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- PDB-8hn9: Human SIRT3 Recognizing CCNE2K348la peptide -

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Basic information

Entry
Database: PDB / ID: 8hn9
TitleHuman SIRT3 Recognizing CCNE2K348la peptide
Components
  • CCNE2 peptide
  • NAD-dependent protein deacetylase sirtuin-3, mitochondrial
KeywordsLYASE
Function / homology
Function and homology information


positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / peptidyl-lysine deacetylation / positive regulation of superoxide dismutase activity / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / protein deacetylation / Regulation of FOXO transcriptional activity by acetylation / NAD+ binding ...positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / peptidyl-lysine deacetylation / positive regulation of superoxide dismutase activity / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / NAD-dependent histone deacetylase activity / protein deacetylation / Regulation of FOXO transcriptional activity by acetylation / NAD+ binding / negative regulation of reactive oxygen species metabolic process / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / aerobic respiration / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / negative regulation of ERK1 and ERK2 cascade / transferase activity / 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
IMIDAZOLE / NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å
AuthorsWang, Y. / Ding, W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)21977121 China
CitationJournal: Embo Rep. / Year: 2023
Title: SIRT3-dependent delactylation of cyclin E2 prevents hepatocellular carcinoma growth.
Authors: Jin, J. / Bai, L. / Wang, D. / Ding, W. / Cao, Z. / Yan, P. / Li, Y. / Xi, L. / Wang, Y. / Zheng, X. / Wei, H. / Ding, C. / Wang, Y.
History
DepositionDec 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1May 17, 2023Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
B: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
C: CCNE2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9687
Polymers62,6993
Non-polymers2694
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)235.676, 235.676, 235.676
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

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


Mass: 30553.260 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT3 / Production host: Escherichia phage EcSzw-2 (virus) / References: UniProt: Q9NTG7
#2: Protein/peptide CCNE2 peptide


Mass: 1592.017 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia phage EcSzw-2 (virus)
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

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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: 8.7 Å3/Da / Density % sol: 85.86 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.8 M succinic acid, pH 7.0, 0.01M Imidazole

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9999 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9999 Å / Relative weight: 1
ReflectionResolution: 3.5→40 Å / Num. obs: 27432 / % possible obs: 99.8 % / Redundancy: 20 % / CC1/2: 0.99 / Net I/σ(I): 14.47
Reflection shellResolution: 3.5→3.63 Å / Num. unique obs: 893 / CC1/2: 0.465

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Processing

Software
NameVersionClassification
PHENIX1.18.2-3874refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.7→38.23 Å / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.74 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2183 1199 5.16 %
Rwork0.1968 --
obs0.2331 23238 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.7→38.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4405 0 12 0 4417
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074525
X-RAY DIFFRACTIONf_angle_d1.0016155
X-RAY DIFFRACTIONf_dihedral_angle_d17.241683
X-RAY DIFFRACTIONf_chiral_restr0.062699
X-RAY DIFFRACTIONf_plane_restr0.01801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.7-3.850.30251310.24662443X-RAY DIFFRACTION94
3.85-4.020.35661240.33052346X-RAY DIFFRACTION92
4.02-4.230.29021300.20772425X-RAY DIFFRACTION95
4.24-4.50.20661370.19862453X-RAY DIFFRACTION95
4.5-4.850.20811040.20322472X-RAY DIFFRACTION96
4.85-5.330.22951310.21052447X-RAY DIFFRACTION95
5.33-6.10.24621420.2552456X-RAY DIFFRACTION95
6.11-7.680.29851430.26562472X-RAY DIFFRACTION94
7.69-38.230.16451540.21032528X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 33.5357204492 Å / Origin y: 49.1548187498 Å / Origin z: 11.9943189386 Å
111213212223313233
T0.356968810318 Å20.0126503853247 Å2-0.0167830856761 Å2-0.462643272884 Å20.181569069066 Å2--0.51333406117 Å2
L-0.00174303304646 °20.17665848549 °2-0.257775634159 °2-0.786492153188 °20.731332220346 °2--0.676548328727 °2
S-0.0229884601241 Å °0.227387895865 Å °0.295984481596 Å °-0.133987330436 Å °-0.0283160237018 Å °-0.049626359687 Å °-0.197339150285 Å °0.044713109601 Å °0.0139196068075 Å °
Refinement TLS groupSelection details: all

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