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- PDB-6zvc: 14-3-3 Sigma in complex with phosphorylated Gab2pT391 peptide - 4... -

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Basic information

Entry
Database: PDB / ID: 6zvc
Title14-3-3 Sigma in complex with phosphorylated Gab2pT391 peptide - 48h incubation
Components
  • 14-3-3 protein sigma
  • phosphorylated Gab2pT391 peptide
KeywordsPROTEIN BINDING / 14-3-3 / Gab2pT391 / 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 cell-cell adhesion / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / phosphoserine residue binding / Activation of BAD and translocation to mitochondria ...regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / regulation of cell-cell adhesion / 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 / negative regulation of protein localization to plasma membrane / 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 / positive regulation of protein localization / RHO GTPases activate PKNs / protein kinase A signaling / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / positive regulation of cell adhesion / 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 / intrinsic apoptotic signaling pathway in response to DNA damage / protein localization / regulation of protein localization / 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 / MOLECULAR REPLACEMENT / Resolution: 2.51 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: To Be Published
Title: A new soaking procedure for X-ray crystallography structural determination of protein-peptide complexes
Authors: Ballone, A. / Lau, R.A. / Zweipfenning, F.P.A. / Ottmann, C.
History
DepositionJul 24, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 31, 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
Revision 1.2Nov 13, 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: phosphorylated Gab2pT391 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8424
Polymers29,7932
Non-polymers492
Water3,513195
1
A: 14-3-3 protein sigma
P: phosphorylated Gab2pT391 peptide
hetero molecules

A: 14-3-3 protein sigma
P: phosphorylated Gab2pT391 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6848
Polymers59,5864
Non-polymers974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area5300 Å2
ΔGint-42 kcal/mol
Surface area23680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.574, 112.508, 62.665
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-418-

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 phosphorylated Gab2pT391 peptide


Mass: 1566.677 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: None / Source: (synth.) Homo sapiens (human)
#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


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O
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: 2.44 Å3/Da / Density % sol: 49.64 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 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: SEALED TUBE / Type: RIGAKU / Wavelength: 1.541 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 16, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 2.51→28.35 Å / Num. obs: 10297 / % possible obs: 99.5 % / Redundancy: 6.1 % / CC1/2: 0.997 / Net I/σ(I): 19
Reflection shellResolution: 2.51→2.55 Å / Num. unique obs: 466 / CC1/2: 0.995

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Processing

Software
NameVersionClassification
REFMAC1.16_3549refinement
PHENIX5.5refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LW1

3lw1


Resolution: 2.51→28.35 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.886 / SU B: 6.782 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.567 / ESU R Free: 0.273 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22894 521 5.1 %RANDOM
Rwork0.17124 ---
obs0.17421 9762 99.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.088 Å2
Baniso -1Baniso -2Baniso -3
1-0.79 Å20 Å2-0 Å2
2---0.54 Å20 Å2
3----0.24 Å2
Refinement stepCycle: 1 / Resolution: 2.51→28.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 2 195 2112
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0131958
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171810
X-RAY DIFFRACTIONr_angle_refined_deg1.3211.6492642
X-RAY DIFFRACTIONr_angle_other_deg1.5961.584196
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8565248
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65322.222108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.63315353
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.6961516
X-RAY DIFFRACTIONr_chiral_restr0.0680.2255
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022216
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02404
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5231.094989
X-RAY DIFFRACTIONr_mcbond_other1.5181.092988
X-RAY DIFFRACTIONr_mcangle_it2.7031.6281235
X-RAY DIFFRACTIONr_mcangle_other2.7031.6311236
X-RAY DIFFRACTIONr_scbond_it1.211.067969
X-RAY DIFFRACTIONr_scbond_other1.2011.062967
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0721.5671406
X-RAY DIFFRACTIONr_long_range_B_refined5.1217.2568374
X-RAY DIFFRACTIONr_long_range_B_other4.9917.0558235
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.51→2.57 Å
RfactorNum. reflection% reflection
Rfree0.236 36 -
Rwork0.168 671 -
obs--96.45 %

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