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- PDB-6y3r: 14-3-3 Sigma in complex with phosphorylated (Thr391) Gab2 peptide -

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Basic information

Entry
Database: PDB / ID: 6y3r
Title14-3-3 Sigma in complex with phosphorylated (Thr391) Gab2 peptide
Components
  • 14-3-3 protein sigma
  • Chain P
KeywordsPROTEIN BINDING / 14-3-3 / Gab2 / complex / protein / protein-protein interactions
Function / homology
Function and homology information


positive regulation of mast cell degranulation / STAT5 Activation / phosphatidylinositol-3,4-bisphosphate binding / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by cytosolic FGFR1 fusion mutants / Interleukin-15 signaling / regulation of epidermal cell division / protein kinase C inhibitor activity / STAT5 activation downstream of FLT3 ITD mutants / positive regulation of epidermal cell differentiation ...positive regulation of mast cell degranulation / STAT5 Activation / phosphatidylinositol-3,4-bisphosphate binding / transmembrane receptor protein tyrosine kinase adaptor activity / Signaling by cytosolic FGFR1 fusion mutants / Interleukin-15 signaling / regulation of epidermal cell division / protein kinase C inhibitor activity / STAT5 activation downstream of FLT3 ITD mutants / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / phosphatidylinositol-3,4,5-trisphosphate binding / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / RET signaling / PI3K Cascade / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / negative regulation of keratinocyte proliferation / establishment of skin barrier / Role of LAT2/NTAL/LAB on calcium mobilization / Interleukin receptor SHC signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / negative regulation of stem cell proliferation / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / protein kinase A signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / protein export from nucleus / negative regulation of innate immune response / protein sequestering activity / osteoclast differentiation / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / release of cytochrome c from mitochondria / positive regulation of protein export from nucleus / phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 / Signaling by SCF-KIT / Constitutive Signaling by Aberrant PI3K in Cancer / Signaling by CSF1 (M-CSF) in myeloid cells / intrinsic apoptotic signaling pathway in response to DNA damage / PIP3 activates AKT signaling / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / positive regulation of cell growth / regulation of cell cycle / cadherin binding / membrane raft / positive regulation of cell population proliferation / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / extracellular exosome / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
GRB2-associated-binding protein 1-4-like / 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 ...GRB2-associated-binding protein 1-4-like / 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 / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
14-3-3 protein sigma / GRB2-associated-binding protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
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: Chain P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7294
Polymers29,6802
Non-polymers492
Water7,800433
1
A: 14-3-3 protein sigma
P: Chain P
hetero molecules

A: 14-3-3 protein sigma
P: Chain P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4578
Polymers59,3604
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5230 Å2
ΔGint-44 kcal/mol
Surface area23740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.438, 111.896, 62.349
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-743-

HOH

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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 Chain P


Mass: 1453.519 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UQC2*PLUS
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 433 / 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: 2.42 Å3/Da / Density % sol: 49.22 %
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: 0.973 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: 0.973 Å / Relative weight: 1
ReflectionResolution: 1.5→66.37 Å / Num. obs: 33470 / % possible obs: 72.1 % / Redundancy: 11 % / Biso Wilson estimate: 12.39 Å2 / CC1/2: 1 / Net I/σ(I): 41.2
Reflection shellResolution: 1.5→1.53 Å / Num. unique obs: 211 / 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→45.44 Å / SU ML: 0.1282 / Cross valid method: FREE R-VALUE / σ(F): 1.48 / Phase error: 26.0454
RfactorNum. reflection% reflection
Rfree0.2196 1630 4.87 %
Rwork0.1823 --
obs0.1841 33458 72.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 18.42 Å2
Refinement stepCycle: LAST / Resolution: 1.5→45.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1927 0 2 433 2362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00581970
X-RAY DIFFRACTIONf_angle_d1.74792657
X-RAY DIFFRACTIONf_chiral_restr0.0415292
X-RAY DIFFRACTIONf_plane_restr0.0052349
X-RAY DIFFRACTIONf_dihedral_angle_d7.73611666
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.540.208220.1482467X-RAY DIFFRACTION12.78
1.54-1.590.2082500.1616980X-RAY DIFFRACTION27.13
1.59-1.650.2215800.16361348X-RAY DIFFRACTION37.27
1.65-1.720.2077880.16851761X-RAY DIFFRACTION48.29
1.72-1.80.22881030.18662207X-RAY DIFFRACTION60.09
1.8-1.890.23291300.19132886X-RAY DIFFRACTION78.95
1.89-2.010.2341830.18553588X-RAY DIFFRACTION97.74
2.01-2.160.21521860.17583668X-RAY DIFFRACTION99.48
2.16-2.380.19262020.17393651X-RAY DIFFRACTION99.82
2.38-2.730.24121950.18953683X-RAY DIFFRACTION99.85
2.73-3.430.21071860.18733738X-RAY DIFFRACTION99.97
3.43-45.40.22472050.18183851X-RAY DIFFRACTION99.51

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