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- PDB-8be4: Crystal structure of SOS1-KRasG12V-Nanobody14 -

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Basic information

Entry
Database: PDB / ID: 8be4
TitleCrystal structure of SOS1-KRasG12V-Nanobody14
Components
  • Isoform 2B of GTPase KRas
  • Nanobody14
  • 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 / 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 / Regulation of KIT signaling / epidermal growth factor receptor binding / leukocyte migration / regulation of T cell proliferation / NRAGE signals death through JNK / roof of mouth development / eyelid development in camera-type eye / Fc-epsilon receptor signaling pathway / GRB2:SOS provides linkage to MAPK signaling for Integrins / B cell homeostasis / neurotrophin TRK receptor signaling pathway / 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 / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Role of LAT2/NTAL/LAB on calcium mobilization / Interleukin receptor SHC signaling / Signal attenuation / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / Schwann cell development / 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 / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / RAC1 GTPase cycle / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / myelination / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / FCERI mediated Ca+2 mobilization / Insulin receptor signalling cascade / GTPase activator activity / guanyl-nucleotide exchange factor activity / insulin-like growth factor receptor signaling pathway / small monomeric GTPase / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / molecular condensate scaffold activity / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / response to ischemia / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / axon guidance / B cell receptor signaling pathway / Constitutive Signaling by EGFRvIII / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / epidermal growth factor receptor signaling pathway / multicellular organism growth / Signaling by SCF-KIT / cytokine-mediated signaling pathway / SH3 domain binding / Signaling by CSF1 (M-CSF) in myeloid cells / G alpha (12/13) signalling events / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / insulin receptor signaling pathway / DAP12 signaling / Ca2+ pathway / 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 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 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. / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Histone-fold / PH-like domain superfamily
Similarity search - Domain/homology
Isoform 2B of GTPase KRas / Son of sevenless homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsFischer, B. / Wohlkonig, A. / Steyaert, J.
Funding support Belgium, 1items
OrganizationGrant numberCountry
Research Foundation - Flanders (FWO) Belgium
CitationJournal: To Be Published
Title: ChILL & DisCO to discover Nanobodies that modulate protein-protein interactions and tune the SOS-Ras nucleotide exchange rate
Authors: Fischer, B. / Wohlkonig, A. / Steyaert, J.
History
DepositionOct 21, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
S: Son of sevenless homolog 1
R: Isoform 2B of GTPase KRas
C000: Nanobody14


Theoretical massNumber of molelcules
Total (without water)95,0953
Polymers95,0953
Non-polymers00
Water9,926551
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4930 Å2
ΔGint-13 kcal/mol
Surface area33590 Å2
Unit cell
Length a, b, c (Å)127.675, 127.675, 152.093
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number79
Space group name H-MI4
Space group name HallI4
Symmetry operation#1: x,y,z
#2: -y,x,z
#3: y,-x,z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1/2,x+1/2,z+1/2
#7: y+1/2,-x+1/2,z+1/2
#8: -x+1/2,-y+1/2,z+1/2

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Components

#1: 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
#2: Protein Isoform 2B of GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 21675.314 Da / Num. of mol.: 1 / Mutation: G12V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01116-2, small monomeric GTPase
#3: Antibody Nanobody14


Mass: 14070.595 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 551 / 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: 3.26 Å3/Da / Density % sol: 62.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 14% PEG 1000, Tris 0.1 M pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97622 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jul 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.895400854→29.59036932 Å / Num. obs: 189905 / % possible obs: 99.6 % / Redundancy: 6.9 % / Biso Wilson estimate: 35.62 Å2 / CC1/2: 0.99 / Net I/σ(I): 15.63
Reflection shellResolution: 1.9→2.01 Å / Num. unique obs: 30042 / CC1/2: 0.72

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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: 1.9→29.59 Å / SU ML: 0.2293 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.1277
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1986 9506 5.01 %
Rwork0.1749 180389 -
obs0.1761 189895 99.58 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.67 Å2
Refinement stepCycle: LAST / Resolution: 1.9→29.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5893 0 0 551 6444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01856215
X-RAY DIFFRACTIONf_angle_d1.38518421
X-RAY DIFFRACTIONf_chiral_restr0.1043916
X-RAY DIFFRACTIONf_plane_restr0.00921100
X-RAY DIFFRACTIONf_dihedral_angle_d15.47872387
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.920.40022770.34835349X-RAY DIFFRACTION87.85
1.92-1.940.31213170.28266039X-RAY DIFFRACTION100
1.94-1.960.29063180.25726055X-RAY DIFFRACTION100
1.96-1.990.27723160.24685946X-RAY DIFFRACTION100
1.99-2.010.27393180.246037X-RAY DIFFRACTION99.98
2.01-2.040.25833180.23286050X-RAY DIFFRACTION100
2.04-2.070.25783260.23226134X-RAY DIFFRACTION100
2.07-2.10.2493140.23435983X-RAY DIFFRACTION100
2.1-2.130.26883190.20686046X-RAY DIFFRACTION100
2.13-2.170.2353170.19635996X-RAY DIFFRACTION100
2.17-2.210.24523190.19456063X-RAY DIFFRACTION100
2.21-2.250.19483180.18756028X-RAY DIFFRACTION100
2.25-2.290.22123200.18866058X-RAY DIFFRACTION100
2.29-2.340.20863150.18445994X-RAY DIFFRACTION100
2.34-2.390.19263160.18046028X-RAY DIFFRACTION100
2.39-2.440.21463210.17786054X-RAY DIFFRACTION100
2.44-2.50.1863200.18336061X-RAY DIFFRACTION100
2.5-2.570.24543190.18986021X-RAY DIFFRACTION100
2.57-2.650.2253170.19366068X-RAY DIFFRACTION100
2.65-2.730.24993180.19626004X-RAY DIFFRACTION100
2.73-2.830.24833200.18296047X-RAY DIFFRACTION100
2.83-2.940.22423190.18096056X-RAY DIFFRACTION99.98
2.94-3.080.1963190.18535991X-RAY DIFFRACTION100
3.08-3.240.20483190.18626012X-RAY DIFFRACTION100
3.24-3.440.23583150.17856080X-RAY DIFFRACTION99.98
3.44-3.710.18853190.16486038X-RAY DIFFRACTION99.97
3.71-4.080.17643190.14636077X-RAY DIFFRACTION100
4.08-4.670.14053190.13025985X-RAY DIFFRACTION100
4.67-5.870.14623210.14966048X-RAY DIFFRACTION100
5.87-29.590.163130.16036041X-RAY DIFFRACTION99.75

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