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- PDB-8ccw: Crystal structure of human Sirt3 in complex with an acetylated HI... -

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Basic information

Entry
Database: PDB / ID: 8ccw
TitleCrystal structure of human Sirt3 in complex with an acetylated HIV1 Tat-46-54 substrate peptide
Components
  • NAD-dependent protein deacetylase sirtuin-3, mitochondrial
  • Protein Tat
KeywordsSIGNALING PROTEIN / Sirtuin / substrate / HIV / Tat / complex
Function / homology
Function and homology information


viral gene expression / trans-activation response element binding / positive regulation of superoxide dismutase activity / positive regulation of catalase activity / regulatory region RNA binding / protein serine/threonine phosphatase inhibitor activity / NAD-dependent protein lysine delactylase activity / positive regulation of ceramide biosynthetic process / positive regulation of viral transcription / peptidyl-lysine deacetylation ...viral gene expression / trans-activation response element binding / positive regulation of superoxide dismutase activity / positive regulation of catalase activity / regulatory region RNA binding / protein serine/threonine phosphatase inhibitor activity / NAD-dependent protein lysine delactylase activity / positive regulation of ceramide biosynthetic process / positive regulation of viral transcription / peptidyl-lysine deacetylation / symbiont-mediated perturbation of host chromatin organization / Maturation of TCA enzymes and regulation of TCA cycle / symbiont-mediated suppression of host translation initiation / 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 / host cell nucleolus / histone deacetylase activity, NAD-dependent / protein deacetylation / positive regulation of oxidative phosphorylation / actinin binding / 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 / RNA-binding transcription regulator activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / cyclin binding / aerobic respiration / positive regulation of transcription elongation by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / negative regulation of ERK1 and ERK2 cascade / positive regulation of insulin secretion / sequence-specific DNA binding / host cell cytoplasm / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / mitochondrial matrix / protein domain specific binding / DNA-templated transcription / enzyme binding / protein-containing complex / mitochondrion / extracellular region / zinc ion binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
Tat domain superfamily / Immunodeficiency virus transactivating regulatory protein (Tat) / Transactivating regulatory protein (Tat) / 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
Protein Tat / NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsAdolph, R.S. / Steegborn, C.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)STE1701/15 Germany
CitationJournal: Life / Year: 2023
Title: Molecular Mechanism of Sirtuin 1 Inhibition by Human Immunodeficiency Virus 1 Tat Protein.
Authors: Adolph, R.S. / Beck, E. / Schweimer, K. / Di Fonzo, A. / Weyand, M. / Rosch, P. / Wohrl, B.M. / Steegborn, C.
History
DepositionJan 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 10, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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: Protein Tat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6303
Polymers32,5652
Non-polymers651
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis, cross-linking, MST
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1610 Å2
ΔGint-6 kcal/mol
Surface area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.721, 127.760, 77.576
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11A-673-

HOH

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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: 31340.084 Da / Num. of mol.: 1
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, protein acetyllysine N-acetyltransferase
#2: Protein/peptide Protein Tat / Transactivating regulatory protein


Mass: 1224.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: acetylated at K50 / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P12506
#3: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.99 Å3/Da / Density % sol: 58.93 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 10 mg/ml human Sirt3-(118-399) in 20 mM Tris/HCl, pH 8.0, 150 mM NaCl, 5% (v/v) glycerol, 1 mM TCEP were incubated with 2 mM ac-Tat-46-54 for 60 min at 293.15 K. The complex was crystallized ...Details: 10 mg/ml human Sirt3-(118-399) in 20 mM Tris/HCl, pH 8.0, 150 mM NaCl, 5% (v/v) glycerol, 1 mM TCEP were incubated with 2 mM ac-Tat-46-54 for 60 min at 293.15 K. The complex was crystallized using the sitting-drop vapor-diffusion method at 293.15 K with 100 mM MES, pH 6.0, 30% (w/v) PEG 200, 5% (w/v) PEG 3000 as reservoir solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 12, 2018
RadiationMonochromator: DCM Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.65→39.36 Å / Num. obs: 47332 / % possible obs: 99.89 % / Redundancy: 11.2 % / Biso Wilson estimate: 31.51 Å2 / CC1/2: 0.999 / CC star: 1 / Net I/σ(I): 13.93
Reflection shellResolution: 1.65→1.709 Å / Redundancy: 11.2 % / Mean I/σ(I) obs: 0.89 / Num. unique obs: 4698 / CC1/2: 0.469 / CC star: 0.799 / % possible all: 99.94

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Processing

Software
NameVersionClassification
XDSdata reduction
PHASERphasing
Cootmodel building
PHENIX1.17.1_3660refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FVT

4fvt


Resolution: 1.65→39.36 Å / SU ML: 0.2872 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.9404
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2089 1090 -
Rwork0.1807 88895 -
obs0.1813 47317 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.94 Å2
Refinement stepCycle: LAST / Resolution: 1.65→39.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2233 0 1 287 2521
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01662302
X-RAY DIFFRACTIONf_angle_d1.3823134
X-RAY DIFFRACTIONf_chiral_restr0.0963353
X-RAY DIFFRACTIONf_plane_restr0.0096409
X-RAY DIFFRACTIONf_dihedral_angle_d20.3968867
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.690.5211400.44545865X-RAY DIFFRACTION98.27
1.69-1.730.42021330.37515856X-RAY DIFFRACTION99.82
1.73-1.780.33941410.31795958X-RAY DIFFRACTION99.92
1.78-1.830.2821420.27295976X-RAY DIFFRACTION99.82
1.83-1.890.27561400.25045912X-RAY DIFFRACTION99.93
1.89-1.950.24251370.23255920X-RAY DIFFRACTION99.85
1.95-2.030.27151420.21925954X-RAY DIFFRACTION99.95
2.03-2.130.18121390.18365948X-RAY DIFFRACTION99.97
2.13-2.240.27451410.1765896X-RAY DIFFRACTION99.95
2.24-2.380.19241390.1715935X-RAY DIFFRACTION99.88
2.38-2.560.16651380.16865936X-RAY DIFFRACTION99.98
2.56-2.820.16861430.1675940X-RAY DIFFRACTION99.98
2.82-3.230.20461380.17075913X-RAY DIFFRACTION99.8
3.23-4.060.19911430.15825944X-RAY DIFFRACTION100
4.07-39.360.1911410.16335942X-RAY DIFFRACTION99.72

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