *A × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	H2B11_XENLA
Isoform	—
PDB entities	7
Chains and sequence ranges	Author chain D； PDBConstruct 1–126； UniProt 1–126 Author chain U； PDBConstruct 1–126； UniProt 1–126

Histone acetyltransferase ESA1

OrganismNot specified

UniProt A0A6A5Q414

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 13 DNA 2	Chromatin modification-related protein EAF6 × 1 （A0A6A5PYU5） Chromatin modification-related protein YNG2 × 1 （P38806） Enhancer of polycomb-like protein 1 × 2 （P43572） Histone H3 × 2 （A0A310TTQ1） H4 × 2 Histone H2A × 2 （Q6AZJ8） Histone H2B 1.1 × 2 （P02281） DNA (207-mer) × 1 DNA (207-mer) × 1 CARBOXYMETHYL COENZYME *A × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A6A5Q414_YEASX
Isoform	—
PDB entities	8
Chains and sequence ranges	Author chain P； PDBConstruct 1–445； UniProt 1–445

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	7vvu
Deposition date deposition_date	2021-11-09
Structure title title	NuA4 HAT module bound to the nucleosome
Keywords keywords	NuA4 nucleosome, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex; DNA BINDING PROTEIN/DNA
Experimental Method method	ELECTRON MICROSCOPY

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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.

7vvu__assembly_1__model_1

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

Download this curve (.dat)

7vvu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

7vvu__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	54.56 Å
Rg (electron density)	52.93 Å
Total Rg	53.28 Å
Atom count	19374
Residues	1825
Excluded volume	321440 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`7vvu__assembly_1__model_1`	pentadecameric （15）	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 (11)

Entity 1 Entity 1 polymer

Description description	Chromatin modification-related protein EAF6
Molecular weight formula_weight	12915.7 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y
Atom count atom_count	19374

MTDELKSYEALKAELKKSLQDRREQEDTFDNLQQEIYDKETEYFSHNSNNNHSGHGGAHGSKSHYSGNIIKGFDTFSKSHHSHADSAFNNNDRIFSLSSATYVKQQHGQSQND

Entity 2 Entity 2 polymer

Description description	Chromatin modification-related protein YNG2
Molecular weight formula_weight	32139.5 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	V

MDPSLVLEQTIQDVSNLPSEFRYLLEEIGSNDLKLIEEKKKYEQKESQIHKFIRQQGSIPKHPQEDGLDKEIKESLLKCQSLQREKCVLANTALFLIARHLNKLEKNIALLEEDGVLAPVEEDGDMDSAAEASRESSVVSNSSVKKRRAASSSGSVPPTLKKKKTSRTSKLQNEIDVSSREKSVTPVSPSIEKKIARTKEFKNSRNGKGQNGSPENEEEDKTLYCFCQRVSFGEMVACDGPNCKYEWFHYDCVNLKEPPKGTWYCPECKIEMEKNKLKRKRN

Entity 3 Entity 3 polymer

Description description	Enhancer of polycomb-like protein 1
Molecular weight formula_weight	96889.9 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	T,X

MPTPSNAIEINDGSHKSGRSTRRSGSRSAHDDGLDSFSKGDSGAGASAGSSNSRFRHRKISVKQHLKIYLPNDLKHLDKDELQQREVVEIETGVEKNEEKEVHLHRILQMGSGHTKHKDYIPTPDASMTWNEYDKFYTGSFQETTSYIKFSATVEDCCGTNYNMDERDETFLNEQVNKGSSDILTEDEFEILCSSFEHAIHERQPFLSMDPESILSFEELKPTLIKSDMADFNLRNQLNHEINSHKTHFITQFDPVSQMNTRPLIQLIEKFGSKIYDYWRERKIEVNGYEIFPQLKFERPGEKEEIDPYVCFRRREVRHPRKTRRIDILNSQRLRALHQELKNAKDLALLVAKRENVSLNWINDELKIFDQRVKIKNLKRSLNISGEDDDLINHKRKRPTIVTVEQREAELRKAELKRAAAAAAAAKAKNNKRNNQLEDKSSRLTKQQQQQLLQQQQQQQQNALKTENGKQLANASSSSTSQPITSHVYVKLPSSKIPDIVLEDVDALLNSKEKNARKFVQEKMEKRKIEDADVFFNLTDDPFNPVFDMSLPKNFSTSNVPFASIASSKFQIDRSFYSSHLPEYLKGISDDIRIYDSNGRSRNKDNYNLDTKRIKKTELYDPFQENLEIHSREYPIKFRKRVGRSNIKYVDRMPNFTTSSTKSACSLMDFVDFDSIEKEQYSREGSNDTDSINVYDSKYDEFVRLYDKWKYDSPQNEYGIKFSDEPARLNQISNDTQVIRFGTMLGTKSYEQLREATIKYRRDYITRLKQKHIQHLQQQQQQQQQQQQQAQQQKQKSQNNNSNSSNSLKKLNDSLINSEAKQNSSITQKNSS

Entity 4 Entity 4 polymer

Description description	Histone H3
Molecular weight formula_weight	15435.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Source Source

Source organism organism	Xenopus laevis
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 5 Entity 5 polymer

Description description	H4
Molecular weight formula_weight	11394.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Source Source

Source organism organism	Xenopus laevis
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 6 Entity 6 polymer

Description description	Histone H2A
Molecular weight formula_weight	14109.4 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	S,N

MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK

Source Source

Source organism organism	Xenopus laevis
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 7 Entity 7 polymer

Description description	Histone H2B 1.1
Molecular weight formula_weight	13965.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U,D

MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKSRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Source Source

Source organism organism	Xenopus laevis
NCBI taxonomy ID ncbi_taxonomy_id	8355
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 8 Entity 8 polymer

Description description	Histone acetyltransferase ESA1
Molecular weight formula_weight	52692.8 kDa
EC 编号 ec_number	2.3.1.48
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

MSHDGKEEPGIAKKINSVDDIIIKCQCWVQKNDEERLAEILSINTRKAPPKFYVHYVNYNKRLDEWITTDRINLDKEVLYPKLKATDEDNKKQKKKKATNTSETPQDSLQDGVDGFSRENTDVMDLDNLNVQGIKDENISHEDEIKKLRTSGSMTQNPHEVARVRNLNRIIMGKYEIEPWYFSPYPIELTDEDFIYIDDFTLQYFGSKKQYERYRKKCTLRHPPGNEIYRDDYVSFFEIDGRKQRTWCRNLCLLSKLFLDHKTLYYDVDPFLFYCMTRRDELGHHLVGYFSKEKESADGYNVACILTLPQYQRMGYGKLLIEFSYELSKKENKVGSPEKPLSDLGLLSYRAYWSDTLITLLVEHQKEITIDEISSMTSMTTTDILHTAKTLNILRYYKGQHIIFLNEDILDRYNRLKAKKRRTIDPNRLIWKPPVFTASQLRFAW

Entity 9 Entity 9 polymer

Description description	DNA (207-mer)
Molecular weight formula_weight	63679.5 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	W

TCCGGAGGACTGTCCTCCGGGGACCCTATACGCGGCCGCCATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCGATAGCTTGTCGAGAAGTACTAG

Entity 10 Entity 10 polymer

Description description	DNA (207-mer)
Molecular weight formula_weight	64150.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I

CTAGTACTTCTCGACAAGCTATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCGATGGCGGCCGCGTATAGGGTCCCCGGAGGACAGTCCTCCGGA

Entity 11 Entity 11 non-polymer

Description description	CARBOXYMETHYL COENZYME *A
Molecular weight formula_weight	825.6 kDa
Source method src_method	syn
Copy count entity_count	1

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	3.40 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	393016

NuA4 HAT module bound to the nucleosome

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

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

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

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

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

Histone H2A

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 H2B 1.1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

7vvu__assembly_1__model_1

7vvu__assembly_1__model_1 | I(q)

7vvu__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Source Source

Entity 5 Entity 5 polymer

Polymer Polymer

Source Source