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- PDB-6vc8: Crystal structure of wild-type KRAS4b(1-169) in complex with GMPP... -

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Basic information

Entry
Database: PDB / ID: 6vc8
TitleCrystal structure of wild-type KRAS4b(1-169) in complex with GMPPNP and Mg ion
ComponentsGTPase KRas
KeywordsONCOPROTEIN / KRAS / RAS / KRAS4b
Function / homology
Function and homology information


forebrain astrocyte development / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants ...forebrain astrocyte development / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / 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 / RUNX3 regulates p14-ARF / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / glial cell proliferation / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / 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:FGFR2 / SHC-mediated cascade:FGFR4 / protein-membrane adaptor activity / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / homeostasis of number of cells within a tissue / positive regulation of glial cell proliferation / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / striated muscle cell differentiation / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Ras activation upon Ca2+ influx through NMDA receptor / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / small monomeric GTPase / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / FCERI mediated MAPK activation / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / visual learning / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cytoplasmic side of plasma membrane / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / GDP binding / 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 / Signaling by CSF1 (M-CSF) in myeloid cells / MAPK cascade / Signaling by BRAF and RAF1 fusions / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling / Ca2+ pathway / gene expression / actin cytoskeleton organization / RAF/MAP kinase cascade / neuron apoptotic process / Ras protein signal transduction / negative regulation of neuron apoptotic process / mitochondrial outer membrane / positive regulation of protein phosphorylation / Golgi membrane / focal adhesion
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsTran, T.H. / Davies, D.R. / Edwards, T.E. / Simanshu, D.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Machine learning-driven multiscale modeling reveals lipid-dependent dynamics of RAS signaling proteins.
Authors: Ingolfsson, H.I. / Neale, C. / Carpenter, T.S. / Shrestha, R. / Lopez, C.A. / Tran, T.H. / Oppelstrup, T. / Bhatia, H. / Stanton, L.G. / Zhang, X. / Sundram, S. / Di Natale, F. / Agarwal, A. ...Authors: Ingolfsson, H.I. / Neale, C. / Carpenter, T.S. / Shrestha, R. / Lopez, C.A. / Tran, T.H. / Oppelstrup, T. / Bhatia, H. / Stanton, L.G. / Zhang, X. / Sundram, S. / Di Natale, F. / Agarwal, A. / Dharuman, G. / Kokkila Schumacher, S.I.L. / Turbyville, T. / Gulten, G. / Van, Q.N. / Goswami, D. / Jean-Francois, F. / Agamasu, C. / Hettige, J.J. / Travers, T. / Sarkar, S. / Surh, M.P. / Yang, Y. / Moody, A. / Liu, S. / Van Essen, B.C. / Voter, A.F. / Ramanathan, A. / Hengartner, N.W. / Simanshu, D.K. / Stephen, A.G. / Bremer, P.T. / Gnanakaran, S. / Glosli, J.N. / Lightstone, F.C. / McCormick, F. / Nissley, D.V. / Streitz, F.H.
History
DepositionDec 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 12, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 11, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)59,6269
Polymers57,9863
Non-polymers1,6406
Water50428
1
A: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8753
Polymers19,3291
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8753
Polymers19,3291
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8753
Polymers19,3291
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.210, 82.330, 88.140
Angle α, β, γ (deg.)90.000, 112.920, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein GTPase KRas / K-Ras 2 / Ki-Ras / c-K-ras / c-Ki-ras


Mass: 19328.811 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli (E. coli) / References: UniProt: P01116
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 1.99 Å3/Da / Density % sol: 38.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 32% PEG 4000, 800 mM LiCl, 100 mM Magnesium Chloride and 100 mM Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 25, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.5→37.91 Å / Num. obs: 15480 / % possible obs: 97.3 % / Redundancy: 2.6 % / Biso Wilson estimate: 46.5 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 15.5
Reflection shellResolution: 2.5→2.56 Å / Rmerge(I) obs: 0.565 / Mean I/σ(I) obs: 2.02 / Num. unique obs: 1571 / % possible all: 97.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.17refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GFT

3gft


Resolution: 2.5→37.91 Å / SU ML: 0.36 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 31.62
RfactorNum. reflection% reflection
Rfree0.2768 749 4.84 %
Rwork0.2124 --
obs0.2155 15475 97.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.56 Å2 / Biso mean: 62.1887 Å2 / Biso min: 27.96 Å2
Refinement stepCycle: final / Resolution: 2.5→37.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3548 0 99 28 3675
Biso mean--51.77 54.23 -
Num. residues----470
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.690.34411380.31112965310398
2.69-2.960.33371560.2772944310099
2.96-3.390.3151740.23852960313499
3.39-4.270.27331310.19352949308098
4.27-37.910.23511500.17692908305895
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)
13.70650.11960.47134.79750.58363.71610.22460.1455-0.1355-0.0997-0.4230.58640.3789-1.1410.13290.316-0.03640.00590.5809-0.04760.27875.3549-18.570312.9702
25.72973.8166-5.43045.5295-5.10467.77770.9121-0.2073-0.24322.10141.731.5834-0.91281.205-1.32350.77280.1027-0.42791.1561-0.17030.6993-1.0254-9.507413.4534
32.59470.11820.8732.19733.95315.7518-0.0106-0.75790.54350.2812-0.38290.41170.1855-0.83790.37280.4619-0.0709-0.02550.7309-0.03540.5944-0.311-24.87289.1855
44.1525-0.3826-0.81562.49887.81899.75610.1182-0.4495-0.1383-0.0036-0.31190.43890.276-0.06280.33890.5623-0.0777-0.00670.50390.0930.43763.6545-27.21428.9456
51.6589-1.1195-0.19253.6768-1.96031.47950.556-0.6676-0.7874-0.36230.0926-0.1919-0.1477-0.88-0.41820.9825-0.3055-0.01110.89350.31270.62857.7348-23.871923.3756
63.0416-0.53210.86490.25580.19584.4889-0.10040.0476-0.24660.20120.2883-0.83130.0697-0.1733-0.25060.22860.040.02660.3208-0.0310.313114.1614-12.611814.9481
77.33025.8957-0.652710.0038-0.6316.99510.1879-0.499-0.79992.7650.0997-2.17270.5881-0.6982-0.18030.6583-0.0837-0.19310.48010.03270.555118.3635-16.98623.2474
87.98262.7017-2.88626.9144.40325.62480.01440.0674-0.51190.7039-0.1449-2.71810.7720.2838-0.04760.363-0.009-0.10840.41860.01360.592318.0013-23.036716.3043
97.20275.92143.32698.74933.11869.7452-0.49660.49660.6738-1.16530.1163-0.6888-1.56760.50660.45010.58-0.04-0.06910.37720.05650.566516.417-2.80698.7887
105.52641.07852.65914.76150.79865.72890.10330.8403-0.28-0.30310.2454-1.17940.06030.7216-0.3150.3274-0.02070.05060.5186-0.13650.505318.5378-13.78238.4852
119.4104-3.91811.60846.6036-2.67267.940.41070.3075-0.4856-1.48730.1091-0.63450.96760.1434-0.45790.4615-0.0357-0.00210.4512-0.12940.451812.8733-27.09517.1399
121.213-2.3257-0.40915.30830.0660.7388-0.5963-0.65110.68191.01690.3971-1.4277-1.1975-0.09760.07990.8732-0.0911-0.28660.4532-0.05220.955527.5754-14.6459-12.2244
132.1793.93361.31195.0357-0.03245.4682-0.45930.03471.0475-0.527-0.23060.2371-0.7651-0.15280.760.47930.0026-0.05950.44720.02380.523418.6783-21.1333-22.685
140.3057-1.4198-0.2565.56480.91620.2594-1.14922.1262.6713-0.79280.35450.1967-0.66550.12450.37890.79540.1633-0.25590.37860.30241.292518.3588-18.4756-28.8728
158.1744-7.2371-2.33038.75743.7037.1776-1.1478-0.20421.68260.616-0.476-0.1922-1.34560.37261.12871.036-0.0686-0.39610.49140.01621.275624.5211-11.2899-19.5257
164.84812.06620.90475.488-1.04114.2714-0.05-0.21390.43060.5001-0.4432-1.188-0.76350.6640.41110.4544-0.0748-0.0910.3779-0.00370.689425.7213-26.0581-14.5695
174.68580.03971.66857.8396-2.0749.1083-0.3178-0.8030.58380.66640.03250.6825-0.3545-0.86290.31590.35780.01330.06980.44-0.12190.481114.0329-28.035-12.2237
184.6404-2.0722-0.94355.4482-1.09286.8424-0.6675-1.66381.71651.0397-0.53520.5713-1.4377-1.11830.98770.79260.0452-0.1260.7108-0.4170.98421.0513-16.2321-6.7332
192.2299-1.92891.42931.6643-1.42881.76010.6192-1.3026-1.06841.6146-0.2617-0.27910.3211-0.4082-0.32940.9306-0.022-0.26780.51450.29790.740432.8126-7.126941.4595
200.17380.4988-0.04922.1771-0.48021.39710.3596-0.5708-1.20580.4747-0.1231-0.13460.37840.0171-0.36861.0542-0.04-0.34430.91560.43851.114437.3854-11.838345.0781
216.8931-0.71821.48740.16370.07350.80930.3517-1.6353-0.47580.4968-0.5998-0.64210.005-0.17790.13371.3174-0.1515-0.27590.94110.45560.860138.4216-5.261948.6437
228.6966-0.218-3.38146.6032-3.11162.02310.5082-2.9415-0.67481.5465-0.0459-0.4507-1.3087-0.8522-0.09431.1110.0051-0.01981.21480.11420.686729.97893.528346.7069
238.9508-0.24584.19486.0745-1.15649.003-0.0769-0.4657-0.1570.89470.1535-0.3056-0.38710.1245-0.07750.4401-0.0025-0.03560.30440.07430.346634.8394-0.324732.1792
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 24 )A2 - 24
2X-RAY DIFFRACTION2chain 'A' and (resid 25 through 37 )A25 - 37
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 46 )A38 - 46
4X-RAY DIFFRACTION4chain 'A' and (resid 47 through 57 )A47 - 57
5X-RAY DIFFRACTION5chain 'A' and (resid 58 through 76 )A58 - 76
6X-RAY DIFFRACTION6chain 'A' and (resid 77 through 86 )A77 - 86
7X-RAY DIFFRACTION7chain 'A' and (resid 87 through 104 )A87 - 104
8X-RAY DIFFRACTION8chain 'A' and (resid 105 through 116 )A105 - 116
9X-RAY DIFFRACTION9chain 'A' and (resid 117 through 126 )A117 - 126
10X-RAY DIFFRACTION10chain 'A' and (resid 127 through 151 )A127 - 151
11X-RAY DIFFRACTION11chain 'A' and (resid 152 through 168 )A152 - 168
12X-RAY DIFFRACTION12chain 'B' and (resid 1 through 9 )B1 - 9
13X-RAY DIFFRACTION13chain 'B' and (resid 10 through 23 )B10 - 23
14X-RAY DIFFRACTION14chain 'B' and (resid 24 through 36 )B24 - 36
15X-RAY DIFFRACTION15chain 'B' and (resid 37 through 45 )B37 - 45
16X-RAY DIFFRACTION16chain 'B' and (resid 46 through 104 )B46 - 104
17X-RAY DIFFRACTION17chain 'B' and (resid 105 through 151 )B105 - 151
18X-RAY DIFFRACTION18chain 'B' and (resid 152 through 168 )B152 - 168
19X-RAY DIFFRACTION19chain 'C' and (resid 2 through 25 )C2 - 25
20X-RAY DIFFRACTION20chain 'C' and (resid 26 through 48 )C26 - 48
21X-RAY DIFFRACTION21chain 'C' and (resid 49 through 57 )C49 - 57
22X-RAY DIFFRACTION22chain 'C' and (resid 58 through 76 )C58 - 76
23X-RAY DIFFRACTION23chain 'C' and (resid 77 through 168 )C77 - 168

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