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- PDB-5wfp: Ligand-bound Ras:SOS:Ras complex -

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Basic information

Entry
Database: PDB / ID: 5wfp
TitleLigand-bound Ras:SOS:Ras complex
Components
  • GTPase HRas
  • Son of sevenless homolog 1
KeywordsSIGNALING PROTEIN / Ras / SOS / ONCOPROTEIN / Protein-protein complex / MAPK
Function / homology
Function and homology information


midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / phospholipase C activator activity / regulation of T cell differentiation in thymus / GTPase complex / Interleukin-15 signaling ...midbrain morphogenesis / regulation of pro-B cell differentiation / vitellogenesis / pericardium morphogenesis / cardiac atrium morphogenesis / heart trabecula morphogenesis / phospholipase C activator activity / regulation of T cell differentiation in thymus / GTPase complex / Interleukin-15 signaling / oncogene-induced cell senescence / positive regulation of small GTPase mediated signal transduction / Activation of RAC1 / blood vessel morphogenesis / positive regulation of miRNA metabolic process / Signaling by LTK / positive regulation of ruffle assembly / epidermal growth factor receptor binding / T-helper 1 type immune response / Regulation of KIT signaling / positive regulation of epidermal growth factor receptor signaling pathway / leukocyte migration / NRAGE signals death through JNK / positive regulation of wound healing / defense response to protozoan / neurotrophin TRK receptor signaling pathway / Fc-epsilon receptor signaling pathway / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / 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 / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RET signaling / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / fibroblast growth factor receptor signaling pathway / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / Role of LAT2/NTAL/LAB on calcium mobilization / positive regulation of protein targeting to membrane / SHC1 events in ERBB4 signaling / Interleukin receptor SHC signaling / hair follicle development / adipose tissue development / Signalling to RAS / Signal attenuation / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Schwann cell development / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / 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 / p38MAPK events / Signaling by FGFR3 in disease / protein-membrane adaptor activity / Tie2 Signaling / Signaling by FGFR2 in disease / RAC1 GTPase cycle / myelination / EPHB-mediated forward signaling / GRB2 events in EGFR signaling / Signaling by FLT3 fusion proteins / 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 / intrinsic apoptotic signaling pathway / Downstream signal transduction / GRB2 events in ERBB2 signaling / insulin-like growth factor receptor signaling pathway / Insulin receptor signalling cascade / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / axon guidance / GTPase activator activity / 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
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
Chem-5UX / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase HRas / Son of sevenless homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.08 Å
AuthorsSun, Q. / Phan, J. / Burns, M.C. / Fesik, S.W.
CitationJournal: Anal. Biochem. / Year: 2018
Title: High-throughput screening identifies small molecules that bind to the RAS:SOS:RAS complex and perturb RAS signaling.
Authors: Burns, M.C. / Howes, J.E. / Sun, Q. / Little, A.J. / Camper, D.V. / Abbott, J.R. / Phan, J. / Lee, T. / Waterson, A.G. / Rossanese, O.W. / Fesik, S.W.
History
DepositionJul 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 23, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 4, 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
Q: GTPase HRas
R: GTPase HRas
N: Son of sevenless homolog 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,3626
Polymers94,4543
Non-polymers9083
Water13,908772
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7370 Å2
ΔGint-28 kcal/mol
Surface area35390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.530, 182.530, 177.314
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

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Protein , 2 types, 3 molecules QRN

#1: Protein GTPase HRas / H-Ras-1 / Ha-Ras / Transforming protein p21 / c-H-ras / p21ras


Mass: 18932.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01112
#2: Protein Son of sevenless homolog 1 / SOS-1


Mass: 56589.781 Da / Num. of mol.: 1
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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Non-polymers , 4 types, 775 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-5UX / 6-chloranyl-~{N}-(3-chloranyl-4-fluoranyl-phenyl)-1,2,3,4-tetrahydroacridin-9-amine


Mass: 361.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H15Cl2FN2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 772 / 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: 3.91 Å3/Da / Density % sol: 68.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M sodium acetate, 2.0 M sodium formate, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 10, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.08→50 Å / Num. obs: 89373 / % possible obs: 100 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.044 / Net I/σ(I): 16.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NYI

4nyi


Resolution: 2.08→48.68 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.03
RfactorNum. reflection% reflection
Rfree0.2035 1988 2.22 %
Rwork0.1624 --
obs0.1633 89373 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.08→48.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6527 0 57 772 7356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086745
X-RAY DIFFRACTIONf_angle_d1.0529131
X-RAY DIFFRACTIONf_dihedral_angle_d14.682596
X-RAY DIFFRACTIONf_chiral_restr0.041000
X-RAY DIFFRACTIONf_plane_restr0.0041184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0779-2.12990.28741390.22176070X-RAY DIFFRACTION98
2.1299-2.18750.24911360.21046196X-RAY DIFFRACTION100
2.1875-2.25190.26651350.19756193X-RAY DIFFRACTION100
2.2519-2.32450.2191430.18676159X-RAY DIFFRACTION100
2.3245-2.40760.20351460.18276213X-RAY DIFFRACTION100
2.4076-2.5040.24821420.18426199X-RAY DIFFRACTION100
2.504-2.6180.20641410.18076209X-RAY DIFFRACTION100
2.618-2.7560.2411420.1836205X-RAY DIFFRACTION100
2.756-2.92860.21061420.17286226X-RAY DIFFRACTION100
2.9286-3.15470.20411370.16466245X-RAY DIFFRACTION100
3.1547-3.47210.1711460.15056274X-RAY DIFFRACTION100
3.4721-3.97430.15581420.13446296X-RAY DIFFRACTION100
3.9743-5.00640.16861450.1286339X-RAY DIFFRACTION100
5.0064-48.69290.22521520.16076561X-RAY DIFFRACTION100

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