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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 / negative regulation of vascular endothelial growth factor production / selenocysteine incorporation / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / negative regulation of striated muscle tissue development / negative regulation of satellite cell differentiation ...selenocysteine-tRNA ligase activity / negative regulation of vascular endothelial growth factor production / selenocysteine incorporation / serine-tRNA ligase / serine-tRNA ligase activity / seryl-tRNA aminoacylation / cellular response to caloric restriction / negative regulation of oligodendrocyte progenitor proliferation / negative regulation of striated muscle tissue development / negative regulation of satellite cell differentiation / histone H4K16 deacetylase activity, NAD-dependent / positive regulation of attachment of spindle microtubules to kinetochore / peptidyl-lysine deacetylation / positive regulation of meiotic nuclear division / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / paranodal junction / tubulin deacetylation / lateral loop / Cytosolic tRNA aminoacylation / regulation of phosphorylation / mitotic nuclear membrane reassembly / tubulin deacetylase activity / NLRP3 inflammasome complex assembly / tRNA modification / negative regulation of NLRP3 inflammasome complex assembly / paranode region of axon / regulation of exit from mitosis / negative regulation of peptidyl-threonine phosphorylation / Schmidt-Lanterman incisure / positive regulation of fatty acid biosynthetic process / protein acetyllysine N-acetyltransferase / NAD-dependent protein lysine deacetylase activity / myelination in peripheral nervous system / rDNA heterochromatin formation / protein deacetylation / histone deacetylase activity, NAD-dependent / positive regulation of oocyte maturation / juxtaparanode region of axon / Initiation of Nuclear Envelope (NE) Reformation / chromatin silencing complex / meiotic spindle / protein lysine deacetylase activity / histone deacetylase activity / regulation of myelination / response to redox state / positive regulation of DNA binding / negative regulation of fat cell differentiation / histone acetyltransferase binding / negative regulation of reactive oxygen species metabolic process / positive regulation of cell division / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / Selenocysteine synthesis / positive regulation of execution phase of apoptosis / glial cell projection / subtelomeric heterochromatin formation / lipid catabolic process / heterochromatin / cellular response to epinephrine stimulus / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / substantia nigra development / epigenetic regulation of gene expression / negative regulation of angiogenesis / negative regulation of autophagy / meiotic cell cycle / ubiquitin binding / centriole / negative regulation of protein catabolic process / autophagy / spindle / histone deacetylase binding / mitotic spindle / myelin sheath / heterochromatin formation / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / chromosome / growth cone / cellular response to oxidative stress / midbody / cellular response to hypoxia / DNA-binding transcription factor binding / molecular adaptor activity / microtubule / proteasome-mediated ubiquitin-dependent protein catabolic process / perikaryon / cytoplasmic translation / tRNA binding / chromosome, telomeric region / regulation of cell cycle / RNA polymerase II cis-regulatory region sequence-specific DNA binding / translation / innate immune response / cell division / negative regulation of DNA-templated transcription / chromatin binding / centrosome / nucleolus / perinuclear region of cytoplasm / 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: To Be Published
Title: Cryo-EM structure of SerRS dimer in complex with one SIRT2
Authors: Yang, J. / Zhang, Q. / Lander, G.C. / Yang, X.
History
DepositionSep 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 18, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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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