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- PDB-1dbh: DBL AND PLECKSTRIN HOMOLOGY DOMAINS FROM HSOS1 -

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Basic information

Entry
Database: PDB / ID: 1dbh
TitleDBL AND PLECKSTRIN HOMOLOGY DOMAINS FROM HSOS1
ComponentsPROTEIN (HUMAN SOS 1)
KeywordsGENE REGULATION / GUANINE NUCLEOTIDE EXCHANGE 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 / positive regulation of small GTPase mediated signal transduction / Interleukin-15 signaling ...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 / positive regulation of small GTPase mediated signal transduction / Interleukin-15 signaling / Activation of RAC1 / blood vessel morphogenesis / positive regulation of epidermal growth factor receptor signaling pathway / epidermal growth factor receptor binding / Regulation of KIT signaling / leukocyte migration / NRAGE signals death through JNK / regulation of T cell proliferation / roof of mouth development / eyelid development in camera-type eye / Fc-epsilon receptor signaling pathway / neurotrophin TRK receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / B cell homeostasis / SOS-mediated signalling / RET signaling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / hair follicle development / SHC1 events in ERBB4 signaling / Signalling to RAS / fibroblast growth factor receptor signaling pathway / Schwann cell development / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Role of LAT2/NTAL/LAB on calcium mobilization / Signal attenuation / Interleukin receptor SHC signaling / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR4 signaling / myelination / Tie2 Signaling / FRS-mediated FGFR1 signaling / molecular condensate scaffold activity / RAC1 GTPase cycle / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / GTPase activator activity / SHC1 events in ERBB2 signaling / Downstream signal transduction / FCERI mediated Ca+2 mobilization / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / guanyl-nucleotide exchange factor activity / insulin-like growth factor receptor signaling pathway / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / response to ischemia / axon guidance / multicellular organism growth / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / B cell receptor signaling pathway / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / epidermal growth factor receptor signaling pathway / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / SH3 domain binding / cytokine-mediated signaling pathway / G alpha (12/13) signalling events / Signaling by CSF1 (M-CSF) in myeloid cells / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling / insulin receptor signaling pathway / regulation of cell population proliferation / RAF/MAP kinase cascade / Ras protein signal transduction / Potential therapeutics for SARS / protein heterodimerization activity / neuronal cell body
Similarity search - Function
Dbl Homology Domain; Chain A / Dbl homology (DH) 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 guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily ...Dbl Homology Domain; Chain A / Dbl homology (DH) 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 guanine-nucleotide exchange factors N-terminal domain profile. / Ras-like guanine nucleotide exchange factor / Ras guanine-nucleotide exchange factor, catalytic domain superfamily / Ras guanine nucleotide exchange factor 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 / 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 / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Son of sevenless homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.3 Å
AuthorsSoisson, S.M. / Kuriyan, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1998
Title: Crystal structure of the Dbl and pleckstrin homology domains from the human Son of sevenless protein.
Authors: Soisson, S.M. / Nimnual, A.S. / Uy, M. / Bar-Sagi, D. / Kuriyan, J.
History
DepositionDec 17, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Dec 23, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (HUMAN SOS 1)


Theoretical massNumber of molelcules
Total (without water)41,3131
Polymers41,3131
Non-polymers00
Water1,24369
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.400, 70.440, 73.830
Angle α, β, γ (deg.)90.00, 96.29, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN (HUMAN SOS 1) / SON OF SEVENLESS PROTEIN


Mass: 41312.812 Da / Num. of mol.: 1 / Fragment: DBL AND PLECKSTRIN HOMOLOGY DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q07889
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 69 / Source method: isolated from a natural source / Formula: H2O

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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: 3.21 Å3/Da / Density % sol: 62 %
Description: SELENOMETHIONINE MAD DATA WERE COLLECTED USING INVERSE-BEAM GEOMETRY
Crystal growpH: 6.5
Details: 5 MG/ML PROTEIN 100 MM BIS-TRIS PH 6.5 1-3% PEG6000 1 MM DTT
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
15 mg/mlprotein1drop
21-3 %PEG60001drop
3100 mMBis-Tris1droppH6.5
41-3 %PEG60001reservoir
5100 mMBis-Tris1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9686, 0.9792, 0.9794, 0.9856
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.96861
20.97921
30.97941
40.98561
ReflectionResolution: 2.3→30 Å / Num. obs: 23805 / % possible obs: 99 % / Redundancy: 19 % / Rsym value: 0.036 / Net I/σ(I): 21.1
Reflection shellResolution: 2.3→2.4 Å / Mean I/σ(I) obs: 5 / Rsym value: 0.187 / % possible all: 96.9
Reflection
*PLUS
Num. measured all: 238642 / Rmerge(I) obs: 0.036
Reflection shell
*PLUS
% possible obs: 96.9 % / Rmerge(I) obs: 0.187

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Processing

Software
NameVersionClassification
MLPHAREphasing
CNSCNS-03refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.3→30 Å / Data cutoff high rms absF: 1000000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: DISORDERED SIDE CHAIN ATOM OCCUPANCIES WERE SET TO ZERO
RfactorNum. reflection% reflectionSelection details
Rfree0.269 2393 10 %RANDOM
Rwork0.229 ---
obs0.229 23586 99.1 %-
Solvent computationSolvent model: DENSITY MODIFICATION / Bsol: 45.4 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso mean: 44.7 Å2
Baniso -1Baniso -2Baniso -3
1-4.595 Å20 Å26.104 Å2
2--5.69 Å20 Å2
3----10.284 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2748 0 0 69 2817
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.256
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.242
X-RAY DIFFRACTIONc_mcangle_it3.592.5
X-RAY DIFFRACTIONc_scbond_it3.322.5
X-RAY DIFFRACTIONc_scangle_it4.713
LS refinement shellResolution: 2.3→2.32 Å / Total num. of bins used: 47 /
RfactorNum. reflection
Rfree0.319 33
Rwork0.274 462
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAM
Software
*PLUS
Name: 'CNS CNS-03' / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 44.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal target
X-RAY DIFFRACTIONc_mcbond_it2
X-RAY DIFFRACTIONc_scbond_it2.5
X-RAY DIFFRACTIONc_mcangle_it2.5
X-RAY DIFFRACTIONc_scangle_it3
LS refinement shell
*PLUS
Rfactor Rfree: 0.319 / Rfactor Rwork: 0.274

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