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- PDB-8v5u: Human SIRT3 bound to p53-AMC peptide and Honokiol -

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Basic information

Entry
Database: PDB / ID: 8v5u
TitleHuman SIRT3 bound to p53-AMC peptide and Honokiol
Components
  • NAD-dependent protein deacetylase sirtuin-3, mitochondrial
  • p53-AMC peptide
KeywordsHYDROLASE / Activator / Complex / Deacylase
Function / homology
Function and homology information


positive regulation of superoxide dismutase activity / positive regulation of catalase activity / NAD-dependent protein lysine delactylase activity / positive regulation of ceramide biosynthetic process / peptidyl-lysine deacetylation / Maturation of TCA enzymes and regulation of TCA cycle / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / histone H3K14 deacetylase activity, NAD-dependent / histone H3K9 deacetylase activity, NAD-dependent ...positive regulation of superoxide dismutase activity / positive regulation of catalase activity / NAD-dependent protein lysine delactylase activity / positive regulation of ceramide biosynthetic process / peptidyl-lysine deacetylation / Maturation of TCA enzymes and regulation of TCA cycle / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / histone H3K14 deacetylase activity, NAD-dependent / histone H3K9 deacetylase activity, NAD-dependent / histone H4K16 deacetylase activity, NAD-dependent / histone H3K18 deacetylase activity, NAD-dependent / histone H3K56 deacetylase activity, NAD-dependent / histone H3K4 deacetylase activity, NAD-dependent / histone deacetylase activity, NAD-dependent / protein deacetylation / positive regulation of oxidative phosphorylation / Regulation of FOXO transcriptional activity by acetylation / protein lysine deacetylase activity / cellular response to stress / negative regulation of reactive oxygen species metabolic process / NAD+ binding / Mitochondrial unfolded protein response (UPRmt) / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / aerobic respiration / Transcriptional activation of mitochondrial biogenesis / negative regulation of ERK1 and ERK2 cascade / positive regulation of insulin secretion / sequence-specific DNA binding / mitochondrial matrix / enzyme binding / protein-containing complex / mitochondrion / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
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
Chem-Y4T / NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.48 Å
AuthorsChakrabarti, R. / Ghosh, A. / Guan, X. / Upadhyay, A. / Dumpati, R.K. / Munshi, S. / Roy, S. / Chall, S. / Rahnamoun, A. / Reverdy, C. ...Chakrabarti, R. / Ghosh, A. / Guan, X. / Upadhyay, A. / Dumpati, R.K. / Munshi, S. / Roy, S. / Chall, S. / Rahnamoun, A. / Reverdy, C. / Errasti, G. / Delacroix, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Phys. Rev. X / Year: 2024
Title: Computationally Driven Discovery and Characterization of SIRT3-Activating Compounds that Fully Recover Catalytic Activity under ${\mathrm{NAD}}^{+}$ Depletion
Authors: Guan, X. / Dumpati, R.K. / Munshi, S. / Chall, S. / Bose, R. / Rahnamoun, A. / Reverdy, C. / Errasti, G. / Delacroix, T. / Ghosh, A. / Chakrabarti, R.
History
DepositionDec 1, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 6, 2024Provider: 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-3, mitochondrial
B: p53-AMC peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3724
Polymers32,0402
Non-polymers3322
Water1,78399
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-6 kcal/mol
Surface area12570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.452, 52.901, 68.753
Angle α, β, γ (deg.)90.00, 92.52, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein NAD-dependent protein deacetylase sirtuin-3, mitochondrial


Mass: 31340.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT3
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q9NTG7
#2: Protein/peptide p53-AMC peptide


Mass: 699.816 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-Y4T / (1P)-3',5-di(prop-2-en-1-yl)[1,1'-biphenyl]-2,4'-diol / Honokiol


Mass: 266.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H18O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / Source method: isolated from a natural source / Formula: H2O
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: 1.95 Å3/Da / Density % sol: 37.04 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion
Details: SIRT3 (118-399) (10.3 mg/ml) was crystallized in complex with FDL (QPKKAC-7-amino-4-methylcoumarin) peptide (3 mM) and honokiol (1 mM) in 25% PEG 3350, 0.2 M Li2SO4 (or 0.2 M NaCl), and 0.1M ...Details: SIRT3 (118-399) (10.3 mg/ml) was crystallized in complex with FDL (QPKKAC-7-amino-4-methylcoumarin) peptide (3 mM) and honokiol (1 mM) in 25% PEG 3350, 0.2 M Li2SO4 (or 0.2 M NaCl), and 0.1M HEPES, pH 7.5 as reservoir. Following formation of the ternary complex, crystals were soaked with carba-NAD (10 mM).

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979257 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979257 Å / Relative weight: 1
ReflectionResolution: 1.48→68.69 Å / Num. obs: 40650 / % possible obs: 97.9 % / Redundancy: 3.4 % / CC1/2: 0.997 / Net I/σ(I): 11.9
Reflection shellResolution: 1.48→1.5 Å / Num. unique obs: 1828 / CC1/2: 0.754

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
PHASERphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.48→68.69 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.939 / SU B: 1.888 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.095 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24628 2908 7.2 %RANDOM
Rwork0.22615 ---
obs0.2276 37737 97.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å20 Å2
2---0.04 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.48→68.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2162 0 21 99 2282
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0122258
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162191
X-RAY DIFFRACTIONr_angle_refined_deg1.81.8483081
X-RAY DIFFRACTIONr_angle_other_deg0.6261.7355038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3445280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg20.6586.2524
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.36310356
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0930.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022645
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02516
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.0232.1061108
X-RAY DIFFRACTIONr_mcbond_other2.022.1031105
X-RAY DIFFRACTIONr_mcangle_it2.9113.7691380
X-RAY DIFFRACTIONr_mcangle_other2.9133.7671379
X-RAY DIFFRACTIONr_scbond_it2.8692.4571150
X-RAY DIFFRACTIONr_scbond_other2.8682.4571151
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.3134.3741698
X-RAY DIFFRACTIONr_long_range_B_refined5.32421.622470
X-RAY DIFFRACTIONr_long_range_B_other5.32321.622471
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.48→1.515 Å
RfactorNum. reflection% reflection
Rfree0.355 197 -
Rwork0.31 2568 -
obs--90.8 %

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