9VKW | pdb_00009vkw

Cryo-EM structure of the NuA3 complex bound to Ace-coenzyme A

• PDB DOI: https://doi.org/10.2210/pdb9VKW/pdb
• EM Map EMD-65145: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Trichoplusia ni
• Mutation(s): No 


• Deposited: 2025-06-24 Released: 2025-12-10 
• Deposition Author(s): Zhang, H.Q., Wang, Y.R.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.13 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of the NuA3 complex bound to Acetyl-coenzyme A

Wang, Y.R., Zhang, H.Q.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 250.72 kDa 
• Atom Count: 10,735 
• Modeled Residue Count: 1,300 
• Deposited Residue Count: 2,155 
• Unique protein chains: 5

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone acetyltransferase SAS3	A	831	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: SAS3, YBL052C, YBL0507, YBL0515 EC: 2.3.1.48
UniProt
Find proteins for P34218 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P34218  Go to UniProtKB:  P34218

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NuA3 HAT complex component NTO1	B	748	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: NTO1, YPR031W
UniProt
Find proteins for Q12311 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12311  Go to UniProtKB:  Q12311

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein YNG1	C	219	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: YNG1, YOR064C, YOR29-15
UniProt
Find proteins for Q08465 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q08465  Go to UniProtKB:  Q08465

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription initiation factor TFIID subunit 14	D [auth E]	244	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: TAF14, ANC1, CST10, SWP29, TAF30, TFG3, YPL129W
UniProt
Find proteins for P35189 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P35189  Go to UniProtKB:  P35189

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromatin modification-related protein EAF6	E [auth D]	113	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: EAF6, YJR082C, J1854
UniProt
Find proteins for P47128 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P47128  Go to UniProtKB:  P47128

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACO (Subject of Investigation/LOI)	G [auth A]	ACETYL COENZYME *A C23 H38 N7 O17 P3 S ZSLZBFCDCINBPY-ZSJPKINUSA-N
ZN (Subject of Investigation/LOI)	F [auth A], H [auth B], I [auth B], J [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.13 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.17.1_3660
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-12-10 
Deposition Author(s): Zhang, H.Q., Wang, Y.R.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2025-12-10
  Type: Initial release