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- PDB-36ok: Tri-complex of RMC-8839, KRAS G13C, and CypA -

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Basic information

Entry
Database: PDB / ID: 36ok
TitleTri-complex of RMC-8839, KRAS G13C, and CypA
Components
  • Isoform 2B of GTPase KRas
  • Peptidyl-prolyl cis-trans isomerase A
KeywordsSIGNALING PROTEIN / inhibitor / complex / small GTPase / cancer / tri-complex / SIGNALING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade ...negative regulation of protein K48-linked ubiquitination / regulation of apoptotic signaling pathway / cell adhesion molecule production / lipid droplet organization / negative regulation of viral life cycle / heparan sulfate binding / regulation of viral genome replication / virion binding / leukocyte chemotaxis / negative regulation of stress-activated MAPK cascade / activation of protein kinase B activity / endothelial cell activation / Basigin interactions / protein peptidyl-prolyl isomerization / cyclosporin A binding / Minus-strand DNA synthesis / Plus-strand DNA synthesis / Uncoating of the HIV Virion / response to mineralocorticoid / GMP binding / forebrain astrocyte development / LRR domain binding / Early Phase of HIV Life Cycle / regulation of synaptic transmission, GABAergic / Integration of provirus / negative regulation of epithelial cell differentiation / response to isolation stress / APOBEC3G mediated resistance to HIV-1 infection / negative regulation of protein phosphorylation / response to gravity / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / myoblast proliferation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / viral release from host cell / RAS signaling downstream of NF1 loss-of-function variants / Binding and entry of HIV virion / Calcineurin activates NFAT / RUNX3 regulates p14-ARF / positive regulation of glial cell proliferation / skeletal muscle cell differentiation / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / cardiac muscle cell proliferation / SHC1 events in ERBB4 signaling / Signalling to RAS / negative regulation of protein kinase activity / negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / positive regulation of viral genome replication / Estrogen-stimulated signaling through PRKCZ / positive regulation of Rac protein signal transduction / SHC-mediated cascade:FGFR3 / glial cell proliferation / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / 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 / neutrophil chemotaxis / striated muscle cell differentiation / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / Tie2 Signaling / protein-membrane adaptor activity / Signaling by FGFR2 in disease / Signaling by FLT3 fusion proteins / GRB2 events in EGFR signaling / 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 / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / Downstream signal transduction / GRB2 events in ERBB2 signaling / homeostasis of number of cells within a tissue / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / response to glucocorticoid / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / Ras activation upon Ca2+ influx through NMDA receptor / :
Similarity search - Function
Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / Small GTPase, Ras-type / Small GTPase Ras domain profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases ...Cyclophilin-type peptidyl-prolyl cis-trans isomerase / Cyclophilin-type peptidyl-prolyl cis-trans isomerase, conserved site / Cyclophilin-type peptidyl-prolyl cis-trans isomerase signature. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain profile. / Cyclophilin-type peptidyl-prolyl cis-trans isomerase domain / Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD / Cyclophilin-like domain superfamily / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
: / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / DI(HYDROXYETHYL)ETHER / GTPase KRas / Peptidyl-prolyl cis-trans isomerase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.21 Å
AuthorsTomlinson, A.C.A. / Saldajeno-Concar, M. / Knox, J.E. / Yano, J.K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Cancer Discov / Year: 2026
Title: Selective Inhibition of KRASG13C Reveals an Increased Dependence on Wild-Type RAS Isoforms in Codon 13 RAS-Mutant Cancers.
Authors: Seamon, K.J. / Zhuang, Y. / Yang, Y.C. / Chakraborty, S. / Cregg, J. / Tomlinson, A.C.A. / Gould, A. / Ahler, E. / Maldonato, B.J. / Spradlin, J.N. / Pota, K. / Weller, C. / Marquez, A. / ...Authors: Seamon, K.J. / Zhuang, Y. / Yang, Y.C. / Chakraborty, S. / Cregg, J. / Tomlinson, A.C.A. / Gould, A. / Ahler, E. / Maldonato, B.J. / Spradlin, J.N. / Pota, K. / Weller, C. / Marquez, A. / Wang, Z. / Koltun, E.S. / Knox, J.E. / Gill, A.L. / Smith, J.A.M. / Singh, M. / Jiang, J. / Wildes, D. / Holderfield, M.
History
DepositionJun 23, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2B of GTPase KRas
B: Isoform 2B of GTPase KRas
C: Peptidyl-prolyl cis-trans isomerase A
D: Peptidyl-prolyl cis-trans isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,39513
Polymers75,0574
Non-polymers3,3389
Water16,916939
1
A: Isoform 2B of GTPase KRas
D: Peptidyl-prolyl cis-trans isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1456
Polymers37,5292
Non-polymers1,6164
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoform 2B of GTPase KRas
C: Peptidyl-prolyl cis-trans isomerase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2517
Polymers37,5292
Non-polymers1,7225
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.960, 101.690, 66.150
Angle α, β, γ (deg.)90.000, 90.970, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

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Protein , 2 types, 4 molecules ABCD

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


Mass: 19404.928 Da / Num. of mol.: 2
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 Peptidyl-prolyl cis-trans isomerase A / PPIase A / Cyclophilin A / Cyclosporin A-binding protein / Rotamase A


Mass: 18123.582 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PPIA, CYPA / Production host: Escherichia coli (E. coli) / References: UniProt: P62937, peptidylprolyl isomerase

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Non-polymers , 6 types, 948 molecules

#3: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 2 / 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.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-A1DKY / (4S)-N-[(2S)-1-{[(1P,6S,8S,10R,14S,21M)-21-{2-[(1S)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-22-(2,2,2-trifluoroethyl)-16-oxa-6,10,22,28-tetraazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2,20,23,26-pentaen-8-yl]amino}-3-methyl-1-oxobutan-2-yl]-N,4-dimethyl-3-propanoyl-1-oxa-3,8-diazaspiro[4.5]decane-8-carboxamide (non-preferred name)


Mass: 1034.216 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C54H74F3N9O8 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 939 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.15 Å3/Da / Density % sol: 42.76 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 25% PEG 3350, 0.1M Bis Tris, pH 5.5, 150 mM NaCl

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.97934 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.21→40.31 Å / Num. obs: 188470 / % possible obs: 97.98 % / Redundancy: 3.8 % / Biso Wilson estimate: 14.3 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.048 / Net I/σ(I): 6.33
Reflection shellResolution: 1.21→1.22 Å / Rmerge(I) obs: 1.153 / Mean I/σ(I) obs: 0.86 / Num. unique obs: 5980 / CC1/2: 0.409 / Rpim(I) all: 0.6671

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.21→40.31 Å / SU ML: 0.1416 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.0503
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1792 9452 5.02 %
Rwork0.1428 179012 -
obs0.1446 188464 97.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 20.89 Å2
Refinement stepCycle: LAST / Resolution: 1.21→40.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5248 0 223 939 6410
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01155735
X-RAY DIFFRACTIONf_angle_d1.31637780
X-RAY DIFFRACTIONf_chiral_restr0.1024829
X-RAY DIFFRACTIONf_plane_restr0.01351008
X-RAY DIFFRACTIONf_dihedral_angle_d13.97852247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.21-1.220.29093410.26665639X-RAY DIFFRACTION93.91
1.22-1.240.29333100.26365750X-RAY DIFFRACTION94.9
1.24-1.250.29892690.26465799X-RAY DIFFRACTION95.14
1.25-1.270.2933010.26095856X-RAY DIFFRACTION96.08
1.27-1.290.28163440.23885799X-RAY DIFFRACTION96.15
1.29-1.30.26993340.23475842X-RAY DIFFRACTION96.39
1.3-1.320.26363300.22875875X-RAY DIFFRACTION96.59
1.32-1.340.28153030.23035874X-RAY DIFFRACTION97.37
1.34-1.360.25783160.2165924X-RAY DIFFRACTION97.27
1.36-1.390.23243070.20045931X-RAY DIFFRACTION97.35
1.39-1.410.23162990.20225960X-RAY DIFFRACTION97.48
1.41-1.430.23442890.18965904X-RAY DIFFRACTION97.73
1.43-1.460.2152750.17356017X-RAY DIFFRACTION97.73
1.46-1.490.21923160.15795933X-RAY DIFFRACTION97.89
1.49-1.520.19563180.1435954X-RAY DIFFRACTION97.83
1.52-1.560.19043080.13256016X-RAY DIFFRACTION98.26
1.56-1.60.17163500.12425947X-RAY DIFFRACTION98.59
1.6-1.640.17333270.12115982X-RAY DIFFRACTION98.59
1.64-1.690.16633370.1246011X-RAY DIFFRACTION99.11
1.69-1.750.16963160.12886026X-RAY DIFFRACTION98.99
1.75-1.810.16693110.13026065X-RAY DIFFRACTION99.28
1.81-1.880.16882910.13416072X-RAY DIFFRACTION99.45
1.88-1.970.18042920.12846084X-RAY DIFFRACTION99.44
1.97-2.070.17733240.12796096X-RAY DIFFRACTION99.69
2.07-2.20.15393630.12456057X-RAY DIFFRACTION99.89
2.2-2.370.17093250.13186091X-RAY DIFFRACTION99.88
2.37-2.610.17353820.13656031X-RAY DIFFRACTION99.8
2.61-2.980.18543010.1426126X-RAY DIFFRACTION99.64
2.98-3.760.14583020.12386117X-RAY DIFFRACTION99.41
3.76-40.310.14932710.12976234X-RAY DIFFRACTION99.59

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