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- PDB-8vm2: Crystal Structure of NRAS Q61K bound to GTP -

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Basic information

Entry
Database: PDB / ID: 8vm2
TitleCrystal Structure of NRAS Q61K bound to GTP
ComponentsGTPase NRas
KeywordsHYDROLASE/ONCOPROTEIN / NRAS / oncogenic mutation / RAS superfamily small GTPases / HYDROLASE / HYDROLASE-ONCOPROTEIN complex
Function / homology
Function and homology information


Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / tertiary granule membrane / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS ...Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / tertiary granule membrane / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / 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 / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR4 / 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 / Tie2 Signaling / positive regulation of endothelial cell proliferation / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / 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 receptor signalling cascade / 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 / VEGFR2 mediated cell proliferation / small monomeric GTPase / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by SCF-KIT / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Regulation of RAS by GAPs / RAS processing / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / GDP binding / Signaling by BRAF and RAF1 fusions / DAP12 signaling / MAPK cascade / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / G protein activity / RAF/MAP kinase cascade / Ras protein signal transduction / Golgi membrane / GTPase activity / Neutrophil degranulation / endoplasmic reticulum membrane / GTP binding / protein-containing complex binding / Golgi apparatus / extracellular exosome / membrane / plasma membrane / cytosol
Similarity search - Function
Small GTPase, Ras-type / Small GTPase Ras domain profile. / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / GTPase NRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.74 Å
AuthorsGebregiworgis, T. / Chan, J.Y.L. / Kuntz, D.A. / Prive, G.G. / Marshall, C.B. / Ikura, M.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)FDN-1542284 Canada
CitationJournal: Eur J Cell Biol / Year: 2024
Title: Crystal structure of NRAS Q61K with a ligand-induced pocket near switch II.
Authors: Gebregiworgis, T. / Chan, J.Y. / Kuntz, D.A. / Prive, G.G. / Marshall, C.B. / Ikura, M.
History
DepositionJan 12, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 1, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase NRas
B: GTPase NRas
C: GTPase NRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,04313
Polymers65,3183
Non-polymers2,72510
Water7,404411
1
A: GTPase NRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8615
Polymers21,7731
Non-polymers1,0894
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTPase NRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8434
Polymers21,7731
Non-polymers1,0713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GTPase NRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3384
Polymers21,7731
Non-polymers5663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.789, 55.699, 149.291
Angle α, β, γ (deg.)90.00, 98.15, 90.00
Int Tables number5
Space group name H-MI121
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

#1: Protein GTPase NRas / Transforming protein N-Ras


Mass: 21772.666 Da / Num. of mol.: 3 / Fragment: residues 1-172 / Mutation: Q61K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRAS, HRAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01111, small monomeric GTPase
#2: Chemical
ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: GTP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 411 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.61 Å3/Da / Density % sol: 52.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.1
Details: PEG/Ion (containing 0.06 M Citric acid, 0.04 M BIS-TRIS propane)/pH 4.1, 16% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.542 Å
DetectorType: DECTRIS EIGER R 1M / Detector: PIXEL / Date: Feb 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.74→29.74 Å / Num. obs: 63393 / % possible obs: 99.9 % / Redundancy: 3.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.056 / Rpim(I) all: 0.032 / Rrim(I) all: 0.065 / Net I/σ(I): 15.8 / Num. measured all: 234839
Reflection shellResolution: 1.74→1.77 Å / % possible obs: 99.5 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.749 / Num. measured all: 7765 / Num. unique obs: 3430 / CC1/2: 0.578 / Rpim(I) all: 0.616 / Rrim(I) all: 0.975 / Net I/σ(I) obs: 1.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
CrysalisProdata collection
CrysalisProdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.74→29.74 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2026 2002 3.16 %
Rwork0.1721 --
obs0.173 63374 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.74→29.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4108 0 165 411 4684
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012
X-RAY DIFFRACTIONf_angle_d2.069
X-RAY DIFFRACTIONf_dihedral_angle_d24.321688
X-RAY DIFFRACTIONf_chiral_restr0.107677
X-RAY DIFFRACTIONf_plane_restr0.014753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.780.30481390.284300X-RAY DIFFRACTION100
1.78-1.830.27811430.26354345X-RAY DIFFRACTION100
1.83-1.890.26731430.24344363X-RAY DIFFRACTION100
1.89-1.950.27141430.21714390X-RAY DIFFRACTION100
1.95-2.020.21051400.20044335X-RAY DIFFRACTION100
2.02-2.10.21551430.18144392X-RAY DIFFRACTION100
2.1-2.190.20761430.17364351X-RAY DIFFRACTION100
2.19-2.310.2091430.16674375X-RAY DIFFRACTION100
2.31-2.450.19521430.1654400X-RAY DIFFRACTION100
2.45-2.640.2041420.16254364X-RAY DIFFRACTION100
2.64-2.910.1831440.16154395X-RAY DIFFRACTION100
2.91-3.330.17681440.15034405X-RAY DIFFRACTION100
3.33-4.190.16211440.14114443X-RAY DIFFRACTION100
4.19-29.740.20731480.16654514X-RAY DIFFRACTION100
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)
15.749-0.70681.8060.764-0.16491.55730.0626-0.1303-0.55910.04140.0915-0.06380.05490.186-0.14020.16140.00550.00260.1634-0.01770.15548.0441-17.6798-16.5166
21.8799-0.53490.34680.8534-0.13650.71250.22241.1942-0.5641-0.6836-0.2261-0.05530.24610.26550.02240.26040.06370.01160.4263-0.09280.12422.0406-18.4593-31.9914
33.40010.47390.70521.42690.50890.6310.03830.0802-0.2649-0.0889-0.0036-0.05230.04710.1023-0.0890.1615-0.01180.00820.165-0.02820.15678.9164-18.3559-20.8864
43.9470.62151.03161.73681.33591.4474-0.1983-0.0793-0.72760.1384-0.05950.440.103-0.1721-0.3150.2448-0.01110.01250.15460.04460.4742-6.4126-25.2251-15.9744
52.8295-0.25810.77041.40140.05781.06650.0281-0.1054-0.07070.0658-0.00430.12990.0389-0.0483-0.03780.1247-0.00330.02340.13330.01370.1092-6.8532-12.004-16.1733
60.70490.1917-0.57030.0654-0.16960.47330.13310.84290.3555-0.6484-0.11230.2291-0.2466-0.0999-0.00430.27350.0162-0.04380.37270.11030.191-7.9515-3.4689-33.038
73.2343-0.0108-0.26482.0843-1.46636.0611-0.02620.00630.5820.1530.10750.1127-0.6231-0.34630.03860.17810.01070.02220.15230.01730.256-8.40060.7841-17.6943
80.972-0.1842-0.60720.57190.09331.8770.05020.55920.5138-0.2032-0.1021-0.133-0.11610.0997-0.24170.16730.00940.04770.30720.11010.09641.7978-5.4302-27.6501
93.7512-0.19590.28952.91190.19383.2788-0.1212-0.13990.48890.26160.0202-0.23-0.26140.3081-0.04210.1382-0.00990.00640.1781-0.01940.1578.4019-8.3969-14.0023
103.45960.5075-0.22410.41350.01680.52870.161-0.4832-0.09160.051-0.13940.08240.0618-0.2645-0.00990.1215-0.02360.00740.25770.01880.1579-40.298-11.0761-11.2507
112.6627-0.8047-0.15691.7469-0.57620.9280.0288-0.48030.38790.23890.06190.0154-0.1713-0.050.00910.1544-0.00440.03770.2576-0.08660.1777-32.90581.7914-3.6776
122.5678-0.15691.52870.2146-0.50982.57830.0224-0.36280.10930.0418-0.0290.0096-0.056-0.1511-0.01830.13890.00630.01410.3104-0.00660.1556-42.0014-6.7735-6.9865
132.7979-0.2488-0.45570.29110.05990.8855-0.0409-0.4171-0.18960.00120.0059-0.01520.0850.0038-0.0070.1416-0.00450.02350.230.04390.1422-28.8523-9.4875-10.0577
144.89742.5168-0.46343.17490.91291.7812-0.1029-0.0691-0.52170.00730.0448-0.2220.37110.09020.02810.16530.01270.01810.16640.01870.218-23.2951-16.79-15.5139
152.4517-0.1801-0.19310.83410.5431.77170.10360.3180.2221-0.2604-0.0908-0.041-0.17240.0705-0.04320.14410.00240.02260.19250.02970.1822-24.1834-2.9796-21.0558
162.2592-0.8757-0.76272.29481.4892.42550.15660.27230.5159-0.2011-0.03460.0057-0.3945-0.1267-0.05910.16210.01680.03030.16880.03580.2489-31.07042.9003-18.0288
173.9580.68680.29741.99880.19813.0619-0.02650.1589-0.0585-0.08350.1049-0.05790.2742-0.0984-0.00880.130.00090.00960.19060.01970.1036-39.7467-9.8964-21.371
182.5971-0.2311-0.32281.55060.08771.47250.06110.19140.0211-0.1079-0.0224-0.1626-0.02010.1455-0.09180.16380.0043-0.00640.09340.00190.1547-35.1613-6.8327-44.2038
192.9674-0.09110.15941.0437-0.42751.09030.01910.00620.33160.1512-0.0549-0.1035-0.07450.0907-0.10790.2069-0.0049-0.01820.12740.02440.2508-34.9407-1.0319-42.058
202.90880.1075-0.2911.5645-0.41461.5470.08090.5089-0.0155-0.2607-0.00980.08160.1348-0.2346-0.0610.2106-0.007-0.05710.1837-0.00210.1853-43.0721-10.7766-48.925
212.3011-0.11570.74081.08470.16691.01550.1634-0.1163-0.43390.06570.05270.02910.4235-0.37220.23820.1989-0.0404-0.03340.1350.01270.2225-45.1323-15.2276-38.6908
221.80890.1725-0.41821.1710.21630.9496-0.0143-0.3804-0.56480.05360.01360.39550.4072-0.16070.02150.274-0.0447-0.0470.11620.03280.337-43.8429-18.7397-35.869
231.3983-1.0099-1.44592.45822.04163.2129-0.02550.0517-0.073-0.09360.0323-0.07680.21640.1176-0.01460.2340.0341-0.02340.1044-0.0180.1917-31.1556-19.4432-46.8296
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid -4 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 36 )
3X-RAY DIFFRACTION3chain 'A' and (resid 37 through 61 )
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 74 )
5X-RAY DIFFRACTION5chain 'A' and (resid 75 through 116 )
6X-RAY DIFFRACTION6chain 'A' and (resid 117 through 126 )
7X-RAY DIFFRACTION7chain 'A' and (resid 127 through 137 )
8X-RAY DIFFRACTION8chain 'A' and (resid 138 through 151 )
9X-RAY DIFFRACTION9chain 'A' and (resid 152 through 170 )
10X-RAY DIFFRACTION10chain 'B' and (resid -4 through 15 )
11X-RAY DIFFRACTION11chain 'B' and (resid 16 through 36 )
12X-RAY DIFFRACTION12chain 'B' and (resid 37 through 46 )
13X-RAY DIFFRACTION13chain 'B' and (resid 47 through 92 )
14X-RAY DIFFRACTION14chain 'B' and (resid 93 through 104 )
15X-RAY DIFFRACTION15chain 'B' and (resid 105 through 137 )
16X-RAY DIFFRACTION16chain 'B' and (resid 138 through 151 )
17X-RAY DIFFRACTION17chain 'B' and (resid 152 through 171 )
18X-RAY DIFFRACTION18chain 'C' and (resid 1 through 25 )
19X-RAY DIFFRACTION19chain 'C' and (resid 26 through 46 )
20X-RAY DIFFRACTION20chain 'C' and (resid 47 through 104 )
21X-RAY DIFFRACTION21chain 'C' and (resid 105 through 126 )
22X-RAY DIFFRACTION22chain 'C' and (resid 127 through 151 )
23X-RAY DIFFRACTION23chain 'C' and (resid 152 through 171 )

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