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5y81

NuA4 TEEAA sub-complex

Method: ELECTRON MICROSCOPY Dmax: 214.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Transcription-associated protein 1

OrganismNot specified

UniProt P38811

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 1–2627 Chain B； UniProt 2630–3744 Fragment：UNP residues 2630-3744 Fragment：UNP residues 1-2627 Chromatin modification-related protein EAF1 × 1 （Q06337） Eaf1-disorder domain × 1 Chromatin modification-related protein EAF5 × 1 （P39995） Actin-related protein 4 × 1 （P80428） Actin × 1 （P60010） Chromatin modification-related protein EAF1 × 1 （Q06337） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.70 Å

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.

Other PDB Difference from Current Entry 5Y81 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5OJS Cryo-EM structure of the SAGA and NuA4 coactivator subunit Tra1 Deposited 2017-07-24 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain T 1–3744（3744 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；Two subsequent applications of protein were required to achieve the desired particle density on grids. Each application was followed by 20 sec waiting time, with a short 0.5 sec blotting after first application and 5 sec blotting after the second.
Resolution 3.70 Å
6IG9 Tra1 subunit from Saccharomyces cerevisiae SAGA complex Deposited 2018-09-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain T 1–3744（3744 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5；20mM HEPES pH 8.5 150mM Nacl
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 4 seconds and wait for 30 seconds before plunging
Resolution 4.60 Å
6T9I cryo-EM structure of transcription coactivator SAGA Deposited 2019-10-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain T 1–3744（3744 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.90 Å
6T9J SAGA Tra1 module Deposited 2019-10-28 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain T 1–3744（3744 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；Solution were made from stock solution
cryo-EM vitrification conditions Cryogen ETHANE；blot for 4 seconds before plunging
Resolution 3.40 Å
7VVY TRA module of NuA4 Deposited 2021-11-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain L 1–3744（3744 aa）
Not recorded MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.10 Å
7VVZ NuA4 bound to the nucleosome Deposited 2021-11-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric
Chain L 1–3744（3744 aa）
Not recorded CMC CARBOXYMETHYL COENZYME *A × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 8.80 Å
7YFN Core module of the NuA4 complex in S. cerevisiae Deposited 2022-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain T 1–3744（3744 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7YFP The NuA4 histone acetyltransferase complex from S. cerevisiae Deposited 2022-07-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain T 1–3744（3744 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8ESC Structure of the Yeast NuA4 Histone Acetyltransferase Complex Deposited 2022-10-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain Z 1–3744（3744 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

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

View Construct and Data Evidence
UniProt name TRA1_YEAST
Isoform —
PDB entities 1, 5
Chains and sequence ranges Author chain B； PDBConstruct 1–1115； UniProt 2630–3744 Author chain A； PDBConstruct 1–2627； UniProt 1–2627

Chromatin modification-related protein EAF1

OrganismNot specified

UniProt Q06337

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain C； UniProt 647–982 Chain E； UniProt 357–397 Fragment：UNP residues 647-982 Fragment：UNP residues 357-397 Transcription-associated protein 1 × 1 （P38811） Eaf1-disorder domain × 1 Chromatin modification-related protein EAF5 × 1 （P39995） Transcription-associated protein 1 × 1 （P38811） Actin-related protein 4 × 1 （P80428） Actin × 1 （P60010） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.70 Å

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.

Other PDB Difference from Current Entry 5Y81 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
7VVY TRA module of NuA4 Deposited 2021-11-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–982（982 aa）
Not recorded MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.10 Å
7VVZ NuA4 bound to the nucleosome Deposited 2021-11-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric
Chain E 1–982（982 aa）
Not recorded CMC CARBOXYMETHYL COENZYME *A × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 8.80 Å
8ESC Structure of the Yeast NuA4 Histone Acetyltransferase Complex Deposited 2022-10-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–982（982 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name EAF1_YEAST
Isoform —
PDB entities 2, 8
Chains and sequence ranges Author chain C； PDBConstruct 2–336； UniProt 647–982 Author chain E； PDBConstruct 1–41； UniProt 357–397

Chromatin modification-related protein EAF5

OrganismNot specified

UniProt P39995

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain H； UniProt 1–279 Not recorded Transcription-associated protein 1 × 1 （P38811） Chromatin modification-related protein EAF1 × 1 （Q06337） Eaf1-disorder domain × 1 Transcription-associated protein 1 × 1 （P38811） Actin-related protein 4 × 1 （P80428） Actin × 1 （P60010） Chromatin modification-related protein EAF1 × 1 （Q06337） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.70 Å

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name EAF5_YEAST
Isoform —
PDB entities 4
Chains and sequence ranges Author chain H； PDBConstruct 1–279； UniProt 1–279

Actin-related protein 4

OrganismNot specified

UniProt P80428

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain F； UniProt 1–489 Not recorded Transcription-associated protein 1 × 1 （P38811） Chromatin modification-related protein EAF1 × 1 （Q06337） Eaf1-disorder domain × 1 Chromatin modification-related protein EAF5 × 1 （P39995） Transcription-associated protein 1 × 1 （P38811） Actin × 1 （P60010） Chromatin modification-related protein EAF1 × 1 （Q06337） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.70 Å

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.

Other PDB Difference from Current Entry 5Y81 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3QB0 Crystal structure of Actin-related protein Arp4 from S. cerevisiae complexed with ATP Deposited 2011-01-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–489（489 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；27 % PEG2000MME, 0.1 M HEPES-NaOH, 6 % D+-Trehalose, 50 mM Glycine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.40 Å R-free 0.221
3QB0 Crystal structure of Actin-related protein Arp4 from S. cerevisiae complexed with ATP Deposited 2011-01-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–489（489 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；27 % PEG2000MME, 0.1 M HEPES-NaOH, 6 % D+-Trehalose, 50 mM Glycine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.40 Å R-free 0.221
3QB0 Crystal structure of Actin-related protein Arp4 from S. cerevisiae complexed with ATP Deposited 2011-01-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–489（489 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；27 % PEG2000MME, 0.1 M HEPES-NaOH, 6 % D+-Trehalose, 50 mM Glycine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.40 Å R-free 0.221
3QB0 Crystal structure of Actin-related protein Arp4 from S. cerevisiae complexed with ATP Deposited 2011-01-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–489（489 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；27 % PEG2000MME, 0.1 M HEPES-NaOH, 6 % D+-Trehalose, 50 mM Glycine, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 3.40 Å R-free 0.221
5I9E Crystal structure of a nuclear actin ternary complex Deposited 2016-02-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–489（489 aa）
Not recorded MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291 K；polyethylene glycol (PEG) 3350, citric acid, BIS-TRIS propane
Resolution 2.80 Å R-free 0.284
5I9E Crystal structure of a nuclear actin ternary complex Deposited 2016-02-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–489（489 aa）
Not recorded MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291 K；polyethylene glycol (PEG) 3350, citric acid, BIS-TRIS propane
Resolution 2.80 Å R-free 0.284
5NBL Crystal structure of the Arp4-N-actin(APO-state) heterodimer bound by a nanobody Deposited 2017-03-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–489（489 aa）
Not recorded CA CALCIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1 mM ADP, 0.2 mM CaCl2, 1.3-1.5 M sodium malonate at pH 6.0, Subtilisin (1/6000; w(subtilisin)/w(protein))
Resolution 2.80 Å R-free 0.204
5NBL Crystal structure of the Arp4-N-actin(APO-state) heterodimer bound by a nanobody Deposited 2017-03-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–489（489 aa）
Not recorded CA CALCIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1 mM ADP, 0.2 mM CaCl2, 1.3-1.5 M sodium malonate at pH 6.0, Subtilisin (1/6000; w(subtilisin)/w(protein))
Resolution 2.80 Å R-free 0.204
5NBM Crystal structure of the Arp4-N-actin(ATP-state) heterodimer bound by a nanobody Deposited 2017-03-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–489（489 aa）
Not recorded CA CALCIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1 mM ATP, 0.2 mM CaCl2, 1.3-1.5 M sodium malonate pH 6.0, Subtilisin (1/6000; w(subtilisin)/w(protein))
Resolution 3.40 Å R-free 0.193
5NBM Crystal structure of the Arp4-N-actin(ATP-state) heterodimer bound by a nanobody Deposited 2017-03-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–489（489 aa）
Not recorded CA CALCIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1 mM ATP, 0.2 mM CaCl2, 1.3-1.5 M sodium malonate pH 6.0, Subtilisin (1/6000; w(subtilisin)/w(protein))
Resolution 3.40 Å R-free 0.193
5NBN Crystal structure of the Arp4-N-actin-Arp8-Ino80HSA module of INO80 Deposited 2017-03-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–489（489 aa）
Not recorded CA CALCIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 LAR LATRUNCULIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M sodium citrate tribasic dihydrate, 18% (w/v) polyethylene glycol 3,350, latrunculin A solved in DMSO molar ration 1:1.5 (protein : latrunculin A)
Resolution 4.00 Å R-free 0.242
5NBN Crystal structure of the Arp4-N-actin-Arp8-Ino80HSA module of INO80 Deposited 2017-03-02 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–489（489 aa）
Not recorded CA CALCIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 LAR LATRUNCULIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M sodium citrate tribasic dihydrate, 18% (w/v) polyethylene glycol 3,350, latrunculin A solved in DMSO molar ration 1:1.5 (protein : latrunculin A)
Resolution 4.00 Å R-free 0.242
7VVY TRA module of NuA4 Deposited 2021-11-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain F 1–489（489 aa）
Not recorded MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.10 Å
7VVZ NuA4 bound to the nucleosome Deposited 2021-11-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric
Chain F 1–489（489 aa）
Not recorded CMC CARBOXYMETHYL COENZYME *A × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 8.80 Å
8A5A Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of INO80 Deposited 2022-06-14 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain W 1–489（489 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8A5O Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of S. cerevisiae INO80 Deposited 2022-06-15 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain W 1–489（489 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8ESC Structure of the Yeast NuA4 Histone Acetyltransferase Complex Deposited 2022-10-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 1–489（489 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å

10 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ARP4_YEAST
Isoform —
PDB entities 6
Chains and sequence ranges Author chain F； PDBConstruct 2–490； UniProt 1–489

Actin

OrganismNot specified

UniProt P60010

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain G； UniProt 1–375 Not recorded Transcription-associated protein 1 × 1 （P38811） Chromatin modification-related protein EAF1 × 1 （Q06337） Eaf1-disorder domain × 1 Chromatin modification-related protein EAF5 × 1 （P39995） Transcription-associated protein 1 × 1 （P38811） Actin-related protein 4 × 1 （P80428） Chromatin modification-related protein EAF1 × 1 （Q06337） ELECTRON MICROSCOPY cryo-EM buffer：pH 8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 4.70 Å

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.

Other PDB Difference from Current Entry 5Y81 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1YAG STRUCTURE OF THE YEAST ACTIN-HUMAN GELSOLIN SEGMENT 1 COMPLEX Deposited 1998-10-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–375（375 aa）
Not recorded MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 1.90 Å R-free 0.231
1YAG STRUCTURE OF THE YEAST ACTIN-HUMAN GELSOLIN SEGMENT 1 COMPLEX Deposited 1998-10-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–375（375 aa）
Not recorded MG MAGNESIUM ION × 2 SO4 SULFATE ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.50
Resolution 1.90 Å R-free 0.231
1YVN THE YEAST ACTIN VAL 159 ASN MUTANT COMPLEX WITH HUMAN GELSOLIN SEGMENT 1. Deposited 1999-03-23 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–375（375 aa）
Mutation：V159N MG MAGNESIUM ION × 1 SO4 SULFATE ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；0.1 M HEPES, 1.60 M (NH4)2SO4, 2 MM MG-ATP, PH=8.0.
Resolution 2.10 Å R-free 0.235
1YVN THE YEAST ACTIN VAL 159 ASN MUTANT COMPLEX WITH HUMAN GELSOLIN SEGMENT 1. Deposited 1999-03-23 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–375（375 aa）
Mutation：V159N MG MAGNESIUM ION × 2 SO4 SULFATE ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；0.1 M HEPES, 1.60 M (NH4)2SO4, 2 MM MG-ATP, PH=8.0.
Resolution 2.10 Å R-free 0.235
5NBL Crystal structure of the Arp4-N-actin(APO-state) heterodimer bound by a nanobody Deposited 2017-03-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–375（375 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1 mM ADP, 0.2 mM CaCl2, 1.3-1.5 M sodium malonate at pH 6.0, Subtilisin (1/6000; w(subtilisin)/w(protein))
Resolution 2.80 Å R-free 0.204
5NBL Crystal structure of the Arp4-N-actin(APO-state) heterodimer bound by a nanobody Deposited 2017-03-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–375（375 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1 mM ADP, 0.2 mM CaCl2, 1.3-1.5 M sodium malonate at pH 6.0, Subtilisin (1/6000; w(subtilisin)/w(protein))
Resolution 2.80 Å R-free 0.204
5NBM Crystal structure of the Arp4-N-actin(ATP-state) heterodimer bound by a nanobody Deposited 2017-03-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–375（375 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1 mM ATP, 0.2 mM CaCl2, 1.3-1.5 M sodium malonate pH 6.0, Subtilisin (1/6000; w(subtilisin)/w(protein))
Resolution 3.40 Å R-free 0.193
5NBM Crystal structure of the Arp4-N-actin(ATP-state) heterodimer bound by a nanobody Deposited 2017-03-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–375（375 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1 mM ATP, 0.2 mM CaCl2, 1.3-1.5 M sodium malonate pH 6.0, Subtilisin (1/6000; w(subtilisin)/w(protein))
Resolution 3.40 Å R-free 0.193
5NBN Crystal structure of the Arp4-N-actin-Arp8-Ino80HSA module of INO80 Deposited 2017-03-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–375（375 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 LAR LATRUNCULIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M sodium citrate tribasic dihydrate, 18% (w/v) polyethylene glycol 3,350, latrunculin A solved in DMSO molar ration 1:1.5 (protein : latrunculin A)
Resolution 4.00 Å R-free 0.242
5NBN Crystal structure of the Arp4-N-actin-Arp8-Ino80HSA module of INO80 Deposited 2017-03-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–375（375 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 LAR LATRUNCULIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M sodium citrate tribasic dihydrate, 18% (w/v) polyethylene glycol 3,350, latrunculin A solved in DMSO molar ration 1:1.5 (protein : latrunculin A)
Resolution 4.00 Å R-free 0.242
7VVY TRA module of NuA4 Deposited 2021-11-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain G 1–375（375 aa）
Not recorded MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.10 Å
7VVZ NuA4 bound to the nucleosome Deposited 2021-11-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 19 PDB declaration: 21-meric
Chain G 1–375（375 aa）
Not recorded CMC CARBOXYMETHYL COENZYME *A × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 8.80 Å
7YFN Core module of the NuA4 complex in S. cerevisiae Deposited 2022-07-08 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 4–375（372 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7YFP The NuA4 histone acetyltransferase complex from S. cerevisiae Deposited 2022-07-08 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 4–375（372 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8A5A Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of INO80 Deposited 2022-06-14 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain V 1–375（375 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8A5O Structure of Arp4-Ies4-N-actin-Arp8-Ino80HSA subcomplex (A-module) of S. cerevisiae INO80 Deposited 2022-06-15 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain V 1–375（375 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 3 MG MAGNESIUM ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8ESC Structure of the Yeast NuA4 Histone Acetyltransferase Complex Deposited 2022-10-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–375（375 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.9
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9GO5 CryoEM Reconstruction of Yeast ADP-Actin Filament at 2.5 A resolution. Deposited 2024-09-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric
Chain A 1–375（375 aa）
Chain B 1–375（375 aa）
Chain C 1–375（375 aa）
Chain D 1–375（375 aa）
Chain E 1–375（375 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 8；50 mM KCl, 1 mM MgCl2, 1 mM EGTA, 10 mM Tris
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å

13 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ACT_YEAST
Isoform —
PDB entities 7
Chains and sequence ranges Author chain G； PDBConstruct 1–375； UniProt 1–375

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 5y81

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5y81
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5y81
Deposition date deposition_date2017-08-18
Structure title titleNuA4 TEEAA sub-complex
Keywords keywordsNuA4 complex, Histone acetyltransferases, Tra1/TRRAP, PIKK family, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier68.82 Å
Radius of gyration Rg (electron density) rg_electron69.27 Å
Forward intensity I(0) i02369650000.00
Molecular weight molecular_weight361480.0 kDa
Excluded volume excluded_volume430940 ų
Envelope volume envelope_volume939900 ų
Hydration-shell volume shell_volume119590 ų
Envelope diameter envelope_diameter233.6 Å
Shell Rg shell_rg62.68 Å
Envelope Rg envelope_rg67.60 Å
Shape Rg shape_rg69.26 Å
Total Rg total_rg69.15 Å
Total atoms total_atoms25712
Residues n_residues4455
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax214.7 Å
Rg (real space) rg_real68.97 Å
Rg uncertainty (real space) rg_real_error1.79 Å
I(0) (real space) i0_real2.3700e+09
I(0) uncertainty (real space) i0_real_error5.2760e+07
Rg (reciprocal space) rg_reciprocal68.10 Å
I(0) (reciprocal space) i0_reciprocal2366000000.0000
Solution quality estimate total_estimate0.8401
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary65.3 Å
Skewness Skewness skewness0.374
Kurtosis Kurtosis kurtosis-0.510
Angular range angular_range— – 0.1150 Å−1
Current regularization parameter α current_alpha0.0003
Highest regularization parameter α highest_alpha213900000.0000
Real-space data points n_real_points24
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.970; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.016
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

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8. Citations (1)

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9. Files and Curves (10)