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- PDB-8anb: 14-3-3 sigma sirtuin-1 phospho-peptide complex -

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Basic information

Entry
Database: PDB / ID: 8anb
Title14-3-3 sigma sirtuin-1 phospho-peptide complex
Components
  • 14-3-3 protein sigma
  • Sirtuin 1 deacetylase
KeywordsPEPTIDE BINDING PROTEIN / Human sirtuin / human 14-3-3 sigma / protein complex / phospho-peptide / NAD / deacetylase
Function / homology
Function and homology information


regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation ...regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / protein kinase A signaling / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / protein export from nucleus / negative regulation of innate immune response / protein sequestering activity / 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 / negative regulation of protein kinase activity / negative regulation of cysteine-type endopeptidase activity involved in apoptotic process / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of cell growth / regulation of cell cycle / cadherin binding / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
14-3-3 protein sigma / 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
Similarity search - Domain/homology
14-3-3 protein sigma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.64 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-1 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

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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: Sirtuin 1 deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3064
Polymers27,2472
Non-polymers602
Water5,819323
1
A: 14-3-3 protein sigma
P: Sirtuin 1 deacetylase
hetero molecules

A: 14-3-3 protein sigma
P: Sirtuin 1 deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,6138
Polymers54,4934
Non-polymers1204
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_567x,-y+1,-z+21
Buried area4410 Å2
ΔGint-55 kcal/mol
Surface area21980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.010, 95.550, 79.940
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 26139.461 Da / Num. of mol.: 1 / Fragment: UNP residues 1-231
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SFN, HME1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21 / References: UniProt: P31947
#2: Protein/peptide Sirtuin 1 deacetylase


Mass: 1107.047 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 323 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.84 Å3/Da / Density % sol: 56.67 %
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: 1.64→48.89 Å / Num. obs: 38275 / % possible obs: 99.6 % / Redundancy: 3.652 % / Biso Wilson estimate: 26.932 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rrim(I) all: 0.05 / Χ2: 0.986 / Net I/σ(I): 18.55 / Num. measured all: 139769
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
1.64-1.683.5480.3214.129618279127110.9040.37997.1
1.68-1.733.5320.2594.999733276227560.9230.30699.8
1.73-1.783.4760.2215.729253266726620.9370.26299.8
1.78-1.833.7140.1817.289553257425720.9590.21299.9
1.83-1.893.8210.1498.829641252625230.9770.17499.9
1.89-1.963.7790.12310.589203243624350.9810.144100
1.96-2.033.7720.09313.368856234823480.990.109100
2.03-2.123.730.07216.358418226022570.9930.08599.9
2.12-2.213.5090.058197575216421590.9950.06999.8
2.21-2.323.5630.0521.857492210821030.9960.05999.8
2.32-2.443.8760.04624.877581195719560.9970.05499.9
2.44-2.593.8280.04326.357265189918980.9970.0599.9
2.59-2.773.7760.03828.856645176317600.9980.04499.8
2.77-2.993.650.03531.446051166816580.9970.04199.4
2.99-3.283.4130.03233.25147151715080.9970.03899.4
3.28-3.663.640.0338.115041139113850.9980.03599.6
3.66-4.233.7410.02840.84609123912320.9980.03399.4
4.23-5.183.5660.02840.423723104910440.9980.03399.5
5.18-7.333.280.02837.3927038328240.9980.03399
7.33-48.893.4340.02842.0516624934840.9980.03398.2

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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: 1.64→48.89 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.95 / SU B: 3.38 / SU ML: 0.06 / SU R Cruickshank DPI: 0.0877 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.088 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2044 1943 5.1 %RANDOM
Rwork0.1757 ---
obs0.1772 36279 99.59 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 80.18 Å2 / Biso mean: 20.754 Å2 / Biso min: 11.14 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20 Å2-0 Å2
2--0.31 Å20 Å2
3----0.53 Å2
Refinement stepCycle: final / Resolution: 1.64→48.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1822 0 3 329 2154
Biso mean--36.13 34.26 -
Num. residues----234
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0122101
X-RAY DIFFRACTIONr_bond_other_d0.0040.0161881
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.642862
X-RAY DIFFRACTIONr_angle_other_deg0.5061.5564418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4855284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.721017
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.53910375
X-RAY DIFFRACTIONr_chiral_restr0.070.2321
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022467
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02405
LS refinement shellResolution: 1.64→1.682 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.288 122 -
Rwork0.247 2588 -
obs--97.48 %
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)
11.33430.4803-0.81581.80140.16081.9135-0.06880.0696-0.1677-0.0445-0.01910.1311-0.0639-0.13560.08790.03040.0046-0.00170.01-0.01050.056111.797628.653380.5526
212.5576-1.9890.126912.8469-0.70042.2994-0.11450.56040.5934-0.13960.14141.1666-0.3584-0.5667-0.02690.09890.0685-0.04340.17510.0570.22631.674231.835275.9696
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 231
2X-RAY DIFFRACTION2P666 - 675

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