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- PDB-4g3x: Crystal Structure of Q61L H-Ras-GppNHp bound to the RBD of Raf Kinase -

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Basic information

Entry
Database: PDB / ID: 4g3x
TitleCrystal Structure of Q61L H-Ras-GppNHp bound to the RBD of Raf Kinase
Components
  • GTPase HRas
  • RAF proto-oncogene serine/threonine-protein kinase
KeywordsHYDROLASE/TRANSFERASE / H-Ras / Ras / Raf kinase / Raf / GTPase / allosteric regulation / intrinsic hydrolysis / protein-protein interaction / kinase / GTP binding / HYDROLASE-TRANSFERASE complex
Function / homology
Function and homology information


death-inducing signaling complex assembly / intermediate filament cytoskeleton organization / regulation of Rho protein signal transduction / phospholipase C activator activity / type B pancreatic cell proliferation / GTPase complex / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / oncogene-induced cell senescence ...death-inducing signaling complex assembly / intermediate filament cytoskeleton organization / regulation of Rho protein signal transduction / phospholipase C activator activity / type B pancreatic cell proliferation / GTPase complex / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / Rap1 signalling / oncogene-induced cell senescence / insulin secretion involved in cellular response to glucose stimulus / positive regulation of miRNA metabolic process / positive regulation of ruffle assembly / T-helper 1 type immune response / Negative feedback regulation of MAPK pathway / IFNG signaling activates MAPKs / GP1b-IX-V activation signalling / positive regulation of wound healing / defense response to protozoan / ERBB2-ERBB3 signaling pathway / neurotrophin TRK receptor signaling pathway / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / face development / pseudopodium / regulation of cell differentiation / thyroid gland development / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / RAS signaling downstream of NF1 loss-of-function variants / extrinsic apoptotic signaling pathway via death domain receptors / somatic stem cell population maintenance / SOS-mediated signalling / positive regulation of peptidyl-serine phosphorylation / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / MAP kinase kinase kinase activity / adipose tissue development / positive regulation of protein targeting to membrane / Signalling to RAS / type II interferon-mediated signaling pathway / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Schwann cell development / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / negative regulation of protein-containing complex assembly / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / p38MAPK events / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / protein-membrane adaptor activity / response to muscle stretch / Tie2 Signaling / Signaling by FGFR2 in disease / myelination / EPHB-mediated forward signaling / GRB2 events in EGFR signaling / Signaling by FLT3 fusion proteins / SHC1 events in EGFR signaling / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / insulin-like growth factor receptor signaling pathway / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / SHC1 events in ERBB2 signaling / Ras activation upon Ca2+ influx through NMDA receptor / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / thymus development / adenylate cyclase activator activity / animal organ morphogenesis / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / small monomeric GTPase / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / wound healing / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by SCF-KIT
Similarity search - Function
Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / : / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) ...Raf-like Ras-binding domain / Raf-like Ras-binding / Ras-binding domain (RBD) profile. / Raf-like Ras-binding domain / Diacylglycerol/phorbol-ester binding / : / Phorbol esters/diacylglycerol binding domain (C1 domain) / Zinc finger phorbol-ester/DAG-type signature. / Zinc finger phorbol-ester/DAG-type profile. / Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains) / Protein kinase C-like, phorbol ester/diacylglycerol-binding domain / C1-like domain superfamily / Small GTPase, Ras-type / Small GTPase Ras domain profile. / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Ubiquitin-like (UB roll) / Small GTP-binding protein domain / Ubiquitin-like domain superfamily / P-loop containing nucleotide triphosphate hydrolases / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase HRas / RAF proto-oncogene serine/threonine-protein kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.25 Å
AuthorsFetics, S.K. / Kearney, B.M. / Buhrman, G. / Mattos, C.
CitationJournal: Structure / Year: 2015
Title: Allosteric Effects of the Oncogenic RasQ61L Mutant on Raf-RBD.
Authors: Fetics, S.K. / Guterres, H. / Kearney, B.M. / Buhrman, G. / Ma, B. / Nussinov, R. / Mattos, C.
History
DepositionJul 15, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 11, 2015Group: Database references
Revision 1.2Mar 18, 2015Group: Derived calculations
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 13, 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 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase HRas
B: RAF proto-oncogene serine/threonine-protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1964
Polymers27,6502
Non-polymers5472
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)91.400, 91.400, 93.110
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

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


Mass: 18860.221 Da / Num. of mol.: 1 / Mutation: Q61L
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / References: UniProt: P01112
#2: Protein RAF proto-oncogene serine/threonine-protein kinase / Proto-oncogene c-RAF / cRaf / Raf-1


Mass: 8789.290 Da / Num. of mol.: 1 / Fragment: UNP residues 55-131
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAF1, RAF / Plasmid: pET302/NT-His / Production host: Escherichia coli (E. coli)
References: UniProt: P04049, non-specific serine/threonine protein kinase
#3: 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
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 4.06 Å3/Da / Density % sol: 69.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.8
Details: Protein solution: 10 - 18 mg/mL, 50 mM HEPES, pH 7.2, 50 mM NaCl, 10mM MgCl2 5% Glycerol, 1mM DTE, 10 M ZnCl2 Reservoir solution:200mM calcium acetate, 100mM sodium cacodylate pH 6.5, 18% ...Details: Protein solution: 10 - 18 mg/mL, 50 mM HEPES, pH 7.2, 50 mM NaCl, 10mM MgCl2 5% Glycerol, 1mM DTE, 10 M ZnCl2 Reservoir solution:200mM calcium acetate, 100mM sodium cacodylate pH 6.5, 18% PEG 8000. Drop: 3uL protein, 3uL reservoir , VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 1, 2011 / Details: crystal
RadiationMonochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.25→32.6 Å / Num. all: 6462 / Num. obs: 6462 / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 4.6 % / Rmerge(I) obs: 0.18

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Processing

Software
NameVersionClassification
MAR345data collection
SERGUIdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB 3K8Y for Chain A and PDB 1GUA for Chain B

3k8y

1gua


Resolution: 3.25→32.6 Å / σ(F): 0 / Phase error: 32.62 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.271 668 10.54 %
Rwork0.2505 --
obs0.2754 6339 85.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0605 Å2-0 Å20 Å2
2--0.0605 Å20 Å2
3----0.1211 Å2
Refinement stepCycle: LAST / Resolution: 3.25→32.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1860 0 33 17 1910
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091934
X-RAY DIFFRACTIONf_angle_d0.5972627
X-RAY DIFFRACTIONf_dihedral_angle_d12.773705
X-RAY DIFFRACTIONf_chiral_restr0.041302
X-RAY DIFFRACTIONf_plane_restr0.002335
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2719-3.52420.5009910.3665788X-RAY DIFFRACTION55
3.5242-3.87840.3781230.31461069X-RAY DIFFRACTION76
3.8784-4.43840.35981350.27911180X-RAY DIFFRACTION82
4.4384-5.58730.26111420.2351264X-RAY DIFFRACTION87
5.5873-32.61450.2421560.24151374X-RAY DIFFRACTION90
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)
10.2780.0704-0.08220.0182-0.0210.02080.08760.0220.0643-0.00690.04780.0326-0.04410.11110.41640.47870.2944-0.19730.2160.24350.564544.96095.2341-15.3303
20.02750.0218-0.04850.1480.02420.0950.03880.0042-0.05450.00920.1157-0.0397-0.0228-0.06710.18590.55250.2983-0.1602-0.3702-0.1060.617732.9185-7.5102-18.0347
30.2565-0.0763-0.00820.09730.06710.06430.17290.20120.10540.06910.06860.0445-0.086-0.0250.2430.52340.20510.0684-0.4441-0.21610.882137.97518.1763-14.2374
40.0154-0.0227-0.00550.04260.00040.0905-0.00560.0042-0.02240.04990.0006-0.0048-0.0140.004-0.16050.45910.2765-0.05210.42240.05370.691144.5871-6.6383-23.6293
50.06570.030.01830.0331-0.00760.01830.032-0.115-0.07380.05160.00180.04180.0149-0.089-0.02110.38710.3261-0.06460.62840.06630.698852.1693-0.7228-23.123
60.0162-0.0183-0.0030.0241-0.00370.01670.04740.0287-0.0421-0.00750.0251-0.0166-0.0079-0.01570.10230.01990.226-0.08260.33070.19580.726650.3304-11.8697-13.7669
70.0684-0.0793-0.0140.19980.0360.3317-0.07010.04680.0154-0.1119-0.2191-0.01780.11260.0423-0.24290.00940.1149-0.02380.04980.07420.6744.4611-11.3414-6.7729
80.0337-0.0331-0.03970.06410.05140.043-0.01330.0087-0.04040.098-0.03940.06090.1323-0.0278-0.12360.34270.3591-0.194-0.0949-0.23630.739144.0744-10.229-3.4569
90.0152-0.00970.00780.0071-0.00310.00040.0192-0.01860.033-0.07460.0135-0.0179-0.00650.0134-0.00330.5605-0.2043-0.11190.06640.08280.640243.84953.2895-5.8022
100.0166-0.02670.00610.0573-0.00210.0052-0.0390.0286-0.0292-0.0323-0.0484-0.05090.0241-0.0221-0.08860.2725-0.11090.14240.39250.06550.283238.3657-1.6029-34.5527
110.0110.03080.02310.26460.14980.087-0.1288-0.05030.00010.0150.0002-0.0161-0.00540.0017-0.07920.42490.30740.17430.21510.27960.557637.00253.424-28.1685
120.00430.00310.00040.00140.00040.00130.02-0.02130.007-0.01080.02290.0210.06740.013601.0080.1110.32650.76320.00321.006926.3499-7.4536-36.6921
130.01660.02240.02030.03060.02740.0249-0.0035-0.0075-0.00510.0208-0.0175-0.0027-0.0079-0.0106-0.00160.49090.2272-0.05330.65020.36780.85427.2196-1.5425-28.3773
140.0009-0.002-0.00070.00210.00070.00020.0047-0.0527-0.0061-0.0021-0.03860.00430.0312-0.0422-0.00011.12550.503-0.28211.0920.25170.874426.09265.1077-25.9304
150.06160.0255-0.02660.0587-0.11010.2168-0.06890.01160.0405-0.0222-0.0328-0.00440.05350.0721-0.0010.5472-0.14640.20520.1056-0.03920.498436.8028.8881-42.8417
160.0033-0.0021-0.0035-0.00010.0021-0.0002-0.0096-0.00030.0118-0.0530.03350.07660.0536-0.077401.0058-0.1092-0.15250.87860.10220.777828.8334-1.2822-41.7021
170.02840.0284-0.01530.0279-0.01130.0217-0.0054-0.00320.0202-0.09330.01040.03870.0484-0.02060.00730.55080.0942-0.22010.2582-0.15620.685433.99266.6279-36.146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 10 )
2X-RAY DIFFRACTION2chain 'A' and (resid 11 through 36 )
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 52 )
4X-RAY DIFFRACTION4chain 'A' and (resid 53 through 66 )
5X-RAY DIFFRACTION5chain 'A' and (resid 67 through 76 )
6X-RAY DIFFRACTION6chain 'A' and (resid 77 through 104 )
7X-RAY DIFFRACTION7chain 'A' and (resid 105 through 127 )
8X-RAY DIFFRACTION8chain 'A' and (resid 128 through 151 )
9X-RAY DIFFRACTION9chain 'A' and (resid 152 through 166 )
10X-RAY DIFFRACTION10chain 'B' and (resid 55 through 62 )
11X-RAY DIFFRACTION11chain 'B' and (resid 63 through 71 )
12X-RAY DIFFRACTION12chain 'B' and (resid 72 through 81 )
13X-RAY DIFFRACTION13chain 'B' and (resid 82 through 86 )
14X-RAY DIFFRACTION14chain 'B' and (resid 87 through 95 )
15X-RAY DIFFRACTION15chain 'B' and (resid 96 through 111 )
16X-RAY DIFFRACTION16chain 'B' and (resid 112 through 123 )
17X-RAY DIFFRACTION17chain 'B' and (resid 124 through 131 )

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