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- PDB-1xdv: Experimentally Phased Structure of Human the Son of Sevenless pro... -

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Basic information

Entry
Database: PDB / ID: 1xdv
TitleExperimentally Phased Structure of Human the Son of Sevenless protein at 4.1 Ang.
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 / 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 / neurotrophin TRK receptor signaling pathway / Fc-epsilon receptor signaling pathway / eyelid development in camera-type eye / GRB2:SOS provides linkage to MAPK signaling for Integrins / roof of mouth development / regulation of T cell proliferation / B cell homeostasis / RET signaling / 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 / hair follicle development / Interleukin receptor SHC signaling / Signalling to RAS / Signal attenuation / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Schwann cell development / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / 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 / Insulin receptor signalling cascade / insulin-like growth factor receptor signaling pathway / SHC1 events in ERBB2 signaling / GTPase activator activity / 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 / guanyl-nucleotide exchange factor activity / T cell activation / response to ischemia / B cell receptor signaling pathway / FCERI mediated MAPK activation / molecular condensate scaffold activity / Signaling by ERBB2 TMD/JMD mutants / Signaling by SCF-KIT / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / SH3 domain binding / multicellular organism growth / epidermal growth factor receptor signaling pathway / cytokine-mediated 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
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. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Histone-fold / PH-like domain superfamily
Similarity search - Domain/homology
Son of sevenless homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / rigid body refinement of previously determined domains positioned in MAD map. / Resolution: 4.1 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 8, 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 1.3Aug 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)197,7732
Polymers197,7732
Non-polymers00
Water00
1
A: Son of sevenless protein homolog 1


Theoretical massNumber of molelcules
Total (without water)98,8861
Polymers98,8861
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)98,8861
Polymers98,8861
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)80.033, 124.710, 245.384
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 98886.367 Da / Num. of mol.: 2 / Fragment: residues 198-1044
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: 3.1 Å3/Da / Density % sol: 60.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: PEG 4000, HEPES, pH 7.5, VAPOR DIFFUSION, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98800, 0.97935, 0.97919, 0.96864
DetectorDate: Dec 15, 1999
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9881
20.979351
30.979191
40.968641
ReflectionResolution: 4.1→49.4 Å / Num. obs: 19738 / % possible obs: 96 %

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
MLPHAREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: rigid body refinement of previously determined domains positioned in MAD map.
Starting model: 1DBH and 1BKD

1dbh

1bkd


Resolution: 4.1→8 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
Details: The four domains of each molecule in this structure are derived from the structures 1BKD and 1DBH; two very well-refined structures. The poor R-value of this preliminary structure reflect ...Details: The four domains of each molecule in this structure are derived from the structures 1BKD and 1DBH; two very well-refined structures. The poor R-value of this preliminary structure reflect the fact that it is at such low resolution, and was not able to be refined due to that serious limitation.
RfactorNum. reflection% reflectionSelection details
Rfree0.449 14092 -10 percent
Rwork0.433 ---
all0.453 17131 --
obs0.45 15630 91 %-
Refinement stepCycle: LAST / Resolution: 4.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12516 0 0 0 12516

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