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- PDB-4c78: Complex of human Sirt3 with Bromo-Resveratrol and ACS2 peptide -

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Basic information

Entry
Database: PDB / ID: 4c78
TitleComplex of human Sirt3 with Bromo-Resveratrol and ACS2 peptide
Components
  • ACETYL-COENZYME A SYNTHETASE 2-LIKE, MITOCHONDRIAL
  • NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
KeywordsHYDROLASE / SIRTUIN / INHIBITOR / ACTIVATION / RESVERATROL / SIRT1 / METABOLIC SENSOR / METABOLISM / AGING
Function / homology
Function and homology information


propionate biosynthetic process / propionate-CoA ligase / acetate biosynthetic process / propionate-CoA ligase activity / positive regulation of superoxide dismutase activity / positive regulation of catalase activity / NAD-dependent protein lysine delactylase activity / positive regulation of ceramide biosynthetic process / acetate-CoA ligase / acetate-CoA ligase activity ...propionate biosynthetic process / propionate-CoA ligase / acetate biosynthetic process / propionate-CoA ligase activity / positive regulation of superoxide dismutase activity / positive regulation of catalase activity / NAD-dependent protein lysine delactylase activity / positive regulation of ceramide biosynthetic process / acetate-CoA ligase / acetate-CoA ligase activity / acetyl-CoA biosynthetic process from acetate / ethanol catabolic process / Ethanol oxidation / peptidyl-lysine deacetylation / Maturation of TCA enzymes and regulation of TCA cycle / acetyl-CoA biosynthetic process / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / protein deacetylation / histone deacetylase activity, NAD-dependent / positive regulation of oxidative phosphorylation / Regulation of FOXO transcriptional activity by acetylation / protein lysine deacetylase activity / AMP binding / 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 / positive regulation of insulin secretion / negative regulation of ERK1 and ERK2 cascade / 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. / TPP-binding domain / ANL, N-terminal 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
5-[(E)-2-(4-bromophenyl)ethenyl]benzene-1,3-diol / 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 Å
AuthorsNguyen, G.T.T. / Gertz, M. / Weyand, M. / Steegborn, C.
CitationJournal: Chem.Biol. / Year: 2013
Title: Crystal Structures of Sirt3 Complexes with 4'-Bromo-Resveratrol Reveal Binding Sites and Inhibition Mechanism.
Authors: Nguyen, G.T.T. / Gertz, M. / Steegborn, C.
History
DepositionSep 19, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Dec 11, 2013Group: Database references
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
C: ACETYL-COENZYME A SYNTHETASE 2-LIKE, MITOCHONDRIAL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0894
Polymers32,7332
Non-polymers3572
Water2,252125
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1170 Å2
ΔGint-9.3 kcal/mol
Surface area12440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.700, 52.600, 159.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
Components on special symmetry positions
IDModelComponents
11A-2039-

HOH

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Components

#1: Protein NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL


Mass: 31484.219 Da / Num. of mol.: 1 / Fragment: RESIDUES 116-399
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PVFT3S / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2
References: UniProt: Q9NTG7, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Protein/peptide ACETYL-COENZYME A SYNTHETASE 2-LIKE, MITOCHONDRIAL


Mass: 1248.523 Da / Num. of mol.: 1 / Fragment: RESIDUES 638-647 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q9NUB1, acetate-CoA ligase
#3: Chemical ChemComp-BVB / 5-[(E)-2-(4-bromophenyl)ethenyl]benzene-1,3-diol


Mass: 291.140 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11BrO2
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.33 Å3/Da / Density % sol: 47.2 % / Description: NONE
Crystal growpH: 6
Details: 250 MM (NH4)2SO4, 100 MM BISTRIS PH 6, 21% (W/V) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 29, 2011 / Details: COLLIMATOR
RadiationMonochromator: SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918 Å / Relative weight: 1
ReflectionResolution: 2→37.4 Å / Num. obs: 37699 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 2.1 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 1.99 / % possible all: 99

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4H8D

4h8d
PDB Unreleased entry


Resolution: 2→37.42 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.939 / SU B: 9.553 / SU ML: 0.137 / Cross valid method: THROUGHOUT / ESU R: 0.184 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED.
RfactorNum. reflection% reflectionSelection details
Rfree0.24056 1025 5 %RANDOM
Rwork0.19375 ---
obs0.19614 19507 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: 40.552 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--1.64 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 2→37.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2112 0 18 125 2255
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192191
X-RAY DIFFRACTIONr_bond_other_d0.0020.022146
X-RAY DIFFRACTIONr_angle_refined_deg1.9232.0012977
X-RAY DIFFRACTIONr_angle_other_deg0.9523.0024925
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7685267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.80222.44794
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.06315357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.161521
X-RAY DIFFRACTIONr_chiral_restr0.1140.2337
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212422
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02497
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_it1.0160.8111071
X-RAY DIFFRACTIONr_mcbond_other1.0140.811070
X-RAY DIFFRACTIONr_mcangle_it1.7291.2031334
X-RAY DIFFRACTIONr_mcangle_other1.7291.2051335
X-RAY DIFFRACTIONr_scbond_it1.2211.7311120
X-RAY DIFFRACTIONr_scbond_other1.221.7311121
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9181.9521643
X-RAY DIFFRACTIONr_long_range_B_refined8.0668.052610
X-RAY DIFFRACTIONr_long_range_B_other8.0157.5542570
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded47.89151
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 75 -
Rwork0.283 1427 -
obs--99.4 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
16.1059-0.62580.16282.93262.58138.17640.1286-0.39870.5604-0.0808-0.1106-0.0968-0.8549-0.0338-0.0180.2384-0.06870.02080.2404-0.0140.2498-13.360835.9439-11.3175
22.63290.07260.6362.22521.979810.907-0.12060.20720.0173-0.48870.325-0.19840.29310.7321-0.20440.4356-0.0082-0.02450.3222-0.03230.2247-9.275516.7542-39.3275
30.24120.4181-0.07152.46282.24744.81750.0433-0.0194-0.09870.18010.2763-0.21320.89180.3213-0.31960.39440.0462-0.11390.3241-0.0340.3047-12.064614.7076-22.7303
42.4865-0.64320.9071.74050.43394.39140.10780.11820.289-0.30940.028-0.0794-0.57580.2248-0.13570.2341-0.03060.0540.2283-0.02110.231-12.09634.784-16.5729
52.48951.6376-3.926514.7773-4.938120.99280.18510.01950.491-0.25210.45180.3606-1.1253-0.5658-0.63690.44820.0328-0.04560.2173-0.00490.3254-16.330724.5024-36.0324
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A122 - 152
2X-RAY DIFFRACTION2A153 - 189
3X-RAY DIFFRACTION3A190 - 311
4X-RAY DIFFRACTION4A312 - 394
5X-RAY DIFFRACTION5C2 - 9

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