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- EMDB-47103: Cryo-EM structure of SerRS dimer in complex with one SIRT2 -

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Basic information

Entry
Database: EMDB / ID: EMD-47103
TitleCryo-EM structure of SerRS dimer in complex with one SIRT2
Map data
Sample
  • Complex: Ternary complex of SerRS dimer with SIRT2
    • Protein or peptide: Serine--tRNA ligase, cytoplasmic
    • Protein or peptide: NAD-dependent protein deacetylase sirtuin-2
  • Ligand: [(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
KeywordsComplex / Enzyme / TRANSLATION
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
Serine--tRNA ligase, cytoplasmic / NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.87 Å
AuthorsYang J / Zhang Q / Zhang H / Lander GC / Yang X
Funding support United States, 1 items
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 GC / Yang X
History
DepositionSep 21, 2024-
Header (metadata) releaseMar 18, 2026-
Map releaseMar 18, 2026-
UpdateMar 18, 2026-
Current statusMar 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47103.png

Downloads & links

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Map

FileDownload / File: emd_47103.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.15 Å/pix.
x 256 pix.
= 294.4 Å		1.15 Å/pix.
x 256 pix.
= 294.4 Å		1.15 Å/pix.
x 256 pix.
= 294.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.15 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.651
Minimum - Maximum-5.6432023 - 7.140884
Average (Standard dev.)0.00045422598 (±0.10897226)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 294.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_47103_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_47103_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of SerRS dimer with SIRT2

EntireName: Ternary complex of SerRS dimer with SIRT2
Components
  • Complex: Ternary complex of SerRS dimer with SIRT2
    • Protein or peptide: Serine--tRNA ligase, cytoplasmic
    • Protein or peptide: NAD-dependent protein deacetylase sirtuin-2
  • Ligand: [(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

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Supramolecule #1: Ternary complex of SerRS dimer with SIRT2

SupramoleculeName: Ternary complex of SerRS dimer with SIRT2 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Serine--tRNA ligase, cytoplasmic

MacromoleculeName: Serine--tRNA ligase, cytoplasmic / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: serine-tRNA ligase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 58.863211 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MVLDLDLFRV DKGGDPALIR ETQEKRFKDP GLVDQLVKAD SEWRRCRFRA DNLNKLKNLC SKTIGEKMKK KEPVGDDESV PENVLSFDD LTADALANLK VSQIKKVRLL IDEAILKCDA ERIKLEAERF ENLREIGNLL HPSVPISNDE DVDNKVERIW G DCTVRKKY ...String:
MVLDLDLFRV DKGGDPALIR ETQEKRFKDP GLVDQLVKAD SEWRRCRFRA DNLNKLKNLC SKTIGEKMKK KEPVGDDESV PENVLSFDD LTADALANLK VSQIKKVRLL IDEAILKCDA ERIKLEAERF ENLREIGNLL HPSVPISNDE DVDNKVERIW G DCTVRKKY SHVDLVVMVD GFEGEKGAVV AGSRGYFLKG VLVFLEQALI QYALRTLGSR GYIPIYTPFF MRKEVMQEVA QL SQFDEEL YKVIGKGSEK SDDNSYDEKY LIATSEQPIA ALHRDEWLRP EDLPIKYAGL STCFRQEVGS HGRDTRGIFR VHQ FEKIEQ FVYSSPHDNK SWEMFEEMIT TAEEFYQSLG IPYHIVNIVS GSLNHAASKK LDLEAWFPGS GAFRELVSCS NCTD YQARR LRIRYGQTKK MMDKVEFVHM LNATMCATTR TICAILENYQ TEKGITVPEK LKEFMPPGLQ ELIPFVKPAP IEQEP SKKQ KKQHEGSKKK AAARDVTLEN RLQNMEVTDA

UniProtKB: Serine--tRNA ligase, cytoplasmic

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Macromolecule #2: NAD-dependent protein deacetylase sirtuin-2

MacromoleculeName: NAD-dependent protein deacetylase sirtuin-2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein acetyllysine N-acetyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.233105 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MAEPDPSHPL ETQAGKVQEA QDSDSDSEGG AAGGEADMDF LRNLFSQTLS LGSQKERLLD ELTLEGVARY MQSERCRRVI CLVGAGIST SAGIPDFRSP STGLYDNLEK YHLPYPEAIF EISYFKKHPE PFFALAKELY PGQFKPTICH YFMRLLKDKG L LLRCYTQN ...String:
MAEPDPSHPL ETQAGKVQEA QDSDSDSEGG AAGGEADMDF LRNLFSQTLS LGSQKERLLD ELTLEGVARY MQSERCRRVI CLVGAGIST SAGIPDFRSP STGLYDNLEK YHLPYPEAIF EISYFKKHPE PFFALAKELY PGQFKPTICH YFMRLLKDKG L LLRCYTQN IDTLERIAGL EQEDLVEAHG TFYTSHCVSA SCRHEYPLSW MKEKIFSEVT PKCEDCQSLV KPDIVFFGES LP ARFFSCM QSDFLKVDLL LVMGTSLQVQ PFASLISKAP LSTPRLLINK EKAGQSDPFL GMIMGLGGGM DFDSKKAYRD VAW LGECDQ GCLALAELLG WKKELEDLVR REHASIDAQS GAGVPNPSTS ASPKKSPPPA KDEARTTERE KPQ

UniProtKB: NAD-dependent protein deacetylase sirtuin-2

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Macromolecule #3: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]ME...

MacromoleculeName: [(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
type: ligand / ID: 3 / Number of copies: 1 / Formula: AR6
Molecular weightTheoretical: 559.316 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE
Details25mM HEPES-Na pH7.5, 150mM NaCl

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.2 µm / Nominal defocus min: 0.7000000000000001 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4l87

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.87 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 590607
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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