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- PDB-6eie: Ras guanine nucleotide exchange factor SOS2 (Rem-cdc25), with sur... -

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Basic information

Entry
Database: PDB / ID: 6eie
TitleRas guanine nucleotide exchange factor SOS2 (Rem-cdc25), with surface mutations
ComponentsSon of sevenless homolog 2
KeywordsSIGNALING PROTEIN / Guanine exchange factor / GEF / SOS2
Function / homology
Function and homology information


regulation of pro-B cell differentiation / regulation of T cell differentiation in thymus / Interleukin-15 signaling / Activation of RAC1 / NRAGE signals death through JNK / regulation of T cell proliferation / B cell homeostasis / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity / insulin receptor signaling pathway ...regulation of pro-B cell differentiation / regulation of T cell differentiation in thymus / Interleukin-15 signaling / Activation of RAC1 / NRAGE signals death through JNK / regulation of T cell proliferation / B cell homeostasis / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity / insulin receptor signaling pathway / G alpha (12/13) signalling events / Ras protein signal transduction / protein heterodimerization activity / plasma membrane / cytosol
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. / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Histone-fold / PH-like domain superfamily / Up-down Bundle / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Son of sevenless homolog 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsHillig, R.C. / Moosmayer, D. / Mastouri, J.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Discovery of potent SOS1 inhibitors that block RAS activation via disruption of the RAS-SOS1 interaction.
Authors: Hillig, R.C. / Sautier, B. / Schroeder, J. / Moosmayer, D. / Hilpmann, A. / Stegmann, C.M. / Werbeck, N.D. / Briem, H. / Boemer, U. / Weiske, J. / Badock, V. / Mastouri, J. / Petersen, K. / ...Authors: Hillig, R.C. / Sautier, B. / Schroeder, J. / Moosmayer, D. / Hilpmann, A. / Stegmann, C.M. / Werbeck, N.D. / Briem, H. / Boemer, U. / Weiske, J. / Badock, V. / Mastouri, J. / Petersen, K. / Siemeister, G. / Kahmann, J.D. / Wegener, D. / Bohnke, N. / Eis, K. / Graham, K. / Wortmann, L. / von Nussbaum, F. / Bader, B.
History
DepositionSep 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Jan 17, 2024Group: 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
A: Son of sevenless homolog 2


Theoretical massNumber of molelcules
Total (without water)57,3711
Polymers57,3711
Non-polymers00
Water1448
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area23860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.970, 53.970, 183.793
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Son of sevenless homolog 2 / SOS-2


Mass: 57370.676 Da / Num. of mol.: 1
Mutation: P564Q, E707Y, Q768H, F769I, K947T, K949R, K949H, C1019P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SOS2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07890
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / 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: 2.33 Å3/Da / Density % sol: 47.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Protein 10.3 mg/ml in 25 mM Tris HCl, pH 7.5, 100 mM NaCl, 1 mM DTT. Reservoir 0,1 M Natriumacetat, 20% w/v PEG 3350. Cryo buffer was reservoir supplemented with 15% glycerol.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: May 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.72→46.54 Å / Num. obs: 13644 / % possible obs: 96.9 % / Redundancy: 4.8 % / Biso Wilson estimate: 69.7 Å2 / CC1/2: 0.998 / Rsym value: 0.067 / Net I/σ(I): 14.1
Reflection shellResolution: 2.72→2.88 Å / Redundancy: 3.2 % / Num. unique obs: 1867 / CC1/2: 0.761 / Rsym value: 0.539 / % possible all: 82.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSVERSION Oct 15, 2015data reduction
XDSVERSION Oct 15, 2015data scaling
PHASER2.6.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NVU

1nvu


Resolution: 2.72→46.54 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.901 / SU B: 51.288 / SU ML: 0.432 / Cross valid method: THROUGHOUT / ESU R Free: 0.433 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28526 683 5 %RANDOM
Rwork0.21836 ---
obs0.22171 12960 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 79.654 Å2
Baniso -1Baniso -2Baniso -3
1--6.06 Å20 Å2-0 Å2
2---6.06 Å2-0 Å2
3---12.12 Å2
Refinement stepCycle: 1 / Resolution: 2.72→46.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3793 0 0 8 3801
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0193895
X-RAY DIFFRACTIONr_bond_other_d0.0010.023696
X-RAY DIFFRACTIONr_angle_refined_deg1.2441.975265
X-RAY DIFFRACTIONr_angle_other_deg0.95138593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2785454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.99923.673196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.66315725
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2631533
X-RAY DIFFRACTIONr_chiral_restr0.0710.2578
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214196
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02801
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.7923.7141819
X-RAY DIFFRACTIONr_mcbond_other2.7933.7141818
X-RAY DIFFRACTIONr_mcangle_it4.7378.3422266
X-RAY DIFFRACTIONr_mcangle_other4.7368.3422267
X-RAY DIFFRACTIONr_scbond_it2.5543.9662076
X-RAY DIFFRACTIONr_scbond_other2.5533.9662077
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.5628.7432998
X-RAY DIFFRACTIONr_long_range_B_refined7.02644.174312
X-RAY DIFFRACTIONr_long_range_B_other7.02644.1744313
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.72→2.791 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.421 41 -
Rwork0.362 766 -
obs--79.35 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.03550.3771-0.87233.18040.51191.67150.22570.0660.04460.1248-0.2295-0.3577-0.3926-0.1850.00370.6814-0-0.07290.55370.0280.051822.62518.19330.254
21.80341.50520.3012.92251.46960.96380.0314-0.35820.28830.1318-0.13220.3310.16630.13020.10080.5560.00690.00550.5468-0.11260.06013.139-14.0158.332
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A561 - 742
2X-RAY DIFFRACTION2A754 - 1040

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