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- PDB-8t72: Crystal structure of WT KRAS4a with bound GMPPNP and Mg ion -

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Basic information

Entry
Database: PDB / ID: 8t72
TitleCrystal structure of WT KRAS4a with bound GMPPNP and Mg ion
ComponentsGTPase KRas
KeywordsONCOPROTEIN / RAS / KRAS
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 / Resolution: 1.6 Å
AuthorsTran, T.H. / Whitley, M.J. / Dharmaiah, S. / Simanshu, D.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)HHSN261200800001E United States
CitationJournal: Sci Adv / Year: 2024
Title: Comparative analysis of KRAS4a and KRAS4b splice variants reveals distinctive structural and functional properties.
Authors: Whitley, M.J. / Tran, T.H. / Rigby, M. / Yi, M. / Dharmaiah, S. / Waybright, T.J. / Ramakrishnan, N. / Perkins, S. / Taylor, T. / Messing, S. / Esposito, D. / Nissley, D.V. / McCormick, F. / ...Authors: Whitley, M.J. / Tran, T.H. / Rigby, M. / Yi, M. / Dharmaiah, S. / Waybright, T.J. / Ramakrishnan, N. / Perkins, S. / Taylor, T. / Messing, S. / Esposito, D. / Nissley, D.V. / McCormick, F. / Stephen, A.G. / Turbyville, T. / Cornilescu, G. / Simanshu, D.K.
History
DepositionJun 19, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)62,94210
Polymers61,2783
Non-polymers1,6647
Water2,936163
1
A: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9974
Polymers20,4261
Non-polymers5713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9733
Polymers20,4261
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,9733
Polymers20,4261
Non-polymers5472
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.901, 102.066, 54.031
Angle α, β, γ (deg.)90.000, 113.770, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 20426.123 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, small monomeric GTPase
#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
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 163 / 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: 1.81 Å3/Da / Density % sol: 31.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.2 M NaBr, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 11, 2017
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.6→44.5 Å / Num. obs: 56159 / % possible obs: 97.5 % / Redundancy: 5.1 % / Biso Wilson estimate: 27.89 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rrim(I) all: 0.069 / Net I/σ(I): 11.59
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
1.6-1.70.88689760.7140.9891
1.7-1.810.585530.8960.5561
1.81-1.960.28379340.9570.3181
1.96-2.140.15873720.9830.1751
2.14-2.40.10166980.9910.1121
2.4-2.770.07458160.9940.0831
2.77-3.380.05749800.9960.0641
3.38-4.770.04737330.9970.0521
4.77-44.50.04420970.9970.0491

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
PHENIX1.20.1_4487refinement
PDB_EXTRACT3.28data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→44.5 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2362 2807 5 %
Rwork0.1917 53322 -
obs0.1939 56129 97.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 157.82 Å2 / Biso mean: 50.3754 Å2 / Biso min: 18.8 Å2
Refinement stepCycle: final / Resolution: 1.6→44.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3708 0 100 163 3971
Biso mean--35.83 44.44 -
Num. residues----463
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.630.35871320.31372502263492
1.63-1.660.31111400.28982653279398
1.66-1.690.31681430.28572710285398
1.69-1.720.35221390.28012659279899
1.72-1.760.40021420.29472699284199
1.76-1.80.28841410.27382675281699
1.8-1.850.33061400.25742661280199
1.85-1.90.32051410.23912692283398
1.9-1.950.27271390.22392632277197
1.95-2.010.27841430.22032716285999
2.01-2.090.23181420.22382699284199
2.09-2.170.31661420.2272688283099
2.17-2.270.24541410.1962697283899
2.27-2.390.22821410.18862676281799
2.39-2.540.2531390.19512626276596
2.54-2.730.22981430.20212722286599
2.73-3.010.24411410.19462675281698
3.01-3.440.2151400.18782669280997
3.44-4.340.21221380.15312616275495
4.34-44.50.19231400.16052655279595
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)
12.0762-0.8382-1.2512.59040.23543.0385-0.3232-0.2785-0.19060.67520.2608-0.080.39660.19010.01360.30190.0729-0.05370.25890.01350.240110.8724-5.448215.0313
29.70473.4488-0.15843.2810.74561.5701-0.3709-1.7414-0.21210.67590.2976-0.18530.67720.2942-0.02780.73710.1631-0.09010.56240.05270.37026.6547-1.983526.1291
30.97870.16970.42455.28942.43921.9239-0.4302-0.19960.04130.75050.30020.04070.23860.1188-0.07310.37150.0947-0.06330.3296-0.04310.286913.5761-10.961812.7499
45.18190.1852-1.43150.1667-0.4331.4195-0.04260.04820.60570.36860.2691-0.83480.03520.2461-0.33610.22750.0339-0.08360.3042-0.09190.414715.68981.776910.5876
57.5705-2.595-2.26883.80670.24913.41160.13740.15570.87980.1420.1223-0.8759-0.26450.1916-0.20150.3106-0.00570.01090.2639-0.02460.42379.397111.769411.3311
65.60531.19862.07513.32322.00675.02340.05630.32850.2323-1.18050.5891-0.8828-1.13030.019-0.39750.67470.11920.22310.5381-0.04030.893621.29026.80381.7327
72.7834-1.9691-1.9623.65351.43292.53810.13790.29820.0716-0.2365-0.1020.1667-0.1501-0.3767-0.05180.25340.0386-0.00760.3020.00790.24581.536.57256.907
85.6121-0.9879-2.69343.50010.95813.3371-0.06440.4726-0.39270.1849-0.08640.16320.1647-0.37810.13930.23060.0027-0.03790.248-0.0060.23116.3283-6.14276.1602
91.94820.0083-1.11520.083-0.08840.88210.2117-0.91390.37031.5636-0.05971.2051-0.8950.1641-0.69721.08590.03810.61110.4052-0.09560.607727.686224.386735.6755
108.2718-2.24310.54765.415-3.10461.84780.4781-1.41931.36271.0837-0.411-0.5041-0.4635-0.1273-0.25641.7377-0.02670.23890.6166-0.13110.610137.201132.087134.649
111.0759-0.1392-0.80280.6981.06042.69160.0556-0.43950.15940.3459-0.13090.2751-0.05560.21180.05830.72820.00110.13510.7237-0.01160.68424.000123.004839.9702
121.5787-0.2118-1.56050.9343-1.03733.1256-0.1686-0.4277-0.17781.19820.10730.5045-0.01650.17090.14830.55870.02750.20170.27310.04610.325534.176816.746727.0009
137.35942.3426-1.05134.2445-3.24914.7656-0.210.5047-1.54670.3819-0.332-0.29370.86130.00950.52090.87950.0850.31230.43580.01420.825732.95096.726132.3347
142.3305-0.0077-0.67122.4054-0.80313.55670.0827-0.00780.11490.00490.17510.8215-0.1149-0.1172-0.210.41530.02040.13170.30070.02160.504730.609720.675521.4251
152.6248-0.4512-0.39073.2653-1.61754.52390.26140.49970.0057-0.89890.21581.3850.0036-0.452-0.36330.4286-0.0006-0.0440.3479-0.01880.629827.543418.315619.1736
161.8634-3.34911.95496.6009-2.51834.22280.44160.12420.25090.00030.51581.4212-0.4611-1.19890.12220.50930.090.39590.46580.01181.091519.385221.318429.8011
173.5091-0.3007-0.11512.29560.80462.66820.11-0.3010.0774-0.2832-0.2902-1.0444-0.21670.51910.11920.2254-0.0210.03420.32320.10340.383915.148237.96496.7475
183.74423.48131.00433.24840.83651.1841-0.8140.1507-0.18770.2408-0.4534-1.35960.98831.20711.26620.7745-0.0830.29130.49910.08961.030222.085530.78753.2641
195.44690.32553.41590.6005-0.23797.0951-0.30560.54680.76070.0546-0.0931-0.223-0.77980.12980.4050.2801-0.0190.05110.45520.1380.414216.831246.7706-1.028
202.6394-1.0222-0.84342.57560.47090.7508-0.2638-0.46220.22370.5018-0.2155-1.2569-0.17670.45780.12310.2818-0.0747-0.14280.54310.07270.417315.197642.577411.2175
212.20060.3763-2.07336.3276-0.36442.9114-0.0133-0.4045-0.0850.6407-0.03690.1992-0.04820.1404-0.00810.2298-0.01-0.04540.2990.02680.21466.029632.80812.0224
225.78120.91970.32263.47463.54544.89860.1405-0.73230.47651.489-0.48881.2366-0.0863-0.52550.49290.5188-0.05430.0370.4342-0.0020.43810.65240.810617.6152
231.02410.6122-0.61455.4249-1.88741.6708-0.19140.0129-0.146-0.17740.19450.39560.2826-0.0411-0.01470.2537-0.0179-0.02640.24430.04410.30810.415429.87475.3607
243.1109-0.10160.53846.6158-3.05823.8697-0.1960.0474-0.157-1.0531-0.002-0.39940.35130.07460.19390.3142-0.04180.02910.31090.0250.24097.898939.53160.1264
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:25)A1 - 25
2X-RAY DIFFRACTION2(chain A and resid 26:37)A26 - 37
3X-RAY DIFFRACTION3(chain A and resid 38:60)A38 - 60
4X-RAY DIFFRACTION4(chain A and resid 71:83)A71 - 83
5X-RAY DIFFRACTION5(chain A and resid 84:100)A84 - 100
6X-RAY DIFFRACTION6(chain A and resid 101:108)A101 - 108
7X-RAY DIFFRACTION7(chain A and resid 109:142)A109 - 142
8X-RAY DIFFRACTION8(chain A and resid 143:169)A143 - 169
9X-RAY DIFFRACTION9(chain B and resid 1:25)B1 - 25
10X-RAY DIFFRACTION10(chain B and resid 26:37)B26 - 37
11X-RAY DIFFRACTION11(chain B and resid 38:72)B38 - 72
12X-RAY DIFFRACTION12(chain B and resid 73:94)B73 - 94
13X-RAY DIFFRACTION13(chain B and resid 95:106)B95 - 106
14X-RAY DIFFRACTION14(chain B and resid 107:126)B107 - 126
15X-RAY DIFFRACTION15(chain B and resid 127:148)B127 - 148
16X-RAY DIFFRACTION16(chain B and resid 149:166)B149 - 166
17X-RAY DIFFRACTION17(chain C and resid 2:25)C2 - 25
18X-RAY DIFFRACTION18(chain C and resid 26:38)C26 - 38
19X-RAY DIFFRACTION19(chain C and resid 39:50)C39 - 50
20X-RAY DIFFRACTION20(chain C and resid 51:72)C51 - 72
21X-RAY DIFFRACTION21(chain C and resid 73:91)C73 - 91
22X-RAY DIFFRACTION22(chain C and resid 92:108)C92 - 108
23X-RAY DIFFRACTION23(chain C and resid 109:141)C109 - 141
24X-RAY DIFFRACTION24(chain C and resid 142:168)C142 - 168

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