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- PDB-8be9: Crystal structure of SOS1-HRas-peptidomimetic5 -

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Basic information

Entry
Database: PDB / ID: 8be9
TitleCrystal structure of SOS1-HRas-peptidomimetic5
Components
  • GTPase HRas
  • SOS1-HRas-peptidomimetic5
  • Son of sevenless homolog 1
KeywordsSIGNALING PROTEIN / Complex / Stabilizer
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 / positive regulation of small GTPase mediated signal transduction / Activation of RAC1 / oncogene-induced cell senescence / blood vessel morphogenesis / negative regulation of GTPase activity / Signaling by LTK / positive regulation of miRNA metabolic process / positive regulation of ruffle assembly / epidermal growth factor receptor binding / Regulation of KIT signaling / positive regulation of epidermal growth factor receptor signaling pathway / T-helper 1 type immune response / leukocyte migration / NRAGE signals death through JNK / positive regulation of wound healing / defense response to protozoan / neurotrophin TRK receptor signaling pathway / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Fc-epsilon receptor signaling pathway / eyelid development in camera-type eye / GRB2:SOS provides linkage to MAPK signaling for Integrins / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / roof of mouth development / Activation of RAS in B cells / B cell homeostasis / regulation of T cell proliferation / RET signaling / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / positive regulation of protein targeting to membrane / fibroblast growth factor receptor signaling pathway / SHC1 events in ERBB4 signaling / hair follicle development / Role of LAT2/NTAL/LAB on calcium mobilization / Interleukin receptor SHC signaling / Signalling to RAS / adipose tissue development / Signal attenuation / positive regulation of MAP kinase activity / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / Schwann cell development / 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 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / protein-membrane adaptor activity / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / positive regulation of GTPase activity / EPHB-mediated forward signaling / GRB2 events in EGFR signaling / RAC1 GTPase cycle / SHC1 events in EGFR signaling / myelination / 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 / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / intrinsic apoptotic signaling pathway / 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
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. / 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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
FORMIC ACID / GTPase HRas / Son of sevenless homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsFischer, B. / Wohlkonig, A. / Steyaert, J.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO) Belgium
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2023
Title: Nanobody Loop Mimetics Enhance Son of Sevenless 1-Catalyzed Nucleotide Exchange on RAS.
Authors: Van Holsbeeck, K. / Fischer, B. / Gonzalez, S. / Gadais, C. / Versees, W. / Martins, J.C. / Martin, C. / Wohlkonig, A. / Steyaert, J. / Ballet, S.
History
DepositionOct 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Feb 7, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.source_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: GTPase HRas
S: Son of sevenless homolog 1
P: SOS1-HRas-peptidomimetic5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,29020
Polymers81,5403
Non-polymers75117
Water2,234124
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6720 Å2
ΔGint-43 kcal/mol
Surface area29010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.410, 150.410, 200.980
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422
Space group name HallI42
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1/2,x+1/2,z+1/2
#11: y+1/2,-x+1/2,z+1/2
#12: x+1/2,-y+1/2,-z+1/2
#13: -x+1/2,y+1/2,-z+1/2
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2

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Components

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Protein , 2 types, 2 molecules RS

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


Mass: 21046.561 Da / Num. of mol.: 1
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, small monomeric GTPase
#2: Protein Son of sevenless homolog 1 / SOS-1


Mass: 59348.816 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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Protein/peptide , 1 types, 1 molecules P

#3: Protein/peptide SOS1-HRas-peptidomimetic5


Mass: 1144.285 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 141 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: CH2O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 124 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.52 Å3/Da / Density % sol: 65.01 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: sodium formate 3 M, Tris 100mM pH 8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980105 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980105 Å / Relative weight: 1
ReflectionResolution: 2.509612595→48.655 Å / Num. obs: 39342 / % possible obs: 99.2 % / Redundancy: 26.2 % / Biso Wilson estimate: 59.58 Å2 / CC1/2: 0.99 / Net I/σ(I): 17.05
Reflection shellResolution: 2.51→2.66 Å / Num. unique obs: 6003 / CC1/2: 0.75

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BKD

1bkd


Resolution: 2.51→48.65 Å / SU ML: 0.343 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.0444
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2285 1965 5 %
Rwork0.19 37351 -
obs0.192 39316 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.68 Å2
Refinement stepCycle: LAST / Resolution: 2.51→48.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5037 0 126 124 5287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00895269
X-RAY DIFFRACTIONf_angle_d1.0137099
X-RAY DIFFRACTIONf_chiral_restr0.0557773
X-RAY DIFFRACTIONf_plane_restr0.0095916
X-RAY DIFFRACTIONf_dihedral_angle_d17.01391999
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.51-2.570.38361220.32872345X-RAY DIFFRACTION89.06
2.57-2.640.36281390.27932651X-RAY DIFFRACTION100
2.64-2.720.31071400.25222657X-RAY DIFFRACTION99.93
2.72-2.810.26851400.23062657X-RAY DIFFRACTION100
2.81-2.910.26841390.232639X-RAY DIFFRACTION100
2.91-3.020.31341400.24552669X-RAY DIFFRACTION100
3.02-3.160.3161400.25572653X-RAY DIFFRACTION100
3.16-3.330.26051410.22532684X-RAY DIFFRACTION100
3.33-3.540.19941410.19792678X-RAY DIFFRACTION100
3.54-3.810.21951420.1812689X-RAY DIFFRACTION100
3.81-4.190.18831420.16122694X-RAY DIFFRACTION100
4.19-4.80.17921420.14242709X-RAY DIFFRACTION100
4.8-6.040.23171450.17122746X-RAY DIFFRACTION100
6.04-48.650.19851520.17152880X-RAY DIFFRACTION99.77

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