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- PDB-3ksy: Crystal structure of the Histone domain, DH-PH unit, and catalyti... -

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Basic information

Entry
Database: PDB / ID: 3ksy
TitleCrystal structure of the Histone domain, DH-PH unit, and catalytic unit of the Ras activator Son of Sevenless (SOS)
ComponentsSon of sevenless homolog 1
KeywordsSIGNALING PROTEIN / Ras / SOS / Ras activator / Son of Sevenless / Disease mutation / Guanine-nucleotide releasing factor
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 / Activation of RAC1 ...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 / Activation of RAC1 / positive regulation of small GTPase mediated signal transduction / Signaling by LTK / blood vessel morphogenesis / epidermal growth factor receptor binding / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / leukocyte migration / NRAGE signals death through JNK / eyelid development in camera-type eye / Fc-epsilon receptor signaling pathway / roof of mouth development / neurotrophin TRK receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / B cell homeostasis / regulation of T cell proliferation / RET signaling / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / hair follicle development / fibroblast growth factor receptor signaling pathway / Role of LAT2/NTAL/LAB on calcium mobilization / Signalling to RAS / Interleukin receptor SHC signaling / Signal attenuation / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Schwann cell development / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / RAC1 GTPase cycle / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / myelination / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / FCERI mediated Ca+2 mobilization / GRB2 events in ERBB2 signaling / Downstream signal transduction / SHC1 events in ERBB2 signaling / Insulin receptor signalling cascade / GTPase activator activity / insulin-like growth factor receptor signaling pathway / axon guidance / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / T cell activation / guanyl-nucleotide exchange factor activity / response to ischemia / B cell receptor signaling pathway / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / molecular condensate scaffold activity / Signaling by SCF-KIT / Constitutive Signaling by EGFRvIII / cytokine-mediated signaling pathway / Signaling by ERBB2 ECD mutants / multicellular organism growth / Signaling by ERBB2 KD Mutants / SH3 domain binding / epidermal growth factor receptor signaling pathway / Signaling by CSF1 (M-CSF) in myeloid cells / insulin receptor signaling pathway / DAP12 signaling / G alpha (12/13) signalling events / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / regulation of cell population proliferation / RAF/MAP kinase cascade / Potential therapeutics for SARS / Ras protein signal transduction
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3060 / Son of sevenless (SoS) protein; Chain S, domain 1 / Son of sevenless (SoS) protein Chain: S domain 1 / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Son of Sevenless (SoS) protein; Chain S, domain 2 / Ras guanine-nucleotide exchange factors catalytic domain / Ras guanine-nucleotide exchange factor, conserved site / Ras Guanine-nucleotide exchange factors domain signature. / RasGEF N-terminal motif ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #3060 / Son of sevenless (SoS) protein; Chain S, domain 1 / Son of sevenless (SoS) protein Chain: S domain 1 / Dbl Homology Domain; Chain A / Dbl homology (DH) domain / Son of Sevenless (SoS) protein; Chain S, domain 2 / Ras guanine-nucleotide exchange factors catalytic 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 / Histone, subunit A / 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. / Histone, subunit A / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Helix non-globular / Special / Core histone H2A/H2B/H3/H4 / Histone-fold / PH-like domain superfamily / Roll / Up-down Bundle / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Son of sevenless homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.178 Å
AuthorsGureasko, J. / Kuchment, O. / Kuriyan, J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Role of the histone domain in the autoinhibition and activation of the Ras activator Son of Sevenless.
Authors: Gureasko, J. / Kuchment, O. / Makino, D.L. / Sondermann, H. / Bar-Sagi, D. / Kuriyan, J.
History
DepositionNov 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 21, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Son of sevenless homolog 1


Theoretical massNumber of molelcules
Total (without water)121,9681
Polymers121,9681
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Son of sevenless homolog 1

A: Son of sevenless homolog 1


Theoretical massNumber of molelcules
Total (without water)243,9352
Polymers243,9352
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556x,-y,-z+11
Buried area2720 Å2
ΔGint-10 kcal/mol
Surface area105260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.961, 160.918, 118.868
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 Son of sevenless homolog 1 / SOS-1


Mass: 121967.727 Da / Num. of mol.: 1 / Fragment: SOS-HDPC, (UNP residues 1-1049)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOS1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07889

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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: 2.96 Å3/Da / Density % sol: 58.44 %
Crystal growMethod: vapor diffusion, hanging drop
Details: Crystals of SOS-HDPC (residues 1-1049) were grown at room temperature using hanging-drop vapor diffusion by mixing equal volumes of protein (20 mg/ml) and reservoir solutions (140-190 mM ...Details: Crystals of SOS-HDPC (residues 1-1049) were grown at room temperature using hanging-drop vapor diffusion by mixing equal volumes of protein (20 mg/ml) and reservoir solutions (140-190 mM sodium thiocyanate, 14%-16% PEG 3350, and 0.1 M SPG (Succinic acid, Phosphate, Glycine) buffer [pH 6.0 or 6.5]). , VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1 Å
DetectorDate: Nov 19, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.18→50 Å / Num. obs: 24554

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.5_2refinement
PDB_EXTRACT3.005data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.178→47.806 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.719 / SU ML: 0.45 / σ(F): 1.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.312 1998 8.14 %R-free is R-work for 8% of reflections selected at random and omitted from refinement
Rwork0.259 ---
obs0.264 24554 99.26 %-
all-538686 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 82.153 Å2 / ksol: 0.302 e/Å3
Displacement parametersBiso max: 615.53 Å2 / Biso mean: 139.989 Å2 / Biso min: 16.16 Å2
Baniso -1Baniso -2Baniso -3
1--5.291 Å2-0 Å20 Å2
2---18.516 Å2-0 Å2
3---23.807 Å2
Refinement stepCycle: LAST / Resolution: 3.178→47.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8234 0 0 0 8234
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028413
X-RAY DIFFRACTIONf_angle_d0.52711363
X-RAY DIFFRACTIONf_chiral_restr0.0341243
X-RAY DIFFRACTIONf_plane_restr0.0031474
X-RAY DIFFRACTIONf_dihedral_angle_d8.1843209
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.178-3.2570.3921290.3181460158991
3.257-3.3450.391430.29716001743100
3.345-3.4440.3061420.28216011743100
3.444-3.5550.3581410.27215981739100
3.555-3.6820.341430.2816181761100
3.682-3.8290.3311420.27115911733100
3.829-4.0040.3331410.25716031744100
4.004-4.2140.2981430.25416111754100
4.214-4.4780.2971430.24316141757100
4.478-4.8240.3341450.23416261771100
4.824-5.3090.3151420.24716161758100
5.309-6.0760.3331460.27316401786100
6.076-7.650.3241460.27116591805100
7.65-47.8110.2161520.2011719187199
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)
18.71883.67081.2136.56640.44132.6644-0.1357-0.2640.20870.3964-0.1872-1.15290.42360.28520.04740.74890.3832-0.39540.476-0.0820.460659.817548.4562110.8839
21.2067-0.8964-1.09111.15870.6715-1.2509-0.50440.57320.12460.38980.03730.0509-0.0634-0.04620.36690.7038-0.147-0.60640.7803-0.16550.943557.533582.299499.0443
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth seq-ID
1X-RAY DIFFRACTION1resid 6:1770
2X-RAY DIFFRACTION2resid 418:5470

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