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- PDB-8be2: Crystal structure of SOS1-Nanobody77 -

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Basic information

Entry
Database: PDB / ID: 8be2
TitleCrystal structure of SOS1-Nanobody77
Components
  • Nanobody 77Single-domain antibody
  • 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 / 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 / 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 / Schwann cell development / 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 / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / RAC1 GTPase cycle / EGFR Transactivation by Gastrin / myelination / Signaling by FLT3 fusion proteins / FLT3 Signaling / GRB2 events in ERBB2 signaling / Signaling by FGFR1 in disease / molecular condensate scaffold activity / NCAM signaling for neurite out-growth / GTPase activator activity / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / FCERI mediated Ca+2 mobilization / 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 / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / B cell receptor signaling pathway / multicellular organism growth / 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 / Signaling by CSF1 (M-CSF) in myeloid cells / G alpha (12/13) signalling events / DAP12 signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / 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
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
Son of sevenless homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89793505929 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

Downloads & links

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Assembly

Deposited unit
S: Son of sevenless homolog 1
N: Nanobody 77
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,7947
Polymers73,3132
Non-polymers4805
Water7,368409
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2470 Å2
ΔGint-60 kcal/mol
Surface area27900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.533, 102.933, 108.494
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,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: Antibody Nanobody 77 / Single-domain antibody


Mass: 13964.427 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)
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 409 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.07 Å3/Da / Density % sol: 59.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: ammonium sulfate 1.5 M, Tris 0.1 M pH 8.5

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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: 1.897935059→29.59 Å / Num. obs: 137616 / % possible obs: 99.8 % / Redundancy: 6.9 % / Biso Wilson estimate: 37.2334274158 Å2 / CC1/2: 0.99 / Net I/σ(I): 14.38
Reflection shellResolution: 1.897935059→2.01 Å / Num. unique obs: 22066 / CC1/2: 0.74

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BKD

1bkd


Resolution: 1.89793505929→29.5898955693 Å / SU ML: 0.246840708845 / Cross valid method: FREE R-VALUE / σ(F): 1.34309844329 / Phase error: 23.0727182879
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.210625047888 6876 5.00043633825 %
Rwork0.181392926296 130632 -
obs0.182832527744 137508 99.8257687952 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 43.683619883 Å2
Refinement stepCycle: LAST / Resolution: 1.89793505929→29.5898955693 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4612 0 25 409 5046
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00749731409484830
X-RAY DIFFRACTIONf_angle_d0.796068940416547
X-RAY DIFFRACTIONf_chiral_restr0.0507537985234709
X-RAY DIFFRACTIONf_plane_restr0.00483796997781848
X-RAY DIFFRACTIONf_dihedral_angle_d23.97568838791864
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89793505929-1.91950.3861512291072200.3444014420014183X-RAY DIFFRACTION95.530483836
1.9195-1.94210.3144048536692280.3065225964614342X-RAY DIFFRACTION100
1.9421-1.96580.3229567596772340.2880570473794369X-RAY DIFFRACTION99.9782797567
1.9658-1.99060.3236116979692290.2731159564814326X-RAY DIFFRACTION99.9341816586
1.9906-2.01680.2964514634262360.2696814293854450X-RAY DIFFRACTION99.8721227621
2.0168-2.04440.2990891361682300.2457510269534315X-RAY DIFFRACTION99.9780026397
2.0444-2.07360.238517675662290.2376406615154368X-RAY DIFFRACTION99.9347826087
2.0736-2.10460.2861064526382280.2292198943324347X-RAY DIFFRACTION99.9563032554
2.1046-2.13750.246615729262280.224571150384358X-RAY DIFFRACTION99.9128540305
2.1375-2.17250.2392568319942290.2210353552234372X-RAY DIFFRACTION99.9782703173
2.1725-2.20990.258670882212330.2145859349324351X-RAY DIFFRACTION99.95638901
2.2099-2.25010.2166757992632270.2018708745734329X-RAY DIFFRACTION99.9561211057
2.2501-2.29340.2823105482032280.2093024582594400X-RAY DIFFRACTION100
2.2934-2.34020.2667622252792300.2082042757324341X-RAY DIFFRACTION100
2.3402-2.3910.2377269200782320.2018413852834376X-RAY DIFFRACTION100
2.391-2.44660.2384163376562290.1992601576724346X-RAY DIFFRACTION100
2.4466-2.50780.2268761743612290.1958325571264365X-RAY DIFFRACTION99.9782372144
2.5078-2.57560.2479928661012270.1864502164164357X-RAY DIFFRACTION99.95638901
2.5756-2.65130.220197942532290.1845437509484376X-RAY DIFFRACTION100
2.6513-2.73680.217824904332280.1853282650824336X-RAY DIFFRACTION100
2.7368-2.83460.2065924733422330.1784738328394375X-RAY DIFFRACTION100
2.8346-2.94790.2353027174352250.1872539842514376X-RAY DIFFRACTION100
2.9479-3.0820.2177478930032270.1898210838344377X-RAY DIFFRACTION100
3.082-3.24430.2020276613752270.193712156354334X-RAY DIFFRACTION100
3.2443-3.44730.2082643776312240.1737527568264376X-RAY DIFFRACTION100
3.4473-3.7130.2052587207422280.168498494324328X-RAY DIFFRACTION100
3.713-4.08570.1673480324182280.1469461185834394X-RAY DIFFRACTION100
4.0857-4.6750.1523599670852350.1322038682464378X-RAY DIFFRACTION100
4.675-5.88240.1754731014132310.1641098742974338X-RAY DIFFRACTION100
5.8824-29.58989556930.2091391588542350.1765746188074349X-RAY DIFFRACTION99.8910438004

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