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- PDB-9vg0: SIRT2 structure in complex with H3K18myr peptide -

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Basic information

Entry
Database: PDB / ID: 9vg0
TitleSIRT2 structure in complex with H3K18myr peptide
Components
  • Histone H3.1
  • NAD-dependent protein deacetylase sirtuin-2
KeywordsHYDROLASE / Deacylated / 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 / tubulin deacetylation / peptidyl-lysine deacetylation / lateral loop / NLRP3 inflammasome complex assembly / mitotic nuclear membrane reassembly / tubulin deacetylase activity / negative regulation of NLRP3 inflammasome complex assembly / 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 / regulation of phosphorylation / protein acetyllysine N-acetyltransferase / 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 / glial cell projection / positive regulation of execution phase of apoptosis / subtelomeric heterochromatin formation / heterochromatin / lipid catabolic process / Chromatin modifying enzymes / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / centriole / cellular response to epinephrine stimulus / substantia nigra development / telomere organization / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / negative regulation of autophagy / epigenetic regulation of gene expression / Assembly of the ORC complex at the origin of replication / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / 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 / Pre-NOTCH Transcription and Translation / Meiotic recombination / histone deacetylase binding / Activation of anterior HOX genes in hindbrain development during early embryogenesis / spindle / RMTs methylate histone arginines / Transcriptional regulation of granulopoiesis / HCMV Early Events / mitotic spindle / structural constituent of chromatin / heterochromatin formation / nucleosome / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / nucleosome assembly
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
MYRISTIC ACID / Histone H3.1 / NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.61 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 12, 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
Revision 1.2Nov 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _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)36,0819
Polymers35,4772
Non-polymers6047
Water3,135174
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2510 Å2
ΔGint19 kcal/mol
Surface area13840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.152, 73.504, 55.731
Angle α, β, γ (deg.)90.000, 94.087, 90.000
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 , 4 types, 181 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2 / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 174 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.08 Å3/Da / Density % sol: 40.91 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / 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: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 17, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.61→55.59 Å / Num. obs: 34600 / % possible obs: 91.8 % / Redundancy: 6.4 % / CC1/2: 0.997 / Net I/σ(I): 17.1
Reflection shellResolution: 1.61→1.64 Å / Num. unique obs: 1925 / CC1/2: 0.939

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X3O

4x3o


Resolution: 1.61→27.81 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.068 / SU ML: 0.073 / Cross valid method: FREE R-VALUE / ESU R: 0.106 / ESU R Free: 0.108
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2313 1746 5.05 %
Rwork0.1883 32826 -
all0.191 --
obs-34572 91.681 %
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: 25.83 Å2
Baniso -1Baniso -2Baniso -3
1--0.348 Å2-0 Å21.88 Å2
2---0.606 Å20 Å2
3---0.678 Å2
Refinement stepCycle: LAST / Resolution: 1.61→27.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2271 0 36 174 2481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132403
X-RAY DIFFRACTIONr_bond_other_d0.0010.0152289
X-RAY DIFFRACTIONr_angle_refined_deg1.9031.6523236
X-RAY DIFFRACTIONr_angle_other_deg1.491.5785278
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8125300
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.27721.327113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83215407
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.291516
X-RAY DIFFRACTIONr_chiral_restr0.0920.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022666
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02538
X-RAY DIFFRACTIONr_nbd_refined0.2380.2491
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1880.22102
X-RAY DIFFRACTIONr_nbtor_refined0.1710.21155
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.21134
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2131
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1840.26
X-RAY DIFFRACTIONr_nbd_other0.1920.243
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1520.212
X-RAY DIFFRACTIONr_mcbond_it1.391.9821197
X-RAY DIFFRACTIONr_mcbond_other1.3881.9821196
X-RAY DIFFRACTIONr_mcangle_it1.9932.9681498
X-RAY DIFFRACTIONr_mcangle_other1.9932.9681499
X-RAY DIFFRACTIONr_scbond_it2.1682.2541206
X-RAY DIFFRACTIONr_scbond_other2.1672.2531207
X-RAY DIFFRACTIONr_scangle_it3.2263.281738
X-RAY DIFFRACTIONr_scangle_other3.2263.281738
X-RAY DIFFRACTIONr_lrange_it4.89624.5842666
X-RAY DIFFRACTIONr_lrange_other4.88224.3492643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.61-1.6520.3161420.2272654X-RAY DIFFRACTION99.8928
1.652-1.6970.2851170.2132551X-RAY DIFFRACTION100
1.697-1.7460.248990.2092073X-RAY DIFFRACTION81.075
1.746-1.80.2451150.1962425X-RAY DIFFRACTION100
1.8-1.8590.261350.1962321X-RAY DIFFRACTION99.9593
1.859-1.9240.27920.2081461X-RAY DIFFRACTION64.2266
1.924-1.9970.2361060.1911801X-RAY DIFFRACTION82.0215
1.997-2.0780.273840.1861766X-RAY DIFFRACTION83.9383
2.078-2.170.2081090.1812018X-RAY DIFFRACTION99.672
2.17-2.2760.248840.1861656X-RAY DIFFRACTION84.5481
2.276-2.3990.226990.1821854X-RAY DIFFRACTION99.7446
2.399-2.5450.288990.1961725X-RAY DIFFRACTION99.4547
2.545-2.720.261080.1941404X-RAY DIFFRACTION87.3484
2.72-2.9380.235870.1871520X-RAY DIFFRACTION99.628
2.938-3.2180.195510.1971428X-RAY DIFFRACTION99.5289
3.218-3.5970.218590.1841157X-RAY DIFFRACTION89.8744
3.597-4.1510.217440.174912X-RAY DIFFRACTION80.8799
4.151-5.080.184600.165951X-RAY DIFFRACTION99.2149
5.08-7.1670.203480.191742X-RAY DIFFRACTION99.1217
7.167-27.810.29680.203407X-RAY DIFFRACTION93.0493
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.4599-0.0484-0.21310.7318-0.21071.1771-0.00120.0639-0.0595-0.07320.02960.06480.0164-0.1475-0.02840.01610.0033-0.01470.0267-0.00810.02337.91928.423219.8146
28.0184-4.44960.42755.24772.99833.7947-0.08510.1184-0.00710.22780.06270.01450.22150.17760.02240.14070.0055-0.03150.16370.02580.18417.971-3.17637.1306
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA57 - 355
2X-RAY DIFFRACTION1ALLA403
3X-RAY DIFFRACTION1ALLA404
4X-RAY DIFFRACTION1ALLA406
5X-RAY DIFFRACTION1ALLA407
6X-RAY DIFFRACTION1ALLA408
7X-RAY DIFFRACTION2ALLC6 - 11

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