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- PDB-6cur: Ras:SOS:Ras in complex with a small molecule activator -

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Basic information

Entry
Database: PDB / ID: 6cur
TitleRas:SOS:Ras in complex with a small molecule activator
Components
  • (GTPase HRas) x 2
  • Son of sevenless homolog 1
KeywordsSIGNALING PROTEIN / Ras / SOS / inhibitor / ONCOPROTEIN / Protein-protein complex / MAPK
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 ruffle assembly / oncogene-induced cell senescence / positive regulation of small GTPase mediated signal transduction / Activation of RAC1 / negative regulation of GTPase activity / Signaling by LTK / blood vessel morphogenesis / positive regulation of miRNA metabolic process / epidermal growth factor receptor binding / positive regulation of epidermal growth factor receptor signaling pathway / Regulation of KIT signaling / T-helper 1 type immune response / leukocyte migration / positive regulation of wound healing / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / NRAGE signals death through JNK / defense response to protozoan / roof of mouth development / eyelid development in camera-type eye / Fc-epsilon receptor signaling pathway / neurotrophin TRK receptor signaling pathway / B cell homeostasis / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / GRB2:SOS provides linkage to MAPK signaling for Integrins / Activation of RAS in B cells / regulation of T cell proliferation / RAS signaling downstream of NF1 loss-of-function variants / RET signaling / SOS-mediated signalling / positive regulation of protein targeting to membrane / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / hair follicle development / SHC1 events in ERBB4 signaling / fibroblast growth factor receptor signaling pathway / Role of LAT2/NTAL/LAB on calcium mobilization / Signalling to RAS / Interleukin receptor SHC signaling / adipose tissue development / Signal attenuation / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Schwann cell development / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / membrane-membrane adaptor activity / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EPHB-mediated forward signaling / EGFR Transactivation by Gastrin / RAC1 GTPase cycle / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / myelination / GRB2 events in ERBB2 signaling / CD209 (DC-SIGN) signaling / NCAM signaling for neurite out-growth / FCERI mediated Ca+2 mobilization / SHC1 events in ERBB2 signaling / Ras activation upon Ca2+ influx through NMDA receptor / Downstream signal transduction / Insulin receptor signalling cascade / GTPase activator activity / intrinsic apoptotic signaling pathway / positive regulation of GTPase activity / positive regulation of MAP kinase 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
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. / Small GTPase, Ras-type / small GTPase Ras family 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 nucleotide triphosphate hydrolases / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-FFY / FORMIC ACID / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase HRas / Son of sevenless homolog 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsPhan, J. / Abbott, J. / Fesik, S.W.
Funding support United States, 1items
OrganizationGrant numberCountry
Lustgarten United States
Citation
Journal: ACS Med Chem Lett / Year: 2018
Title: Discovery of Quinazolines That Activate SOS1-Mediated Nucleotide Exchange on RAS.
Authors: Abbott, J.R. / Patel, P.A. / Howes, J.E. / Akan, D.T. / Kennedy, J.P. / Burns, M.C. / Browning, C.F. / Sun, Q. / Rossanese, O.W. / Phan, J. / Waterson, A.G. / Fesik, S.W.
#1: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2014
Title: Approach for targeting Ras with small molecules that activate SOS-mediated nucleotide exchange.
Authors: Burns, M.C. / Sun, Q. / Daniels, R.N. / Camper, D. / Kennedy, J.P. / Phan, J. / Olejniczak, E.T. / Lee, T. / Waterson, A.G. / Rossanese, O.W. / Fesik, S.W.
History
DepositionMar 26, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 6, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id
Revision 1.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase HRas
B: Son of sevenless homolog 1
C: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,84615
Polymers94,3783
Non-polymers1,46812
Water22,5731253
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8900 Å2
ΔGint-38 kcal/mol
Surface area35790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.045, 184.045, 179.131
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11B-2594-

HOH

21B-2596-

HOH

31B-2907-

HOH

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Components

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Protein , 3 types, 3 molecules ABC

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


Mass: 18856.146 Da / Num. of mol.: 1 / Mutation: Y64A
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
#2: Protein Son of sevenless homolog 1 / SOS-1


Mass: 56589.781 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
#3: Protein GTPase HRas / H-Ras-1 / Ha-Ras / Transforming protein p21 / c-H-ras / p21ras


Mass: 18932.242 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

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Non-polymers , 7 types, 1265 molecules

#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-FFY / N~2~-(3-chloro-4-fluorophenyl)-N~4~-[(1R)-1-cyclopropylethyl]-8-(1,2,3,6-tetrahydropyridin-4-yl)quinazoline-2,4-diamine


Mass: 437.940 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H25ClFN5
#7: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1253 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 4 Å3/Da / Density % sol: 69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4 / Details: 0.1 M sodium acetate, 2.0 M sodium formate, pH 4.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jan 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 158342 / % possible obs: 100 % / Redundancy: 11.4 % / Rpim(I) all: 0.029 / Net I/σ(I): 22.11
Reflection shellResolution: 1.73→1.76 Å / Rpim(I) all: 0.316

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Processing

Software
NameVersionClassification
PHENIX(1.13rc1_2961: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4NYI

4nyi


Resolution: 1.73→35.166 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.25
RfactorNum. reflection% reflection
Rfree0.1763 2000 1.26 %
Rwork0.1574 --
obs0.1576 158313 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.73→35.166 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6534 0 95 1261 7890
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077064
X-RAY DIFFRACTIONf_angle_d0.859588
X-RAY DIFFRACTIONf_dihedral_angle_d14.6664349
X-RAY DIFFRACTIONf_chiral_restr0.0531038
X-RAY DIFFRACTIONf_plane_restr0.0051290
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7293-1.77260.25051430.213811053X-RAY DIFFRACTION100
1.7726-1.82050.24191470.20511062X-RAY DIFFRACTION100
1.8205-1.87410.22771300.200111079X-RAY DIFFRACTION100
1.8741-1.93460.22271510.188811062X-RAY DIFFRACTION100
1.9346-2.00370.21141410.170811123X-RAY DIFFRACTION100
2.0037-2.08390.20211440.161811088X-RAY DIFFRACTION100
2.0839-2.17870.15221390.151711099X-RAY DIFFRACTION100
2.1787-2.29360.17211380.15511136X-RAY DIFFRACTION100
2.2936-2.43730.20451450.157111139X-RAY DIFFRACTION100
2.4373-2.62540.1711410.158111164X-RAY DIFFRACTION100
2.6254-2.88950.17681420.159511171X-RAY DIFFRACTION100
2.8895-3.30730.14641440.154111252X-RAY DIFFRACTION100
3.3073-4.16580.14631450.134611316X-RAY DIFFRACTION100
4.1658-35.17340.17241500.148711569X-RAY DIFFRACTION99
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)
10.0170.02280.01190.02140.02690.0330.0349-0.01290.0108-0.0112-0.00270.0510.0641-0.012100.1177-0.02680.01270.1294-0.00770.12819.495750.260662.3884
20.0090.00210.02550.0003-0.00340.0172-0.054-0.0611-0.01410.03450.0381-0.0235-0.0390.0494-00.1217-0.04540.01470.1511-0.00810.103629.139545.102556.7989
30.00920.00220.01180.0014-0.00250.0079-0.0015-0.0968-0.07990.1382-0.04070.0510.0933-0.00800.1799-0.03750.02070.14580.00890.107923.984346.077473.3813
40.01360.0090.0050.01950.00170.00130.1208-0.18340.08360.07-0.04780.0307-0.04310.0683-00.151-0.050.02180.1653-0.02910.118627.120457.209574.7797
50.01320.0389-0.02630.0171-0.0240.01610.0627-0.00880.1236-0.0118-0.03010.0686-0.08650.0628-00.1599-0.02940.02960.1111-0.01550.177124.573566.132765.8011
60.0062-0.0066-0.0079-0.0015-0.00150.0060.00560.00110.02440.0142-0.084-0.0175-0.04030.0749-00.141-0.04240.01680.1639-0.00360.118734.589653.981960.7036
70.0433-0.1144-0.07880.0490.01670.068-0.0161-0.01530.02580.01350.02370.00370.00420.0672-00.1178-0.01640.00220.11760.00660.088215.342330.67280.3792
80.11630.12670.0072-0.07-0.01980.1494-0.00320.00530.0083-0.02220.01120.0303-0.0196-0.0537-0.00010.0891-0.0060.00870.09220.00740.10089.329540.209649.1748
90.12340.1529-0.10790.1921-0.09740.321-0.08190.046-0.0288-0.03380.0629-0.04590.00790.01540.0110.0476-0.03630.02510.0585-0.00920.04923.959633.119131.9911
10-0.001-0.00930.00530.0247-0.01330.0055-0.03320.03160.08180.0570.0067-0.14220.0308-0.040500.10910.01720.01080.10350.00990.202731.521512.172741.8713
110.0011-0.0019-0.00040.0018-0.00230.00070.02680.0332-0.02830.01340.03640.00050.03580.0001-00.28280.01-0.11830.14220.05860.409232.189512.683555.8857
12-0.00090.0036-0.01110.0018-0.00070.0003-0.0213-0.0404-0.00180.0059-0.0869-0.0261-0.05510.063200.18250.045-0.08620.19880.00050.382240.186614.200545.9734
130.00480.02360.03020.04150.0223-0.0056-0.0662-0.0034-0.0609-0.0505-0.0061-0.1646-0.0259-0.0753-00.0932-0.00340.03060.0640.00790.167129.331619.034636.396
14-0.00850.0026-0.03060.06330.02050.01350.14050.0208-0.0488-0.128-0.0930.0302-0.01750.0228-00.14160.03940.0240.10680.00140.119323.32448.792431.7905
150.00650.00180.00270.0073-0.00180.00510.0971-0.0155-0.0187-0.0574-0.05950.15870.06730.0177-00.17420.01450.00310.1247-0.03650.197218.0816-1.791636.523
160.0018-0.00560.00240.0104-0.00260.00090.0168-0.04440.01260.0058-0.0328-0.0211-0.01830.004900.12040.0224-0.00120.1139-0.00720.138326.35351.168643.3708
170.0044-0.0037-0.00060.00290.00160.00130.0453-0.00120.0351-0.0488-0.0793-0.13910.0666-0.010700.11110.04110.03040.09690.00150.187137.0033.452137.1303
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 36 )
2X-RAY DIFFRACTION2chain 'A' and (resid 37 through 52 )
3X-RAY DIFFRACTION3chain 'A' and (resid 53 through 76 )
4X-RAY DIFFRACTION4chain 'A' and (resid 77 through 116 )
5X-RAY DIFFRACTION5chain 'A' and (resid 117 through 151 )
6X-RAY DIFFRACTION6chain 'A' and (resid 152 through 166 )
7X-RAY DIFFRACTION7chain 'B' and (resid 565 through 699 )
8X-RAY DIFFRACTION8chain 'B' and (resid 700 through 818 )
9X-RAY DIFFRACTION9chain 'B' and (resid 819 through 1046 )
10X-RAY DIFFRACTION10chain 'C' and (resid 0 through 24 )
11X-RAY DIFFRACTION11chain 'C' and (resid 25 through 34 )
12X-RAY DIFFRACTION12chain 'C' and (resid 35 through 48 )
13X-RAY DIFFRACTION13chain 'C' and (resid 49 through 74 )
14X-RAY DIFFRACTION14chain 'C' and (resid 75 through 117 )
15X-RAY DIFFRACTION15chain 'C' and (resid 118 through 137 )
16X-RAY DIFFRACTION16chain 'C' and (resid 138 through 151 )
17X-RAY DIFFRACTION17chain 'C' and (resid 152 through 166 )

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