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- PDB-5h4d: Crystal structure of hSIRT3 in complex with a specific agonist Am... -

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Basic information

Entry
Database: PDB / ID: 5h4d
TitleCrystal structure of hSIRT3 in complex with a specific agonist Amiodarone hydrochloride
Components
  • ARG-HIS-LYS
  • NAD-dependent protein deacetylase sirtuin-3, mitochondrial
KeywordsHYDROLASE / SIRT3 Amiodarone agonist
Function / homology
Function and homology information


positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / positive regulation of superoxide dismutase activity / Maturation of TCA enzymes and regulation of TCA cycle / peptidyl-lysine deacetylation / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / histone deacetylase activity, NAD-dependent / protein deacetylation / Regulation of FOXO transcriptional activity by acetylation ...positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / positive regulation of superoxide dismutase activity / Maturation of TCA enzymes and regulation of TCA cycle / peptidyl-lysine deacetylation / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / histone deacetylase activity, NAD-dependent / 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
SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily ...SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / TPP-binding domain / DHS-like NAD/FAD-binding domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-BBI / 7-AMINO-4-METHYL-CHROMEN-2-ONE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.21 Å
AuthorsZhang, S. / Fu, L. / Liu, J. / Liu, B.
CitationJournal: To Be Published
Title: Crystal structure of hSIRT3 in complex with a specific agonist Amiodarone hydrochloride
Authors: Zhang, S. / Fu, L. / Liu, J. / Liu, B.
History
DepositionOct 31, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 8, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Data collection / Category: diffrn_detector / diffrn_source
Item: _diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_beamline ..._diffrn_detector.detector / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.type
Revision 2.0Apr 5, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_sheet_hbond / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / pdbx_validate_rmsd_angle / struct_conn / struct_conn_type / struct_ref_seq / struct_sheet / struct_sheet_order / struct_sheet_range / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight / _entity.pdbx_description / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_src_id / _pdbx_entity_nonpoly.comp_id / _pdbx_entity_nonpoly.name / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_conn_type.id / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end

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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
D: ARG-HIS-LYS
H: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
C: ARG-HIS-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,97716
Polymers61,6174
Non-polymers3,36012
Water00
1
A: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
C: ARG-HIS-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3827
Polymers30,8092
Non-polymers1,5745
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: ARG-HIS-LYS
H: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5949
Polymers30,8092
Non-polymers1,7867
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.560, 114.560, 123.404
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3

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Components

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Protein / Protein/peptide , 2 types, 4 molecules AHDC

#1: Protein NAD-dependent protein deacetylase sirtuin-3, mitochondrial / hSIRT3 / Regulatory protein SIR2 homolog 3 / SIR2-like protein 3


Mass: 30195.838 Da / Num. of mol.: 2 / Fragment: UNP residues 121-391
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT3, SIR2L3 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NTG7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide ARG-HIS-LYS


Mass: 612.744 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 12 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-BBI / (2-butyl-1-benzofuran-3-yl){4-[2-(diethylamino)ethoxy]-3,5-diiodophenyl}methanone


Mass: 645.312 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H29I2NO3 / Comment: medication, antiarrhythmic*YM
#6: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#7: Chemical ChemComp-MCM / 7-AMINO-4-METHYL-CHROMEN-2-ONE / 7-AMINO-4-METHYLCOUMARIN


Mass: 175.184 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H9NO2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3

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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: 2.51 Å3/Da / Density % sol: 51.05 %
Crystal growTemperature: 293 K / Method: evaporation
Details: 0.1M HEPES sodium pH 7.5, 10%(v/v) 2-Propanol, 20%(w/v) Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 197 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.2→77.32 Å / Num. obs: 5871 / % possible obs: 59.5 % / Redundancy: 1.2 % / Rmerge(I) obs: 0.174 / Net I/av σ(I): 2.75 / Net I/σ(I): 2.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
3.2-3.261.10.7430.323165.7
3.26-3.311.20.6520.525165.3
3.31-3.381.10.3840.64166.3
3.38-3.451.20.6370.522162.6
3.45-3.521.10.4290.516164
3.52-3.61.20.3420.675162
3.6-3.691.20.3450.55161
3.69-3.791.20.2050.867157.3
3.79-3.911.10.2510.862162.4
3.91-4.031.10.2880.75155.1
4.03-4.181.20.220.887156.8
4.18-4.341.20.1880.894158.6
4.34-4.541.30.1480.915161.4
4.54-4.781.30.1610.914160.1
4.78-5.081.30.1380.954158.6
5.08-5.471.30.1710.904159.4
5.47-6.021.30.1570.881156.3
6.02-6.891.30.160.904153.4
6.89-8.671.30.0830.979153.2
8.67-501.60.0820.959150.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
REFMAC5.8.0049refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.21→77.32 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.613 / SU B: 47.808 / SU ML: 0.813 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 1.299
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.3716 285 4.9 %RANDOM
Rwork0.2129 ---
obs0.2202 5583 59.21 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 212.55 Å2 / Biso mean: 35.979 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20.44 Å2-0 Å2
2--0.89 Å2-0 Å2
3----2.88 Å2
Refinement stepCycle: final / Resolution: 3.21→77.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4365 0 161 0 4526
Biso mean--97.23 --
Num. residues----551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0194645
X-RAY DIFFRACTIONr_bond_other_d0.0030.024452
X-RAY DIFFRACTIONr_angle_refined_deg1.3092.0326329
X-RAY DIFFRACTIONr_angle_other_deg0.9053.00810234
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8555544
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57622.667195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.74415715
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6291540
X-RAY DIFFRACTIONr_chiral_restr0.060.2698
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215089
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021059
X-RAY DIFFRACTIONr_mcbond_it1.4613.4642196
X-RAY DIFFRACTIONr_mcbond_other1.463.4642196
X-RAY DIFFRACTIONr_mcangle_it2.6075.1952732
LS refinement shellResolution: 3.206→3.29 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.494 22 -
Rwork0.286 429 -
all-451 -
obs--61.44 %

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