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- PDB-1bkd: COMPLEX OF HUMAN H-RAS WITH HUMAN SOS-1 -

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Basic information

Entry
Database: PDB / ID: 1bkd
TitleCOMPLEX OF HUMAN H-RAS WITH HUMAN SOS-1
Components
  • H-RAS
  • SON OF SEVENLESS-1
KeywordsCOMPLEX(ONCOGENE PROTEIN/EXCHANGE FACTOR) / COMPLEX (ONCOGENE PROTEIN-EXCHANGE FACTOR) / SMALL GTPASE / EXCHANGE FACTOR / COMPLEX(ONCOGENE PROTEIN-EXCHANGE FACTOR) COMPLEX
Function / homology
Function and homology information


GTPase complex / phospholipase C activator activity / Interleukin-15 signaling / oncogene-induced cell senescence / Activation of RAC1 / positive regulation of miRNA metabolic process / Signaling by LTK / leukocyte migration / T-helper 1 type immune response / epidermal growth factor receptor binding ...GTPase complex / phospholipase C activator activity / Interleukin-15 signaling / oncogene-induced cell senescence / Activation of RAC1 / positive regulation of miRNA metabolic process / Signaling by LTK / leukocyte migration / T-helper 1 type immune response / epidermal growth factor receptor binding / Regulation of KIT signaling / neurotrophin TRK receptor signaling pathway / NRAGE signals death through JNK / positive regulation of ruffle assembly / defense response to protozoan / positive regulation of wound healing / Fc-epsilon receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / adipose tissue development / RET signaling / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / Role of LAT2/NTAL/LAB on calcium mobilization / Interleukin receptor SHC signaling / SOS-mediated signalling / Signal attenuation / positive regulation of protein targeting to membrane / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / Schwann cell development / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / positive regulation of Rac protein signal transduction / SHC-mediated cascade:FGFR3 / positive regulation of epidermal growth factor receptor signaling pathway / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / 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 / p38MAPK events / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / RAC1 GTPase cycle / Tie2 Signaling / protein-membrane adaptor activity / Signaling by FGFR2 in disease / myelination / EPHB-mediated forward signaling / insulin-like growth factor receptor signaling pathway / Signaling by FLT3 fusion proteins / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / FCERI mediated Ca+2 mobilization / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / positive regulation of epithelial cell proliferation / GRB2 events in ERBB2 signaling / Downstream signal transduction / intrinsic apoptotic signaling pathway / Insulin receptor signalling cascade / guanyl-nucleotide exchange factor activity / SHC1 events in ERBB2 signaling / response to ischemia / Constitutive Signaling by Overexpressed ERBB2 / Ras activation upon Ca2+ influx through NMDA receptor / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / axon guidance / animal organ morphogenesis / B cell receptor signaling pathway / GTPase activator activity / VEGFR2 mediated cell proliferation / T cell activation / regulation of actin cytoskeleton organization / small monomeric GTPase / FCERI mediated MAPK activation / regulation of long-term neuronal synaptic plasticity / molecular condensate scaffold activity / Signaling by ERBB2 TMD/JMD mutants / Signaling by SCF-KIT / RAF activation / Constitutive Signaling by EGFRvIII
Similarity search - Function
Son of sevenless (SoS) protein; Chain S, domain 1 / Son of sevenless (SoS) protein Chain: S domain 1 / 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 ...Son of sevenless (SoS) protein; Chain S, domain 1 / Son of sevenless (SoS) protein Chain: S domain 1 / 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. / Small GTPase, Ras-type / Small GTPase Ras domain profile. / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Histone-fold / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GTPase HRas / Son of sevenless homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.8 Å
AuthorsBoriack-Sjodin, P.A. / Margarit, S.M. / Sagi, D.B. / Kuriyan, J.
CitationJournal: Nature / Year: 1998
Title: The structural basis of the activation of Ras by Sos.
Authors: Boriack-Sjodin, P.A. / Margarit, S.M. / Bar-Sagi, D. / Kuriyan, J.
History
DepositionJul 6, 1998Processing site: BNL
Revision 1.0Jan 13, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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
R: H-RAS
S: SON OF SEVENLESS-1


Theoretical massNumber of molelcules
Total (without water)74,8942
Polymers74,8942
Non-polymers00
Water46826
1
R: H-RAS
S: SON OF SEVENLESS-1

R: H-RAS
S: SON OF SEVENLESS-1

R: H-RAS
S: SON OF SEVENLESS-1

R: H-RAS
S: SON OF SEVENLESS-1


Theoretical massNumber of molelcules
Total (without water)299,5778
Polymers299,5778
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-y+1,x,z1
crystal symmetry operation4_565y,-x+1,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Unit cell
Length a, b, c (Å)142.700, 142.700, 207.900
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein H-RAS / P21


Mass: 18875.191 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-166
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Cellular location: CYTOPLASM / Organ: BRAIN / Plasmid: PROEX HTB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P01112
#2: Protein SON OF SEVENLESS-1 / SOS


Mass: 56019.098 Da / Num. of mol.: 1 / Fragment: RAS GUANINE NUCLEOTIDE EXCHANGE FACTOR FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Cellular location: MEMBRANE-ANCHORED / Organ: BRAIN / Plasmid: PROEX HTB / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: Q07889
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 3.5 Å3/Da / Density % sol: 65 %
Crystal growpH: 8 / Details: pH 8.0
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
220 mMTris-HCl1drop
3100 mM1dropNaCl
42.7-3.2 Msodium formate1reservoir
5100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1
DetectorType: BRANDEIS / Detector: CCD / Date: Feb 1, 1998
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 26562 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Rmerge(I) obs: 0.53 / Net I/σ(I): 34
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.287 / Mean I/σ(I) obs: 5.9 / % possible all: 100
Reflection
*PLUS
Num. measured all: 283114
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameVersionClassification
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.3phasing
RefinementMethod to determine structure: MIR / Resolution: 2.8→30 Å / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.281 1327 5 %RANDOM
Rwork0.222 ---
obs0.222 26502 99.1 %-
Solvent computationSolvent model: STANDARD / Bsol: 10.78 Å2 / ksol: 0.273 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--6.191 Å20 Å20 Å2
2---6.191 Å20 Å2
3---12.382 Å2
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4984 0 0 26 5010
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.26
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_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.8→2.84 Å / Total num. of bins used: 26
RfactorNum. reflection% reflection
Rfree0.484 48 5 %
Rwork0.362 937 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor obs: 0.362

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