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- PDB-6y3m: 14-3-3 Sigma in complex with phosphorylated ATPase peptide -

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Basic information

Entry
Database: PDB / ID: 6y3m
Title14-3-3 Sigma in complex with phosphorylated ATPase peptide
Components
  • 14-3-3 protein sigma
  • ATPase peptide
KeywordsPROTEIN BINDING / 14-3-3 / ATPase / complex / protein / protein-protein interactions
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)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsBallone, A. / Lau, R.A. / Zweipfenning, F.P.A. / Ottmann, C.
Funding support Netherlands, 1items
OrganizationGrant numberCountry
Marie Sklodowska-Curie Actions, FragNET ITN675179 Netherlands
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2020
Title: A new soaking procedure for X-ray crystallographic structural determination of protein-peptide complexes.
Authors: Ballone, A. / Lau, R.A. / Zweipfenning, F.P.A. / Ottmann, C.
History
DepositionFeb 18, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_residues
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 14-3-3 protein sigma
P: ATPase peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0166
Polymers28,9032
Non-polymers1134
Water8,629479
1
A: 14-3-3 protein sigma
P: ATPase peptide
hetero molecules

A: 14-3-3 protein sigma
P: ATPase peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,03212
Polymers57,8064
Non-polymers2268
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area4340 Å2
ΔGint-59 kcal/mol
Surface area23720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.254, 112.452, 62.885
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

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Components

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


Mass: 28226.518 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 (E. coli) / References: UniProt: P31947
#2: Protein/peptide ATPase peptide


Mass: 676.610 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#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.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 479 / 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: 2.53 Å3/Da / Density % sol: 51.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 28% (v/v) PEG400, 1.25% glycerol, 0.2M CaCl, 0.1M HEPES pH 7.5, 2mM BME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Dec 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.5→34.42 Å / Num. obs: 36795 / % possible obs: 78.7 % / Redundancy: 10.1 % / Biso Wilson estimate: 14.09 Å2 / CC1/2: 1 / Net I/σ(I): 19.7
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 207 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
REFMAC1.16_3549refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LW1

3lw1


Resolution: 1.5→34.42 Å / SU ML: 0.0866 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.426
RfactorNum. reflection% reflection
Rfree0.1966 1878 5.11 %
Rwork0.1629 --
obs0.1646 36770 78.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.76 Å2
Refinement stepCycle: LAST / Resolution: 1.5→34.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1837 0 41 479 2357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00571916
X-RAY DIFFRACTIONf_angle_d0.77962585
X-RAY DIFFRACTIONf_chiral_restr0.041286
X-RAY DIFFRACTIONf_plane_restr0.0042337
X-RAY DIFFRACTIONf_dihedral_angle_d7.00531623
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.590.2615500.18651090X-RAY DIFFRACTION32.29
1.59-1.640.1951880.16181654X-RAY DIFFRACTION49.07
1.64-1.70.19521180.1632189X-RAY DIFFRACTION64.42
1.7-1.770.19871390.16862572X-RAY DIFFRACTION77.02
1.77-1.850.21081570.16752967X-RAY DIFFRACTION86.9
1.85-1.940.20141820.16863283X-RAY DIFFRACTION97.55
1.94-2.070.20022020.16013370X-RAY DIFFRACTION100
2.07-2.230.18691960.15263406X-RAY DIFFRACTION100
2.23-2.450.1981800.15943403X-RAY DIFFRACTION99.97
2.45-2.80.20051750.16523459X-RAY DIFFRACTION99.97
2.8-3.530.19741800.16263460X-RAY DIFFRACTION100
3.53-34.40.19041870.16363601X-RAY DIFFRACTION99.89

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