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- PDB-9vge: SIRT2 demyristoylation intermediate I structure -

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Basic information

Entry
Database: PDB / ID: 9vge
TitleSIRT2 demyristoylation intermediate I structure
Components
  • Histone H3.1
  • NAD-dependent protein deacetylase sirtuin-2
KeywordsHYDROLASE / Deacylase / Cell Cycle regulation / Metabolic regulation
Function / homology
Function and homology information


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 / positive regulation of meiotic nuclear division / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / paranodal junction ...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 / positive regulation of meiotic nuclear division / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / paranodal junction / peptidyl-lysine deacetylation / tubulin deacetylation / lateral loop / NLRP3 inflammasome complex assembly / negative regulation of NLRP3 inflammasome complex assembly / mitotic nuclear membrane reassembly / tubulin deacetylase activity / paranode region of axon / regulation of exit from mitosis / Schmidt-Lanterman incisure / positive regulation of fatty acid biosynthetic process / negative regulation of peptidyl-threonine phosphorylation / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / regulation of phosphorylation / 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 / response to redox state / regulation of myelination / positive regulation of DNA binding / histone deacetylase activity / histone acetyltransferase binding / negative regulation of fat cell differentiation / negative regulation of reactive oxygen species metabolic process / positive regulation of cell division / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / glial cell projection / positive regulation of execution phase of apoptosis / subtelomeric heterochromatin formation / heterochromatin / lipid catabolic process / Chromatin modifying enzymes / cellular response to epinephrine stimulus / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / centriole / substantia nigra development / telomere organization / Interleukin-7 signaling / negative regulation of autophagy / RNA Polymerase I Promoter Opening / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / epigenetic regulation of gene expression / Condensation of Prophase Chromosomes / ubiquitin binding / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / meiotic cell cycle / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / negative regulation of protein catabolic process / NoRC negatively regulates rRNA expression / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / autophagy / Meiotic recombination / Pre-NOTCH Transcription and Translation / spindle / histone deacetylase binding / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / mitotic spindle / structural constituent of chromatin / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / nucleosome / heterochromatin formation / myelin sheath
Similarity search - Function
Sirtuin, class I / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily / Histone H3 signature 1. / Histone H3 signature 2. ...Sirtuin, class I / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold
Similarity search - Domain/homology
NICOTINAMIDE / Chem-YDD / Histone H3.1 / NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.56 Å
AuthorsZhang, N. / Hao, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)2023B0303000003 China
CitationJournal: Rsc Chem Biol / Year: 2025
Title: Structural basis of SIRT2 pre-catalysis NAD + binding dynamics and mechanism.
Authors: Zhang, N. / Pow, K.C. / Chen, L. / Hao, Q.
History
DepositionJun 13, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NAD-dependent protein deacetylase sirtuin-2
C: Histone H3.1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,5126
Polymers35,4772
Non-polymers1,0354
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-5 kcal/mol
Surface area13660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.059, 77.646, 55.955
Angle α, β, γ (deg.)90, 97.988, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AC

#1: Protein NAD-dependent protein deacetylase sirtuin-2 / NAD-dependent protein defatty-acylase sirtuin-2 / Regulatory protein SIR2 homolog 2 / SIR2-like protein 2


Mass: 34692.004 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(DE3) (bacteria)
References: UniProt: Q8IXJ6, protein acetyllysine N-acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
#2: Protein/peptide Histone H3.1 / Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone ...Histone H3/a / Histone H3/b / Histone H3/c / Histone H3/d / Histone H3/f / Histone H3/h / Histone H3/i / Histone H3/j / Histone H3/k / Histone H3/l


Mass: 784.946 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P68431

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Non-polymers , 5 types, 29 molecules

#3: Chemical ChemComp-NCA / NICOTINAMIDE


Mass: 122.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-YDD / [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4R,5S)-3,4-bis(oxidanyl)-5-tetradecoxy-oxolan-2-yl]methyl hydrogen phosphate


Mass: 755.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H51N5O14P2 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.27 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: Tris 8.0, 25% PEG 2000MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 29, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.56→55.474 Å / Num. obs: 9655 / % possible obs: 94.4 % / Redundancy: 5.1 % / CC1/2: 0.994 / Net I/σ(I): 11.4
Reflection shellResolution: 2.56→2.67 Å / Num. unique obs: 1023 / CC1/2: 0.491

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X3O

4x3o


Resolution: 2.56→55.474 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.896 / SU B: 14.567 / SU ML: 0.311 / Cross valid method: FREE R-VALUE / ESU R Free: 0.385
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2819 521 5.406 %
Rwork0.2029 9117 -
all0.207 --
obs-9638 94.37 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 55.879 Å2
Baniso -1Baniso -2Baniso -3
1-7.082 Å2-0 Å23.682 Å2
2---3.976 Å2-0 Å2
3----3.983 Å2
Refinement stepCycle: LAST / Resolution: 2.56→55.474 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2297 0 66 25 2388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0270.0122428
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162274
X-RAY DIFFRACTIONr_angle_refined_deg1.6281.8433276
X-RAY DIFFRACTIONr_angle_other_deg0.5151.7565277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8495296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.54516
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg1.48855
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.03510410
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.3011099
X-RAY DIFFRACTIONr_chiral_restr0.0690.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022781
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02539
X-RAY DIFFRACTIONr_nbd_refined0.2180.2510
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2210.22206
X-RAY DIFFRACTIONr_nbtor_refined0.1830.21187
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.21286
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2101
X-RAY DIFFRACTIONr_metal_ion_refined0.1550.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2290.210
X-RAY DIFFRACTIONr_nbd_other0.2380.247
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2960.24
X-RAY DIFFRACTIONr_mcbond_it3.4075.4961190
X-RAY DIFFRACTIONr_mcbond_other3.4015.4971190
X-RAY DIFFRACTIONr_mcangle_it5.0889.8641484
X-RAY DIFFRACTIONr_mcangle_other5.0869.8661485
X-RAY DIFFRACTIONr_scbond_it3.3095.8711238
X-RAY DIFFRACTIONr_scbond_other3.3085.8731239
X-RAY DIFFRACTIONr_scangle_it5.26210.7111792
X-RAY DIFFRACTIONr_scangle_other5.26110.7121793
X-RAY DIFFRACTIONr_lrange_it8.5754.5962687
X-RAY DIFFRACTIONr_lrange_other8.5754.6082687
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.56-2.6260.254430.2667200.2657630.9490.9431000.248
2.626-2.6980.405370.2844440.2937200.9050.9366.80560.267
2.698-2.7760.358440.2456630.2527110.9090.95699.43740.229
2.776-2.8610.308410.2436600.2477010.9330.9591000.224
2.861-2.9550.289310.246220.2426530.9520.9621000.226
2.955-3.0580.426320.2396290.2486610.9040.9651000.223
3.058-3.1730.277380.2265710.236090.9560.9651000.211
3.173-3.3020.343300.2155910.226210.8970.9681000.207
3.302-3.4490.283150.2264280.2285600.9230.96479.10710.217
3.449-3.6160.373230.2145230.2195470.9030.97199.81720.213
3.616-3.8110.303220.2184050.2225340.9190.97279.96250.222
3.811-4.0410.264160.1833860.1864960.9510.97381.04840.188
4.041-4.3190.157200.1724570.1714770.9850.9831000.185
4.319-4.6620.151240.164080.1594350.9840.98499.31030.181
4.662-5.1040.258210.1733860.1774070.9520.9841000.204
5.104-5.70.33250.1933400.2013650.9520.9821000.222
5.7-6.570.306200.2093010.2143230.9530.97799.38080.238
6.57-8.0190.249230.1892560.1932800.9590.97999.64290.221
8.019-11.2230.287110.1472010.1522150.9660.98798.60470.188
11.223-55.4740.33250.2151260.221310.9510.9711000.266

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