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- PDB-5y4h: Human SIRT3 in complex with halistanol sulfate -

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Basic information

Entry
Database: PDB / ID: 5y4h
TitleHuman SIRT3 in complex with halistanol sulfate
Components
  • NAD-dependent protein deacetylase sirtuin-3, mitochondrial
  • THr-Arg-Ser-GLY-ALY-VAL-MET-ARG-ARG-LEU-ARG-ARG
KeywordsHYDROLASE/INHIBITOR / sirtuin / NAD-dependent deacetylase / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


propionate biosynthetic process / propionate-CoA ligase / acetate biosynthetic process / propionate-CoA ligase activity / positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / Ethanol oxidation ...propionate biosynthetic process / propionate-CoA ligase / acetate biosynthetic process / propionate-CoA ligase activity / positive regulation of catalase activity / positive regulation of ceramide biosynthetic process / acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / Ethanol oxidation / positive regulation of superoxide dismutase activity / Maturation of TCA enzymes and regulation of TCA cycle / peptidyl-lysine deacetylation / acetyl-CoA biosynthetic process / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / histone deacetylase activity, NAD-dependent / protein deacetylation / Regulation of FOXO transcriptional activity by acetylation / AMP binding / 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 / ATP binding / nucleus
Similarity search - Function
Acetate-CoA ligase / Acetyl-coenzyme A synthetase, N-terminal domain / Acetyl-coenzyme A synthetase N-terminus / SIR2/SIRT2 'Small Domain' / SIR2/SIRT2 'Small Domain' / Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain ...Acetate-CoA ligase / Acetyl-coenzyme A synthetase, N-terminal domain / Acetyl-coenzyme A synthetase N-terminus / 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. / ANL, N-terminal domain / TPP-binding domain / AMP-binding enzyme, C-terminal domain / AMP-binding enzyme C-terminal domain / AMP-binding, conserved site / Putative AMP-binding domain signature. / AMP-dependent synthetase/ligase / AMP-binding enzyme / DHS-like NAD/FAD-binding domain superfamily / AMP-binding enzyme, C-terminal domain superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-8QF / NAD-dependent protein deacetylase sirtuin-3, mitochondrial / Acetyl-coenzyme A synthetase 2-like, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKudo, N. / Ito, A. / Yoshida, M.
Funding support Japan, 2items
OrganizationGrant numberCountry
JSPSKAKENHI 26221204 Japan
JSPSP-Direct Japan
Citation
Journal: J. Antibiot. / Year: 2018
Title: Halistanol sulfates I and J, new SIRT1-3 inhibitory steroid sulfates from a marine sponge of the genus Halichondria
Authors: Nakamura, F. / Kudo, N. / Tomachi, Y. / Nakata, A. / Takemoto, M. / Ito, A. / Tabei, H. / Arai, D. / de Voogd, N. / Yoshida, M. / Nakao, Y. / Fusetani, N.
#1: Journal: J. Antibiot. / Year: 2018
Title: Correction to: Halistanol sulfates I and J, new SIRT1-3 inhibitory steroid sulfates from a marine sponge of the genus Halichondria
Authors: Nakamura, F. / Kudo, N. / Tomachi, Y. / Nakata, A. / Takemoto, M. / Ito, A. / Tabei, H. / Arai, D. / de Voogd, N. / Yoshida, M. / Nakao, Y. / Fusetani, N.
History
DepositionAug 3, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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: THr-Arg-Ser-GLY-ALY-VAL-MET-ARG-ARG-LEU-ARG-ARG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9164
Polymers33,1752
Non-polymers7402
Water905
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-7 kcal/mol
Surface area12750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.840, 127.840, 127.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number207
Space group name H-MP432

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Components

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


Mass: 31612.348 Da / Num. of mol.: 1 / Fragment: UNP residues 118-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT3, SIR2L3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q9NTG7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide THr-Arg-Ser-GLY-ALY-VAL-MET-ARG-ARG-LEU-ARG-ARG


Mass: 1562.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9NUB1*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-8QF / [(2~{S},3~{S},5~{S},6~{S},8~{S},9~{S},10~{R},13~{R},14~{R},17~{R})-17-[(2~{R})-6,6-dimethylheptan-2-yl]-10,13-dimethyl-2,3-disulfooxy-2,3,4,5,6,7,8,9,11,12,14,15,16,17-tetradecahydro-1~{H}-cyclopenta[a]phenanthren-6-yl] hydrogen sulfate


Mass: 674.884 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C28H50O12S3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
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: 2.68 Å3/Da / Density % sol: 54.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: Potassium phosphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 11529 / % possible obs: 99.9 % / Redundancy: 16.3 % / Net I/σ(I): 88.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GLU

3glu


Resolution: 2.6→20 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.922 / SU B: 11.164 / SU ML: 0.236 / Cross valid method: THROUGHOUT / ESU R: 0.535 / ESU R Free: 0.315 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.26914 616 5.4 %RANDOM
Rwork0.21514 ---
obs0.21793 10892 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 61.284 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2071 0 44 5 2120
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192167
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5152.0132961
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6885260
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.23122.58193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.71315341
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0911520
X-RAY DIFFRACTIONr_chiral_restr0.1030.2344
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0221613
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.6216.0191049
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.2179.0161306
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8056.1951118
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.88782.5553078
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.6→2.666 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 55 -
Rwork0.294 761 -
obs--100 %

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