9DPD | pdb_00009dpd

Cryo-EM structure of SerRS dimer in complex with one SIRT2

• PDB DOI: https://doi.org/10.2210/pdb9DPD/pdb
• EM Map EMD-47103: EMDB EMDataResource

• Classification: TRANSLATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): No 


• Deposited: 2024-09-21 Released: 2026-03-18 
• Deposition Author(s): Yang, J., Zhang, Q., Zhang, H., Lander, G.C., Yang, X.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.87 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

A metabolite-bridged complex between SerRS and SIRT2 couples NAD+ metabolism to translation control.

Zhang, Q., Zhang, H., Hirschi, M., Li, S., Lander, G.C., Yang, J., Yang, X.L.

(2026) Nat Commun 17

• PubMed: 42420298 
• DOI: https://doi.org/10.1038/s41467-026-75266-4
• Primary Citation Related Structures: 
  9DPD, 9DPI


• PubMed Abstract: 
  

  Cellular homeostasis requires tight coordination between metabolic and translational networks. Here we identify a direct molecular link between these processes through a cryo-EM structure of human cytosolic seryl-tRNA synthetase (SerRS) in complex with the NAD⁺-dependent deacetylase SIRT2. This interaction is promoted by the NAD⁺ metabolite ADP-ribose (ADPR), which acts as a molecular bridge between the two enzymes. Within the SIRT2 active site, ADPR engages SerRS residue K414 located in a flexible catalytic-domain loop. Acetylation of K414 is dispensable for binding. Functionally, complex formation inhibits SIRT2 deacetylase activity by blocking substrate access, while SIRT2 association suppresses SerRS aminoacylation activity by preventing tRNA binding. Thus, SerRS and SIRT2 mutually regulate each other, with ADPR enhancing while tRNA attenuating their interaction. Oxidative stress promotes this interaction via a PARP1-dependent pathway, revealing an ADPR-responsive regulatory module that couples metabolic state to translational output. This regulatory module is likely conserved across vertebrates.

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Organizational Affiliation: 
• Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, China.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
Department of Medicine and UCSD DXMS proteomics Resource, University of California, San Diego, La Jolla, CA, USA.
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. [e-mail].
Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA. [e-mail].
Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA. [e-mail].
Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 161.52 kDa 
• Atom Count: 6,664 
• Modeled Residue Count: 831 
• Deposited Residue Count: 1,417 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine--tRNA ligase, cytoplasmic	A [auth B], B [auth D]	514	Homo sapiens	Mutation(s): 0  Gene Names: SARS1, SARS, SERS EC: 6.1.1.11
UniProt & NIH Common Fund Data Resources
Find proteins for P49591 (Homo sapiens) Explore P49591  Go to UniProtKB:  P49591
PHAROS:  P49591 GTEx:  ENSG00000031698

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-2	C	389	Homo sapiens	Mutation(s): 0  Gene Names: SIRT2, SIR2L, SIR2L2 EC: 2.3.1.286 (PDB Primary Data), 2.3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IXJ6 (Homo sapiens) Explore Q8IXJ6  Go to UniProtKB:  Q8IXJ6
PHAROS:  Q8IXJ6 GTEx:  ENSG00000068903

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AR6 (Subject of Investigation/LOI)	D [auth C]	[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL[HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-ZQSHOCFMSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.87 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-03-18 
Deposition Author(s): Yang, J., Zhang, Q., Zhang, H., Lander, G.C., Yang, X.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History  

• Version 1.0: 2026-03-18
  Type: Initial release
  
• Version 1.1: 2026-09-30
  Changes: Data collection, Database references