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- PDB-8ccz: Crystal structure of human Sirt3 in complex with an inhibiting HI... -

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Basic information

Entry
Database: PDB / ID: 8ccz
TitleCrystal structure of human Sirt3 in complex with an inhibiting HIV1 Tat-37-59 peptide
Components
  • NAD-dependent protein deacetylase sirtuin-3, mitochondrial
  • Protein Tat
KeywordsSIGNALING PROTEIN / Sirtuin / inhibitor / HIV / complex
Function / homology
Function and homology information


viral gene expression / trans-activation response element binding / positive regulation of catalase activity / regulatory region RNA binding / positive regulation of ceramide biosynthetic process / positive regulation of viral transcription / protein serine/threonine phosphatase inhibitor activity / modulation by virus of host chromatin organization / peptidyl-lysine deacetylation / symbiont-mediated suppression of host translation initiation ...viral gene expression / trans-activation response element binding / positive regulation of catalase activity / regulatory region RNA binding / positive regulation of ceramide biosynthetic process / positive regulation of viral transcription / protein serine/threonine phosphatase inhibitor activity / modulation by virus of host chromatin organization / peptidyl-lysine deacetylation / symbiont-mediated suppression of host translation initiation / positive regulation of superoxide dismutase activity / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / host cell nucleolus / protein deacetylation / NAD-dependent histone deacetylase activity / actinin binding / Regulation of FOXO transcriptional activity by acetylation / negative regulation of peptidyl-threonine phosphorylation / NAD+ binding / negative regulation of reactive oxygen species metabolic process / RNA-binding transcription regulator activity / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / aerobic respiration / cyclin binding / positive regulation of transcription elongation by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / positive regulation of insulin secretion / negative regulation of ERK1 and ERK2 cascade / transferase activity / sequence-specific DNA binding / host cell cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / mitochondrial matrix / protein domain specific binding / virus-mediated perturbation of host defense response / DNA-templated transcription / enzyme binding / protein-containing complex / mitochondrion / zinc ion binding / extracellular region / nucleoplasm / nucleus / metal ion binding
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: 1.95 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 28, 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

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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: Protein Tat
D: Protein Tat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2946
Polymers68,1634
Non-polymers1312
Water8,503472
1
A: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
C: Protein Tat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1473
Polymers34,0812
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1600 Å2
ΔGint-3 kcal/mol
Surface area13730 Å2
MethodPISA
2
B: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
D: Protein Tat
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1473
Polymers34,0812
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-6 kcal/mol
Surface area13490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.545, 78.124, 76.575
Angle α, β, γ (deg.)90.000, 96.093, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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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.: 2
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: 2741.274 Da / Num. of mol.: 2 / Mutation: C37A / Source method: obtained synthetically / Details: C37A / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P12506
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 472 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.38 Å3/Da / Density % sol: 48.32 % / Description: Plates
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 Tat-37-59 in 10% (v/v) DMSO for 60 min at 293.15 K. The complex ...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 Tat-37-59 in 10% (v/v) DMSO 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 CHES, pH 9.0, 20% (w/v) PEG 8000 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: Jun 13, 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: 1.95→54.24 Å / Num. obs: 46174 / % possible obs: 98.83 % / Redundancy: 5.5 % / Biso Wilson estimate: 30.86 Å2 / CC1/2: 0.949 / CC star: 0.987 / Net I/σ(I): 11.97
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 0.55 / Num. unique obs: 4615 / CC1/2: 0.445 / CC star: 0.785 / % possible all: 98.88

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Processing

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

4bvb


Resolution: 1.95→54.24 Å / SU ML: 0.2762 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.4121
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2763 2335 5.06 %
Rwork0.2269 43774 -
obs0.2293 46109 98.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.87 Å2
Refinement stepCycle: LAST / Resolution: 1.95→54.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4554 0 2 472 5028
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00194675
X-RAY DIFFRACTIONf_angle_d0.51136350
X-RAY DIFFRACTIONf_chiral_restr0.0415709
X-RAY DIFFRACTIONf_plane_restr0.0043830
X-RAY DIFFRACTIONf_dihedral_angle_d19.43491768
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.990.34841480.32372501X-RAY DIFFRACTION98.48
1.99-2.030.33121300.31292592X-RAY DIFFRACTION99.38
2.03-2.080.30491530.27992547X-RAY DIFFRACTION99.08
2.08-2.130.30861620.28442510X-RAY DIFFRACTION97.66
2.13-2.190.33231360.26652551X-RAY DIFFRACTION97.46
2.19-2.250.3571310.26142564X-RAY DIFFRACTION99.59
2.25-2.330.30471370.2592601X-RAY DIFFRACTION99.38
2.33-2.410.30641180.25452583X-RAY DIFFRACTION99.52
2.41-2.510.30871160.25612606X-RAY DIFFRACTION99.23
2.51-2.620.30571240.24752598X-RAY DIFFRACTION99.05
2.62-2.760.3481640.25012541X-RAY DIFFRACTION98.29
2.76-2.930.30891440.24192522X-RAY DIFFRACTION98.49
2.93-3.160.29431390.23242600X-RAY DIFFRACTION99.42
3.16-3.480.26411770.2232572X-RAY DIFFRACTION99.46
3.48-3.980.26031230.19962603X-RAY DIFFRACTION98.98
3.98-5.010.20321000.18112643X-RAY DIFFRACTION98.35
5.01-54.240.20971330.19952640X-RAY DIFFRACTION98.51

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