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- PDB-8anc: 14-3-3 sigma sirtuin-3 phospho-peptide complex -

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Basic information

Entry
Database: PDB / ID: 8anc
Title14-3-3 sigma sirtuin-3 phospho-peptide complex
Components
  • 14-3-3 protein sigma
  • NAD-dependent protein deacetylase sirtuin-3, mitochondrial
KeywordsPEPTIDE BINDING PROTEIN / Human sirtuin / human 14-3-3 sigma / protein complex / phospho-peptide / NAD / deacetylase
Function / homology
Function and homology information


positive regulation of superoxide dismutase activity / positive regulation of catalase activity / NAD-dependent protein lysine delactylase activity / positive regulation of ceramide biosynthetic process / peptidyl-lysine deacetylation / Maturation of TCA enzymes and regulation of TCA cycle / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / protein deacetylation / histone deacetylase activity, NAD-dependent ...positive regulation of superoxide dismutase activity / positive regulation of catalase activity / NAD-dependent protein lysine delactylase activity / positive regulation of ceramide biosynthetic process / peptidyl-lysine deacetylation / Maturation of TCA enzymes and regulation of TCA cycle / 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 / regulation of epidermal cell division / protein kinase C inhibitor activity / cellular response to stress / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / negative regulation of reactive oxygen species metabolic process / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / NAD+ binding / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / Mitochondrial unfolded protein response (UPRmt) / establishment of skin barrier / negative regulation of protein localization to plasma membrane / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of protein kinase activity / positive regulation of protein localization / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of cell adhesion / protein sequestering activity / negative regulation of innate immune response / protein export from nucleus / aerobic respiration / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / stem cell proliferation / Translocation of SLC2A4 (GLUT4) to the plasma membrane / TP53 Regulates Metabolic Genes / Transcriptional activation of mitochondrial biogenesis / negative regulation of ERK1 and ERK2 cascade / positive regulation of insulin secretion / intrinsic apoptotic signaling pathway in response to DNA damage / intracellular protein localization / regulation of protein localization / positive regulation of cell growth / sequence-specific DNA binding / regulation of cell cycle / cadherin binding / mitochondrial matrix / protein kinase binding / enzyme binding / negative regulation of transcription by RNA polymerase II / signal transduction / protein-containing complex / mitochondrion / extracellular space / extracellular exosome / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 protein sigma / DHS-like NAD/FAD-binding domain superfamily ...Sirtuin, catalytic core small domain superfamily / Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / 14-3-3 domain / Delta-Endotoxin; domain 1 / 14-3-3 protein sigma / DHS-like NAD/FAD-binding domain superfamily / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
14-3-3 protein sigma / NAD-dependent protein deacetylase sirtuin-3, mitochondrial
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.11 Å
AuthorsWeyand, M. / Steegborn, C. / Debbert, L.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)DFG STE-1701/15 Germany
CitationJournal: To Be Published
Title: 14-3-3 sigma sirtuin-3 phospho-peptide complex
Authors: Weyand, M. / Steegborn, C.
History
DepositionAug 5, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 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: 14-3-3 protein sigma
P: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9668
Polymers27,7772
Non-polymers1896
Water7,206400
1
A: 14-3-3 protein sigma
P: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules

A: 14-3-3 protein sigma
P: NAD-dependent protein deacetylase sirtuin-3, mitochondrial
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,93116
Polymers55,5544
Non-polymers37712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5530 Å2
ΔGint-104 kcal/mol
Surface area23760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.600, 112.390, 62.690
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-302-

MG

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Components

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Protein / Protein/peptide , 2 types, 2 molecules AP

#1: Protein 14-3-3 protein sigma / Epithelial cell marker protein 1 / Stratifin


Mass: 26558.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P31947
#2: Protein/peptide NAD-dependent protein deacetylase sirtuin-3, mitochondrial / hSIRT3 / Regulatory protein SIR2 homolog 3 / SIR2-like protein 3 / Sirtuin-3


Mass: 1218.259 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: Q9NTG7, protein acetyllysine N-acetyltransferase

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Non-polymers , 4 types, 406 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 400 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.62 Å3/Da / Density % sol: 53.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes/NaOH pH 7.5, 0.2 M CaCl2, 26% (v/v) PEG 400, 5% (v/v) glycerol, 1 mM TCEP

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.918409 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.918409 Å / Relative weight: 1
ReflectionResolution: 1.11→45.68 Å / Num. obs: 111528 / % possible obs: 97.6 % / Redundancy: 3.504 % / Biso Wilson estimate: 12.932 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.051 / Rrim(I) all: 0.061 / Χ2: 0.937 / Net I/σ(I): 13.19 / Num. measured all: 390760 / Scaling rejects: 33
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.11-1.142.7780.6361.7519502840670200.6330.7883.5
1.14-1.173.2810.4632.5125607815478040.7950.55395.7
1.17-1.213.1470.3972.8124068794976490.8290.47796.2
1.21-1.243.4520.3383.4825845767674880.8760.39997.6
1.24-1.283.4820.2914.0525720753473870.9030.34398
1.28-1.333.4740.2384.9524896723071670.930.2899.1
1.33-1.383.380.25.6923610701769860.9460.23899.6
1.38-1.443.620.1766.7224162670766750.960.20699.5
1.44-1.53.7660.139.124375649264720.980.15199.7
1.5-1.573.7480.10211.2523037617261460.9880.11999.6
1.57-1.663.6360.08413.1621416591058900.990.09899.7
1.66-1.763.4950.06715.4719496559555790.9930.07999.7
1.76-1.883.8780.05819.2320299525452350.9960.06799.6
1.88-2.033.8230.04524.0718732491449000.9970.05399.7
2.03-2.223.740.03530.116821451744980.9980.0499.6
2.22-2.493.4490.0333.4614093411540860.9980.03699.3
2.49-2.873.8440.02838.8413951363536290.9990.03399.8
2.87-3.523.7740.02644.411688311330970.9990.0399.5
3.52-4.973.4130.02346.598283244024270.9990.02799.5
4.97-45.683.7040.02548.085159140713930.9990.02999

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMAC5.8.0352refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YWT

1ywt


Resolution: 1.11→45.68 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.976 / SU B: 0.855 / SU ML: 0.018 / SU R Cruickshank DPI: 0.0289 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.029 / ESU R Free: 0.029 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1456 5111 5.1 %RANDOM
Rwork0.1269 ---
obs0.1278 95338 87.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 242.89 Å2 / Biso mean: 13.818 Å2 / Biso min: 5.45 Å2
Baniso -1Baniso -2Baniso -3
1--0.49 Å2-0 Å20 Å2
2---0.62 Å2-0 Å2
3---1.11 Å2
Refinement stepCycle: final / Resolution: 1.11→45.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1893 0 6 405 2304
Biso mean--21.53 32.9 -
Num. residues----246
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0122324
X-RAY DIFFRACTIONr_bond_other_d0.0270.0162165
X-RAY DIFFRACTIONr_angle_refined_deg1.7461.6463211
X-RAY DIFFRACTIONr_angle_other_deg1.1461.5545127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7345348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.3691019
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.91910453
X-RAY DIFFRACTIONr_chiral_restr0.0960.2362
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.022789
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02463
X-RAY DIFFRACTIONr_rigid_bond_restr16.64634489
LS refinement shellResolution: 1.112→1.141 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.356 171 -
Rwork0.35 3189 -
all-3360 -
obs--39.96 %

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