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- PDB-9v7w: SIRT2 structure in complex with H3K18myr peptide and native NAD: ... -

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Basic information

Entry
Database: PDB / ID: 9v7w
TitleSIRT2 structure in complex with H3K18myr peptide and native NAD: pre-catalysis state 3
Components
  • NAD-dependent protein deacetylase sirtuin-2
  • PRO-ARG-LYS-GLN-LEU-ALA
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 / positive regulation of fatty acid biosynthetic process / Schmidt-Lanterman incisure / 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 / 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 / positive regulation of execution phase of apoptosis / glial cell projection / subtelomeric heterochromatin formation / heterochromatin / lipid catabolic process / cellular response to epinephrine stimulus / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / substantia nigra development / centriole / negative regulation of autophagy / epigenetic regulation of gene expression / ubiquitin binding / meiotic cell cycle / negative regulation of protein catabolic process / autophagy / spindle / histone deacetylase binding / mitotic spindle / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / heterochromatin formation / myelin sheath / chromosome / growth cone / cellular response to oxidative stress / midbody / perikaryon / cellular response to hypoxia / DNA-binding transcription factor binding / proteasome-mediated ubiquitin-dependent protein catabolic process / microtubule / chromosome, telomeric region / regulation of cell cycle / innate immune response / cell division / negative regulation of DNA-templated transcription / centrosome / chromatin binding / nucleolus / perinuclear region of cytoplasm / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / mitochondrion / zinc ion binding / nucleus / plasma membrane / cytosol / cytoplasm
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
Similarity search - Domain/homology
MYRISTIC ACID / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / NAD-dependent protein deacetylase sirtuin-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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
DepositionMay 28, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release

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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: PRO-ARG-LYS-GLN-LEU-ALA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,16416
Polymers35,4062
Non-polymers1,75814
Water1,62190
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)37.76, 76.57, 55.94
Angle α, β, γ (deg.)90, 97.881, 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 PRO-ARG-LYS-GLN-LEU-ALA


Mass: 713.868 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 7 types, 104 molecules

#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-ZN / ZINC ION


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


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


Mass: 18.015 Da / Num. of mol.: 90 / 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: 2.26 Å3/Da / Density % sol: 45.64 %
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 PILATUS3 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: 1.86→44.93 Å / Num. obs: 31715 / % possible obs: 90.8 % / Redundancy: 5.8 % / CC1/2: 0.999 / Net I/σ(I): 10.4
Reflection shellResolution: 1.86→1.9 Å / Num. unique obs: 1522 / CC1/2: 0.29

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.86→44.93 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.95 / SU B: 5.493 / SU ML: 0.148 / Cross valid method: FREE R-VALUE / ESU R: 0.156 / ESU R Free: 0.146
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2314 1306 4.982 %
Rwork0.1858 24908 -
all0.188 --
obs-26214 98.738 %
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: 40.033 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20 Å20.928 Å2
2---0.504 Å20 Å2
3----0.967 Å2
Refinement stepCycle: LAST / Resolution: 1.86→44.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2442 0 112 90 2644
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122698
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162566
X-RAY DIFFRACTIONr_angle_refined_deg1.8461.8483626
X-RAY DIFFRACTIONr_angle_other_deg0.6141.7515954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9495326
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.929519
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.6652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1610469
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.69110115
X-RAY DIFFRACTIONr_chiral_restr0.0870.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023086
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02605
X-RAY DIFFRACTIONr_nbd_refined0.2370.2617
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.22443
X-RAY DIFFRACTIONr_nbtor_refined0.1850.21285
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.21397
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1790.2141
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0980.22
X-RAY DIFFRACTIONr_metal_ion_refined0.140.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1440.214
X-RAY DIFFRACTIONr_nbd_other0.2230.270
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1310.29
X-RAY DIFFRACTIONr_mcbond_it3.5933.7441283
X-RAY DIFFRACTIONr_mcbond_other3.5873.7441283
X-RAY DIFFRACTIONr_mcangle_it4.9416.6941616
X-RAY DIFFRACTIONr_mcangle_other4.946.6981617
X-RAY DIFFRACTIONr_scbond_it4.3494.2741415
X-RAY DIFFRACTIONr_scbond_other4.3484.2771416
X-RAY DIFFRACTIONr_scangle_it6.2847.6292010
X-RAY DIFFRACTIONr_scangle_other6.2827.6322011
X-RAY DIFFRACTIONr_lrange_it8.54540.1113080
X-RAY DIFFRACTIONr_lrange_other8.539.943070
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
1.86-1.9080.365930.38217390.38219670.8470.82193.13680.388
1.908-1.960.496810.44117290.44318730.7240.78696.63640.459
1.96-2.0170.304940.26417660.26618600.9310.9471000.258
2.017-2.0790.317900.25617200.25918100.930.9541000.247
2.079-2.1470.264990.21516350.21717350.9560.96799.94240.2
2.147-2.2220.276790.21916080.22216870.9430.9681000.199
2.222-2.3060.414900.37114110.37316180.8510.89292.76880.358
2.306-2.40.25630.214980.20215610.9580.9731000.175
2.4-2.5060.227780.16414470.16715260.970.98499.93450.141
2.506-2.6280.228670.16313690.16614360.9660.9851000.14
2.628-2.770.29620.16113070.16613700.9530.98499.9270.139
2.77-2.9370.228650.16112330.16412990.9660.98599.9230.138
2.937-3.1390.229630.14811660.15212290.9750.9871000.13
3.139-3.3890.192610.15810640.1611270.9770.98499.82250.145
3.389-3.7110.246500.17410020.17710580.9610.98299.43290.164
3.711-4.1450.164480.1528940.1539440.980.98799.78810.15
4.145-4.7790.159450.1257990.1278450.9870.99199.88170.127
4.779-5.8370.194370.1516740.1537110.9760.9891000.155
5.837-8.1860.177310.1685300.1695610.9830.9861000.17
8.186-44.930.182100.1423170.1433310.9880.98698.79150.159

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