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- PDB-7lc1: Crystal Structure of KRAS4b (GMPPNP-bound) in complex with the RB... -

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Basic information

Entry
Database: PDB / ID: 7lc1
TitleCrystal Structure of KRAS4b (GMPPNP-bound) in complex with the RBD-PH domains of SIN1
Components
  • Isoform 2B of GTPase KRas
  • Target of rapamycin complex 2 subunit MAPKAP1
KeywordsONCOPROTEIN / Hydrolase / KRAS / RAS / K-RAS / GMPPNP / GppNHp / SIN1 / MAPKAP1 / PH DOMAIN / RBD / RAS-BINDING DOMAIN / EFFECTOR / SMALL GTPase
Function / homology
Function and homology information


TORC2 signaling / TORC2 complex / regulation of cellular response to oxidative stress / phosphatidic acid binding / negative regulation of Ras protein signal transduction / serine/threonine protein kinase complex / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,5-bisphosphate binding / response to mineralocorticoid / GMP binding ...TORC2 signaling / TORC2 complex / regulation of cellular response to oxidative stress / phosphatidic acid binding / negative regulation of Ras protein signal transduction / serine/threonine protein kinase complex / phosphatidylinositol-3,4-bisphosphate binding / phosphatidylinositol-3,5-bisphosphate binding / response to mineralocorticoid / GMP binding / forebrain astrocyte development / LRR domain binding / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / response to isolation stress / response to gravity / epithelial tube branching involved in lung morphogenesis / Constitutive Signaling by AKT1 E17K in Cancer / type I pneumocyte differentiation / Rac protein signal transduction / phosphatidylinositol-3,4,5-trisphosphate binding / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / myoblast proliferation / skeletal muscle cell differentiation / RAS signaling downstream of NF1 loss-of-function variants / RUNX3 regulates p14-ARF / positive regulation of glial cell proliferation / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / CD28 dependent PI3K/Akt signaling / SHC1 events in ERBB4 signaling / cardiac muscle cell proliferation / Signalling to RAS / enzyme-substrate adaptor activity / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / glial cell proliferation / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / cellular response to nutrient levels / 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 / Signaling by CSF3 (G-CSF) / 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 / Tie2 Signaling / striated muscle cell differentiation / Signaling by FGFR2 in disease / phosphatidylinositol-4,5-bisphosphate binding / GRB2 events in EGFR signaling / cytoskeleton organization / 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 / substantia nigra development / homeostasis of number of cells within a tissue / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / negative regulation of insulin receptor signaling pathway / Ras activation upon Ca2+ influx through NMDA receptor / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / response to glucocorticoid / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / small monomeric GTPase / VEGFR2 mediated vascular permeability / FCERI mediated MAPK activation / liver development / RAF activation / Signaling by ERBB2 TMD/JMD mutants / female pregnancy / Signaling by SCF-KIT / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / regulation of long-term neuronal synaptic plasticity / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants
Similarity search - Function
Sin1, N-terminal / Stress-activated map kinase interacting protein 1 (SIN1) / TORC2 component Sin1/Avo1 / SAPK-interacting protein 1, Pleckstrin-homology domain / Sin1, middle CRIM domain / SAPK-interacting protein 1 (Sin1), middle CRIM domain / SAPK-interacting protein 1 (Sin1), Pleckstrin-homology / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Small GTPase, Ras-type ...Sin1, N-terminal / Stress-activated map kinase interacting protein 1 (SIN1) / TORC2 component Sin1/Avo1 / SAPK-interacting protein 1, Pleckstrin-homology domain / Sin1, middle CRIM domain / SAPK-interacting protein 1 (Sin1), middle CRIM domain / SAPK-interacting protein 1 (Sin1), Pleckstrin-homology / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / Small GTPase, Ras-type / Small GTPase Ras domain 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 / PH-like domain superfamily / Roll / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase KRas / Target of rapamycin complex 2 subunit MAPKAP1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsDharmaiah, S. / Simanshu, D.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)HHSN261200800001E United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: RAS interaction with Sin1 is dispensable for mTORC2 assembly and activity.
Authors: Castel, P. / Dharmaiah, S. / Sale, M.J. / Messing, S. / Rizzuto, G. / Cuevas-Navarro, A. / Cheng, A. / Trnka, M.J. / Urisman, A. / Esposito, D. / Simanshu, D.K. / McCormick, F.
History
DepositionJan 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 4, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.pdbx_database_id_DOI ..._citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 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

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Assembly

Deposited unit
A: Isoform 2B of GTPase KRas
B: Target of rapamycin complex 2 subunit MAPKAP1
C: Isoform 2B of GTPase KRas
D: Target of rapamycin complex 2 subunit MAPKAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,5648
Polymers92,4714
Non-polymers1,0934
Water75742
1
A: Isoform 2B of GTPase KRas
B: Target of rapamycin complex 2 subunit MAPKAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7824
Polymers46,2352
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-24 kcal/mol
Surface area18260 Å2
MethodPISA
2
C: Isoform 2B of GTPase KRas
D: Target of rapamycin complex 2 subunit MAPKAP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7824
Polymers46,2352
Non-polymers5472
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2960 Å2
ΔGint-23 kcal/mol
Surface area18660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.760, 97.070, 96.620
Angle α, β, γ (deg.)90.000, 92.320, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 19271.760 Da / Num. of mol.: 2 / Mutation: Q25A
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: Protein Target of rapamycin complex 2 subunit MAPKAP1 / TORC2 subunit MAPKAP1 / Mitogen-activated protein kinase 2-associated protein 1 / Stress-activated ...TORC2 subunit MAPKAP1 / Mitogen-activated protein kinase 2-associated protein 1 / Stress-activated map kinase-interacting protein 1 / mSIN1


Mass: 26963.545 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAPKAP1, MIP1, SIN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BPZ7
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3 / Feature type: SUBJECT OF INVESTIGATION
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.17 Å3/Da / Density % sol: 43.23 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 200 mM ammonium sulfate, 100 mM HEPES (N-2-hydroxyethyl piperazine-N-ethane sulfonic acid) pH 7.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.35→48.54 Å / Num. obs: 32468 / % possible obs: 98.6 % / Redundancy: 3.38 % / Biso Wilson estimate: 63.266 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.088 / Χ2: 0.916 / Net I/σ(I): 10.16 / Num. measured all: 109727
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.35-2.493.4370.8531.8117864523451980.6781.01299.3
2.49-2.663.3810.5123.0116443492548630.8560.60998.7
2.66-2.853.3170.3374.6213847425441740.9090.40298.1
2.85-3.13.5650.2047.5814417408540440.9710.2499
3.1-3.433.4260.11611.812712374037100.9870.13799.2
3.43-3.93.2740.07416.0410870339533200.9920.08997.8
3.9-4.63.2640.05120.49025281827650.9960.06198.1
4.6-5.93.3830.04722.547748232322900.9960.05598.6
5.9-10.33.2130.03723.395450172716960.9980.04498.2
10.3-48.543.3110.03227.413514134080.9980.03898.8

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3VOQ

3voq


Resolution: 2.35→48.54 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2792 2005 6.18 %
Rwork0.2314 30454 -
obs0.2344 32459 98.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 155.98 Å2 / Biso mean: 70.2582 Å2 / Biso min: 27.12 Å2
Refinement stepCycle: final / Resolution: 2.35→48.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5930 0 66 42 6038
Biso mean--47.34 54.56 -
Num. residues----766
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.35-2.410.35251400.35642184232499
2.41-2.470.43561380.34532168230699
2.47-2.550.38931440.3612183232799
2.55-2.630.34141430.32882155229898
2.63-2.720.3311410.31472142228398
2.72-2.830.3591370.30222168230599
2.83-2.960.34991460.30192174232099
2.96-3.120.30951450.28652188233399
3.12-3.310.29841380.25712192233099
3.31-3.570.29271400.23662204234499
3.57-3.930.27521430.21522141228497
3.93-4.490.281450.18472132227798
4.49-5.660.24751500.18562202235299
5.66-48.540.20521550.18942221237698
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)
14.3932-0.59040.35934.15850.35192.8274-0.02560.1524-0.0283-0.33060.0580.25280.0115-0.0775-0.01270.2857-0.0474-0.01640.26230.01410.40547.66996.4358-54.4036
22.37051.7749-0.59073.1653-0.70870.8612-0.0325-0.1199-0.06840.0677-0.0533-0.1719-0.0731-0.08970.08370.29830.0546-0.03080.42120.03380.4018-10.82457.2362-35.2338
33.43591.62721.95463.36370.63995.96590.115-0.0133-0.0450.3296-0.19220.00460.88840.15630.08150.53940.02940.12140.4122-0.04140.4001-22.1307-5.7467-82.209
42.8852-2.679-2.01092.23531.45281.1764-0.08240.348-0.05060.0728-0.0542-0.0732-0.06750.05640.16640.4892-0.1245-0.0160.7238-0.06570.612-4.1681.8275-99.9015
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 1 through 167)A1 - 167
2X-RAY DIFFRACTION2(chain 'B' and resid 278 through 500)B278 - 500
3X-RAY DIFFRACTION3(chain 'C' and resid 0 through 166)C0 - 166
4X-RAY DIFFRACTION4(chain 'D' and resid 277 through 496)D277 - 496

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