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- PDB-8uf2: Apo SOS2 crystal structure in P1 space group -

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Basic information

Entry
Database: PDB / ID: 8uf2
TitleApo SOS2 crystal structure in P1 space group
ComponentsSon of sevenless homolog 2
KeywordsSIGNALING PROTEIN / SOS2 / Nucleotide Exchange Factor / GEF / KRAS / RAS / Fragment screening / FBLD
Function / homology
Function and homology information


regulation of pro-B cell differentiation / regulation of T cell differentiation in thymus / positive regulation of small GTPase mediated signal transduction / 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 ...regulation of pro-B cell differentiation / regulation of T cell differentiation in thymus / positive regulation of small GTPase mediated signal transduction / 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 / G alpha (12/13) signalling events / insulin receptor signaling pathway / Ras protein signal transduction / protein heterodimerization activity / plasma membrane / cytosol
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 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGunn, R.J. / Lawson, J.D.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: J.Med.Chem. / Year: 2024
Title: Discovery of Five SOS2 Fragment Hits with Binding Modes Determined by SOS2 X-Ray Cocrystallography.
Authors: Smith, C.R. / Chen, D. / Christensen, J.G. / Coulombe, R. / Fethiere, J. / Gunn, R.J. / Hollander, J. / Jones, B. / Ketcham, J.M. / Khare, S. / Kuehler, J. / Lawson, J.D. / Marx, M.A. / ...Authors: Smith, C.R. / Chen, D. / Christensen, J.G. / Coulombe, R. / Fethiere, J. / Gunn, R.J. / Hollander, J. / Jones, B. / Ketcham, J.M. / Khare, S. / Kuehler, J. / Lawson, J.D. / Marx, M.A. / Olson, P. / Pearson, K.E. / Ren, C. / Tsagris, D. / Ulaganathan, T. / Van't Veer, I. / Wang, X. / Ivetac, A.
History
DepositionOct 3, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 10, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Son of sevenless homolog 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4092
Polymers57,3131
Non-polymers961
Water11,692649
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.665, 52.002, 61.865
Angle α, β, γ (deg.)85.581, 75.304, 76.949
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Son of sevenless homolog 2


Mass: 57312.637 Da / Num. of mol.: 1
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: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 649 / 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: 2.47 Å3/Da / Density % sol: 50.16 %
Crystal growTemperature: 281 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9796 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 11, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 53261 / % possible obs: 73.65 % / Redundancy: 2.3 % / Biso Wilson estimate: 13.01 Å2 / CC1/2: 0.99 / Net I/σ(I): 19.4
Reflection shellResolution: 1.6→1.63 Å / Num. unique obs: 576 / CC1/2: 0.67

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Processing

Software
NameVersionClassification
PHENIX1.19.1_4122refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→44.09 Å / SU ML: 0.1812 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 27.3479
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2315 2588 4.86 %
Rwork0.1958 50673 -
obs0.1976 53261 73.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.86 Å2
Refinement stepCycle: LAST / Resolution: 1.6→44.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3633 0 5 649 4287
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00793729
X-RAY DIFFRACTIONf_angle_d0.84975054
X-RAY DIFFRACTIONf_chiral_restr0.0514562
X-RAY DIFFRACTIONf_plane_restr0.0081648
X-RAY DIFFRACTIONf_dihedral_angle_d12.98931411
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.630.376220.2985269X-RAY DIFFRACTION20
3.33-4.190.19092070.16233651X-RAY DIFFRACTION95.87
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)
10.08568763410830.00719918634045-0.03111763097740.0274186533010.0005984550583620.02545967357880.0228175622258-0.1033256735050.07666701519950.07990568527910.03925928880950.04794364251550.0103938449342-0.07575766785850.116663364145-0.1521405562770.1214531259830.105677568590.021521642335-0.0528700997258-0.009861177043127.3720130650636.849528767912.7342256348
20.2092558013330.07616707328740.08595839087170.159336249447-0.04422403831630.407173980999-0.1686882029910.02230870779590.0878289361818-0.0970058757882-0.0934159696192-0.0161092493711-0.0746331281190.0747921958704-0.574358783030.000787895674866-0.0119908056473-0.03072774401040.01416688601310.00191122924673-0.01020781586285.97849545875.52208196431-11.9133278878
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 565 through 721 )565 - 7211 - 137
22chain 'A' and (resid 722 through 1041 )722 - 1041138 - 444

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