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- PDB-6y44: 14-3-3 Sigma in complex with phosphorylated SOS1 peptide -

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Basic information

Entry
Database: PDB / ID: 6y44
Title14-3-3 Sigma in complex with phosphorylated SOS1 peptide
Components
  • 14-3-3 protein sigma
  • Son of sevenless homolog 1
KeywordsPROTEIN BINDING / 14-3-3 / SOS1 / complex / protein / protein-protein interactions
Function / homology
Function and homology information


midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / regulation of T cell differentiation in thymus / GTPase complex / Interleukin-15 signaling / positive regulation of small GTPase mediated signal transduction ...midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / regulation of T cell differentiation in thymus / GTPase complex / Interleukin-15 signaling / positive regulation of small GTPase mediated signal transduction / Activation of RAC1 / blood vessel morphogenesis / Signaling by LTK / epidermal growth factor receptor binding / Regulation of KIT signaling / positive regulation of epidermal growth factor receptor signaling pathway / leukocyte migration / NRAGE signals death through JNK / regulation of epidermal cell division / protein kinase C inhibitor activity / positive regulation of epidermal cell differentiation / keratinocyte development / keratinization / neurotrophin TRK receptor signaling pathway / Fc-epsilon receptor signaling pathway / eyelid development in camera-type eye / regulation of cell-cell adhesion / GRB2:SOS provides linkage to MAPK signaling for Integrins / roof of mouth development / regulation of T cell proliferation / B cell homeostasis / RET signaling / cAMP/PKA signal transduction / Regulation of localization of FOXO transcription factors / keratinocyte proliferation / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / fibroblast growth factor receptor signaling pathway / Role of LAT2/NTAL/LAB on calcium mobilization / SHC1 events in ERBB4 signaling / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / hair follicle development / Interleukin receptor SHC signaling / negative regulation of keratinocyte proliferation / Signalling to RAS / establishment of skin barrier / Signal attenuation / negative regulation of protein localization to plasma membrane / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Schwann cell development / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / negative regulation of protein kinase activity / negative regulation of stem cell proliferation / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / FRS-mediated FGFR3 signaling / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / positive regulation of protein localization / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / Tie2 Signaling / Signaling by FGFR2 in disease / RAC1 GTPase cycle / myelination / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / FCERI mediated Ca+2 mobilization / NCAM signaling for neurite out-growth / GRB2 events in ERBB2 signaling / Downstream signal transduction / positive regulation of cell adhesion / Insulin receptor signalling cascade / insulin-like growth factor receptor signaling pathway / SHC1 events in ERBB2 signaling / GTPase activator activity / axon guidance / protein sequestering activity / protein export from nucleus / negative regulation of innate immune response / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Constitutive Signaling by Overexpressed ERBB2
Similarity search - Function
Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / RasGEF domain ...Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif / Guanine nucleotide exchange factor for Ras-like GTPases; N-terminal motif / Ras-like guanine nucleotide exchange factor, N-terminal / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factors N-terminal domain profile. / Ras guanine nucleotide exchange factor domain superfamily / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / RasGEF domain / Ras guanine-nucleotide exchange factors catalytic domain profile. / Guanine nucleotide exchange factor for Ras-like small GTPases / Ras guanine-nucleotide exchange factors catalytic domain / : / SOS1/NGEF-like PH domain / Dbl homology (DH) domain superfamily / RhoGEF domain / Guanine nucleotide exchange factor for Rho/Rac/Cdc42-like GTPases / Dbl homology (DH) domain / Dbl homology (DH) domain profile. / 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 profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Histone-fold / PH-like domain superfamily
Similarity search - Domain/homology
14-3-3 protein sigma / Son of sevenless homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.71 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 19, 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
Revision 1.2Nov 20, 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

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Assembly

Deposited unit
A: 14-3-3 protein sigma
P: Son of sevenless homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,00410
Polymers29,7492
Non-polymers2558
Water4,288238
1
A: 14-3-3 protein sigma
P: Son of sevenless homolog 1
hetero molecules

A: 14-3-3 protein sigma
P: Son of sevenless homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,00820
Polymers59,4984
Non-polymers51016
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area6510 Å2
ΔGint-155 kcal/mol
Surface area21630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.769, 111.627, 62.792
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-301-

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: 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 Son of sevenless homolog 1 / SOS-1


Mass: 1522.537 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q07889

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Non-polymers , 4 types, 246 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2.41 Å3/Da / Density % sol: 48.93 %
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: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.541 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Oct 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.541 Å / Relative weight: 1
ReflectionResolution: 1.71→29.81 Å / Num. obs: 31307 / % possible obs: 99.85 % / Redundancy: 6 % / CC1/2: 0.9 / Net I/σ(I): 8
Reflection shellResolution: 1.712→1.773 Å / Num. unique obs: 3088 / CC1/2: 0.9 / % possible all: 99.01

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
REFMAC5.5refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LW1

3lw1


Resolution: 1.71→29.81 Å / SU ML: 0.1878 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.0858
RfactorNum. reflection% reflection
Rfree0.2019 1553 4.96 %
Rwork0.1743 --
obs0.1756 31302 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 30.07 Å2
Refinement stepCycle: LAST / Resolution: 1.71→29.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1833 0 8 238 2079
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00642046
X-RAY DIFFRACTIONf_angle_d0.78172807
X-RAY DIFFRACTIONf_chiral_restr0.0436318
X-RAY DIFFRACTIONf_plane_restr0.0048365
X-RAY DIFFRACTIONf_dihedral_angle_d5.33922049
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.770.35871350.2292657X-RAY DIFFRACTION98.9
1.77-1.830.24811270.21162689X-RAY DIFFRACTION99.96
1.83-1.90.22151410.19562674X-RAY DIFFRACTION100
1.9-1.990.20261440.18632668X-RAY DIFFRACTION99.96
1.99-2.10.22091540.1752663X-RAY DIFFRACTION100
2.1-2.230.20831540.16932671X-RAY DIFFRACTION100
2.23-2.40.20031540.16282687X-RAY DIFFRACTION100
2.4-2.640.19391270.17112707X-RAY DIFFRACTION100
2.64-3.020.18261270.17752738X-RAY DIFFRACTION100
3.02-3.810.19821460.16532732X-RAY DIFFRACTION100
3.81-29.810.19131440.17292863X-RAY DIFFRACTION99.93

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