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- PDB-1xd4: Crystal structure of the DH-PH-cat module of Son of Sevenless (SOS) -

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Basic information

Entry
Database: PDB / ID: 1xd4
TitleCrystal structure of the DH-PH-cat module of Son of Sevenless (SOS)
ComponentsSon of sevenless protein homolog 1
KeywordsSIGNALING PROTEIN / nucleotide exchange factor / Ras / Cdc25 / Ras exchanger motif (Rem) / Dbl homology(DH) / pleckstrin homology (PH)
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
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 ...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 / 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. / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / 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: 3.64 Å
AuthorsSondermann, H. / Soisson, S.M. / Boykevisch, S. / Yang, S.S. / Bar-Sagi, D. / Kuriyan, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2004
Title: Structural analysis of autoinhibition in the ras activator son of sevenless.
Authors: Sondermann, H. / Soisson, S.M. / Boykevisch, S. / Yang, S.S. / Bar-Sagi, D. / Kuriyan, J.
History
DepositionSep 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 23, 2023Group: 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
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: Son of sevenless protein homolog 1
B: Son of sevenless protein homolog 1


Theoretical massNumber of molelcules
Total (without water)198,7922
Polymers198,7922
Non-polymers00
Water00
1
A: Son of sevenless protein homolog 1


Theoretical massNumber of molelcules
Total (without water)99,3961
Polymers99,3961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Son of sevenless protein homolog 1


Theoretical massNumber of molelcules
Total (without water)99,3961
Polymers99,3961
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.470, 127.360, 279.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe asymmetric unit consists of 2 molecules. The biological assembly is a monomer.

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Components

#1: Protein Son of sevenless protein homolog 1 / SOS-1


Mass: 99395.953 Da / Num. of mol.: 2 / Fragment: residues 198-1049
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOS1 / Plasmid: pProExHTa / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / 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: 3.2 Å3/Da / Density % sol: 62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG200, ethylene glycol, strontium chloride, HEPES, sucrose, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 7, 2003
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 3.62→50 Å / Num. all: 30085 / Num. obs: 29501 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.1 % / Biso Wilson estimate: 82.3 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.041 / Net I/σ(I): 20.6
Reflection shellResolution: 3.62→3.75 Å / Rmerge(I) obs: 0.631 / Mean I/σ(I) obs: 2.2 / Rsym value: 0.518 / % possible all: 90.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
CCP4phasing
REFMACrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entris 1DBH, 1BKD, 1NVV

1dbh

1bkd

1nvv


Resolution: 3.64→11.99 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 221147.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.371 2033 7.6 %RANDOM
Rwork0.307 ---
obs0.307 26917 92 %-
all-28950 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 36.9047 Å2 / ksol: 0.169641 e/Å3
Displacement parametersBiso mean: 153.8 Å2
Baniso -1Baniso -2Baniso -3
1-33.79 Å20 Å20 Å2
2---27.34 Å20 Å2
3----6.45 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.74 Å0.61 Å
Luzzati d res low-5 Å
Luzzati sigma a1.17 Å0.93 Å
Refinement stepCycle: LAST / Resolution: 3.64→11.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13542 0 0 0 13542
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d20.5
X-RAY DIFFRACTIONc_improper_angle_d1.09
LS refinement shellResolution: 3.64→3.84 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.5 236 7.4 %
Rwork0.427 2964 -
obs--65.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP

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