5j9u

Crystal structure of the NuA4 core complex

Method: X-RAY DIFFRACTION Dmax: 163.3 Å Quality: REASONABLE

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

Histone acetyltransferase ESA1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt Q08649

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 141–445 Fragment:UNP residues 141-445) Non-standard monomer:Yes (specific site not provided by mmCIF) Chromatin modification-related protein EAF6 × 1 (P47128) Enhancer of polycomb-like protein 1 × 1 (P43572) Chromatin modification-related protein YNG2 × 1 (P38806) X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;298 K;100mM NaCitrate (pH 6.5), 1.79M ammonium sulfate, 5%(w/v) glycerol Resolution 2.95 Å R-free 0.246
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 141–445 Fragment:UNP residues 141-445) Non-standard monomer:Yes (specific site not provided by mmCIF) Chromatin modification-related protein EAF6 × 1 (P47128) Enhancer of polycomb-like protein 1 × 1 (P43572) Chromatin modification-related protein YNG2 × 1 (P38806) X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;298 K;100mM NaCitrate (pH 6.5), 1.79M ammonium sulfate, 5%(w/v) glycerol Resolution 2.95 Å R-free 0.246
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain I; UniProt 141–445 Fragment:UNP residues 141-445) Non-standard monomer:Yes (specific site not provided by mmCIF) Chromatin modification-related protein EAF6 × 1 (P47128) Enhancer of polycomb-like protein 1 × 1 (P43572) Chromatin modification-related protein YNG2 × 1 (P38806) X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;298 K;100mM NaCitrate (pH 6.5), 1.79M ammonium sulfate, 5%(w/v) glycerol Resolution 2.95 Å R-free 0.246

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

13 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

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 Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain F; UniProt 1–113 Not recorded Histone acetyltransferase ESA1 × 1 (Q08649) Enhancer of polycomb-like protein 1 × 1 (P43572) Chromatin modification-related protein YNG2 × 1 (P38806) X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;298 K;100mM NaCitrate (pH 6.5), 1.79M ammonium sulfate, 5%(w/v) glycerol Resolution 2.95 Å R-free 0.246
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain B; UniProt 1–113 Not recorded Histone acetyltransferase ESA1 × 1 (Q08649) Enhancer of polycomb-like protein 1 × 1 (P43572) Chromatin modification-related protein YNG2 × 1 (P38806) X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;298 K;100mM NaCitrate (pH 6.5), 1.79M ammonium sulfate, 5%(w/v) glycerol Resolution 2.95 Å R-free 0.246
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain J; UniProt 1–113 Not recorded Histone acetyltransferase ESA1 × 1 (Q08649) Enhancer of polycomb-like protein 1 × 1 (P43572) Chromatin modification-related protein YNG2 × 1 (P38806) X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;298 K;100mM NaCitrate (pH 6.5), 1.79M ammonium sulfate, 5%(w/v) glycerol Resolution 2.95 Å R-free 0.246

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

7 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

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 Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain G; UniProt 50–400 Fragment:UNP residues 50-400 Histone acetyltransferase ESA1 × 1 (Q08649) Chromatin modification-related protein EAF6 × 1 (P47128) Chromatin modification-related protein YNG2 × 1 (P38806) X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;298 K;100mM NaCitrate (pH 6.5), 1.79M ammonium sulfate, 5%(w/v) glycerol Resolution 2.95 Å R-free 0.246
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 50–400 Fragment:UNP residues 50-400 Histone acetyltransferase ESA1 × 1 (Q08649) Chromatin modification-related protein EAF6 × 1 (P47128) Chromatin modification-related protein YNG2 × 1 (P38806) X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;298 K;100mM NaCitrate (pH 6.5), 1.79M ammonium sulfate, 5%(w/v) glycerol Resolution 2.95 Å R-free 0.246
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain N; UniProt 50–400 Fragment:UNP residues 50-400 Histone acetyltransferase ESA1 × 1 (Q08649) Chromatin modification-related protein EAF6 × 1 (P47128) Chromatin modification-related protein YNG2 × 1 (P38806) X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;298 K;100mM NaCitrate (pH 6.5), 1.79M ammonium sulfate, 5%(w/v) glycerol Resolution 2.95 Å R-free 0.246

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

9 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

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 Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain H; UniProt 1–120 Fragment:UNP residues 1-120 Histone acetyltransferase ESA1 × 1 (Q08649) Chromatin modification-related protein EAF6 × 1 (P47128) Enhancer of polycomb-like protein 1 × 1 (P43572) X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;298 K;100mM NaCitrate (pH 6.5), 1.79M ammonium sulfate, 5%(w/v) glycerol Resolution 2.95 Å R-free 0.246
2 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain D; UniProt 1–120 Fragment:UNP residues 1-120 Histone acetyltransferase ESA1 × 1 (Q08649) Chromatin modification-related protein EAF6 × 1 (P47128) Enhancer of polycomb-like protein 1 × 1 (P43572) X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;298 K;100mM NaCitrate (pH 6.5), 1.79M ammonium sulfate, 5%(w/v) glycerol Resolution 2.95 Å R-free 0.246
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain K; UniProt 1–120 Fragment:UNP residues 1-120 Histone acetyltransferase ESA1 × 1 (Q08649) Chromatin modification-related protein EAF6 × 1 (P47128) Enhancer of polycomb-like protein 1 × 1 (P43572) X-RAY DIFFRACTION X-ray crystallization conditions:EVAPORATION;298 K;100mM NaCitrate (pH 6.5), 1.79M ammonium sulfate, 5%(w/v) glycerol Resolution 2.95 Å R-free 0.246

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

6 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

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.

SAXS scattering curve SAXS Profile

SAXS profile for 5j9u

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5j9u
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5j9u
Deposition date deposition_date2016-04-11
Structure title titleCrystal structure of the NuA4 core complex
Keywords keywordsNuA4, nucleosome, histone, acetylation, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier48.05
Radius of gyration Rg (electron density) rg_electron47.78
Forward intensity I(0) i01114200000.00
Molecular weight molecular_weight278850.0 kDa
Excluded volume excluded_volume350120 ų
Envelope volume envelope_volume492990 ų
Hydration-shell volume shell_volume87057 ų
Envelope diameter envelope_diameter175.5
Shell Rg shell_rg50.92
Envelope Rg envelope_rg48.19
Shape Rg shape_rg47.72
Total Rg total_rg48.11
Total atoms total_atoms19676
Residues n_residues2350
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax163.3
Rg (real space) rg_real48.16
Rg uncertainty (real space) rg_real_error1.52
I(0) (real space) i0_real1.1140e+09
I(0) uncertainty (real space) i0_real_error1.9870e+07
Rg (reciprocal space) rg_reciprocal48.05
I(0) (reciprocal space) i0_reciprocal1114000000.0000
Solution quality estimate total_estimate0.6384
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary54.4
Skewness Skewness skewness0.455
Kurtosis Kurtosis kurtosis-0.110
Angular range angular_range— – 0.1650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha110200000.0000
Real-space data points n_real_points34
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.805; Stabil: 1.000; Sysdev: 0.044; Positv: 1.000; Valcen: 0.999; Smooth: 0.750

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd5j9ua_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamilyd.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family familyd.108.1.1 — N-acetyl transferase, NAT
Domain ID domain_idd5j9ue_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamilyd.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family familyd.108.1.1 — N-acetyl transferase, NAT
Domain ID domain_idd5j9ui_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.108 — Acyl-CoA N-acyltransferases (Nat)
Superfamily Superfamily superfamilyd.108.1 — Acyl-CoA N-acyltransferases (Nat)
Family Family familyd.108.1.1 — N-acetyl transferase, NAT

CATH v4.4 (9 domains)

Domain ID domain_id5j9uA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily60 — N-acetyl transferase-like
Domain ID domain_id5j9uA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily30 — Gcn5-related N-acetyltransferase (GNAT)
Domain ID domain_id5j9uA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id5j9uE01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily60 — N-acetyl transferase-like
Domain ID domain_id5j9uE02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily30 — Gcn5-related N-acetyltransferase (GNAT)
Domain ID domain_id5j9uE03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
Domain ID domain_id5j9uI01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily60 — N-acetyl transferase-like
Domain ID domain_id5j9uI02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology630 — Aminopeptidase
Homologous superfamily homologous superfamily30 — Gcn5-related N-acetyltransferase (GNAT)
Domain ID domain_id5j9uI03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

8. Citations (1)

9. Files and Curves (10)