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- PDB-9dpd: Cryo-EM structure of SerRS dimer in complex with one SIRT2 -

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Basic information

Entry
Database: PDB / ID: 9dpd
TitleCryo-EM structure of SerRS dimer in complex with one SIRT2
Components
  • NAD-dependent protein deacetylase sirtuin-2
  • Serine--tRNA ligase, cytoplasmic
KeywordsTRANSLATION / Complex / Enzyme
Function / homology
Function and homology information


selenocysteine-tRNA ligase activity / tRNA C3-cytosine methylation / negative regulation of vascular endothelial growth factor production / selenocysteine incorporation / selenium compound metabolic process / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / cellular response to caloric restriction / histone methacryllysine demethacrylase activity ...selenocysteine-tRNA ligase activity / tRNA C3-cytosine methylation / negative regulation of vascular endothelial growth factor production / selenocysteine incorporation / selenium compound metabolic process / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / cellular response to caloric restriction / histone methacryllysine demethacrylase activity / histone benzoyllysine debenzoylase activity / positive regulation of oocyte maturation / negative regulation of striated muscle tissue development / negative regulation of oligodendrocyte progenitor proliferation / negative regulation of satellite cell differentiation / histone H4K16 deacetylase activity, NAD-dependent / positive regulation of attachment of spindle microtubules to kinetochore / tRNA methyltransferase complex / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / peptidyl-lysine deacetylation / positive regulation of meiotic nuclear division / paranodal junction / lateral loop / Cytosolic tRNA aminoacylation / mitotic nuclear membrane reassembly / regulation of exit from mitosis / tubulin deacetylase activity / regulation of phosphorylation / paranode region of axon / myelination in peripheral nervous system / tubulin deacetylation / negative regulation of peptidyl-threonine phosphorylation / tRNA modification / regulation of myelination / positive regulation of fatty acid biosynthetic process / Schmidt-Lanterman incisure / protein acetyllysine N-acetyltransferase / NAD-dependent protein lysine deacetylase activity / histone deacetylase activity, NAD-dependent / rDNA heterochromatin formation / juxtaparanode region of axon / Initiation of Nuclear Envelope (NE) Reformation / protein deacetylation / chromatin silencing complex / histone deacetylase activity / meiotic spindle / negative regulation of reactive oxygen species metabolic process / protein lysine deacetylase activity / positive regulation of cell division / positive regulation of DNA binding / negative regulation of fat cell differentiation / response to redox state / histone acetyltransferase binding / lipid catabolic process / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / subtelomeric heterochromatin formation / glial cell projection / positive regulation of execution phase of apoptosis / Selenocysteine synthesis / negative regulation of angiogenesis / heterochromatin / centriole / cellular response to epinephrine stimulus / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / substantia nigra development / negative regulation of autophagy / ubiquitin binding / negative regulation of protein catabolic process / myelin sheath / epigenetic regulation of gene expression / mitotic spindle / spindle / histone deacetylase binding / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / growth cone / cellular response to oxidative stress / midbody / heterochromatin formation / cellular response to hypoxia / microtubule / DNA-binding transcription factor binding / tRNA binding / proteasome-mediated ubiquitin-dependent protein catabolic process / molecular adaptor activity / regulation of cell cycle / perikaryon / cytoplasmic translation / chromosome, telomeric region / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromosome / translation / negative regulation of DNA-templated transcription / centrosome / chromatin binding / nucleolus / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / enzyme binding
Similarity search - Function
Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Sirtuin, class I / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : ...Serine-tRNA synthetase, type1, N-terminal / Seryl-tRNA synthetase N-terminal domain / Serine-tRNA ligase, type1 / Serine-tRNA ligase catalytic core domain / Serine-tRNA synthetase, type1, N-terminal domain superfamily / Sirtuin, class I / Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Aminoacyl-tRNA synthetase, class II (G/ P/ S/T) / tRNA synthetase class II core domain (G, H, P, S and T) / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / Aminoacyl-tRNA synthetase, class II / Aminoacyl-transfer RNA synthetases class-II family profile. / DHS-like NAD/FAD-binding domain superfamily / Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
Similarity search - Domain/homology
Chem-AR6 / Serine--tRNA ligase, cytoplasmic / NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.87 Å
AuthorsYang, J. / Zhang, Q. / Zhang, H. / Lander, G.C. / Yang, X.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Nat Commun / Year: 2026
Title: A metabolite-bridged complex between SerRS and SIRT2 couples NAD⁺ metabolism to translation control.
Authors: Qian Zhang / Huimin Zhang / Marscha Hirschi / Sheng Li / Gabriel C Lander / Jie Yang / Xiang-Lei Yang /
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 ...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.
History
DepositionSep 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Serine--tRNA ligase, cytoplasmic
D: Serine--tRNA ligase, cytoplasmic
C: NAD-dependent protein deacetylase sirtuin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,5194
Polymers160,9603
Non-polymers5591
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Serine--tRNA ligase, cytoplasmic / Seryl-tRNA synthetase / SerRS / Seryl-tRNA(Ser/Sec) synthetase


Mass: 58863.211 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SARS1, SARS, SERS
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P49591, serine-tRNA ligase
#2: Protein NAD-dependent protein deacetylase sirtuin-2 / NAD-dependent protein defatty-acylase sirtuin-2 / Regulatory protein SIR2 homolog 2 / SIR2-like protein 2


Mass: 43233.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT2, SIR2L, SIR2L2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q8IXJ6, protein acetyllysine N-acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#3: Chemical ChemComp-AR6 / [(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 / Adenosine-5-Diphosphoribose


Mass: 559.316 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex of SerRS dimer with SIRT2 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 25mM HEPES-Na pH7.5, 150mM NaCl
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1200 nm / Nominal defocus min: 700 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
8PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
3D reconstructionResolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 590607 / Symmetry type: POINT
RefinementHighest resolution: 3.87 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036817
ELECTRON MICROSCOPYf_angle_d0.6649231
ELECTRON MICROSCOPYf_dihedral_angle_d8.364953
ELECTRON MICROSCOPYf_chiral_restr0.0451021
ELECTRON MICROSCOPYf_plane_restr0.0051177

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