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- PDB-9gtk: KRAS in complex with DARPin 784_F5 -

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Basic information

Entry
Database: PDB / ID: 9gtk
TitleKRAS in complex with DARPin 784_F5
Components
  • DARPin 784_F5
  • Isoform 2B of GTPase KRas
KeywordsSIGNALING PROTEIN / Small GTPase / Designed Ankyrin Repeat Protein
Function / homology
Function and homology information


forebrain astrocyte development / negative regulation of epithelial cell differentiation / type I pneumocyte differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / positive regulation of Rac protein signal transduction / skeletal muscle cell differentiation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants ...forebrain astrocyte development / negative regulation of epithelial cell differentiation / type I pneumocyte differentiation / regulation of synaptic transmission, GABAergic / epithelial tube branching involved in lung morphogenesis / Rac protein signal transduction / positive regulation of Rac protein signal transduction / skeletal muscle cell differentiation / 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 / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / glial cell proliferation / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by CSF3 (G-CSF) / Erythropoietin activates RAS / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / protein-membrane adaptor activity / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / positive regulation of glial cell proliferation / Tie2 Signaling / FRS-mediated FGFR1 signaling / homeostasis of number of cells within a tissue / Signaling by FGFR2 in disease / striated muscle cell differentiation / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / EGFR Transactivation by Gastrin / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / Insulin receptor signalling cascade / 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 / RAF activation / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 TMD/JMD mutants / Signaling by high-kinase activity BRAF mutants / Signaling by SCF-KIT / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / visual learning / Signaling by ERBB2 KD Mutants / cytoplasmic side of plasma membrane / Regulation of RAS by GAPs / RAS processing / Signaling by CSF1 (M-CSF) in myeloid cells / Signaling by RAF1 mutants / Negative regulation of MAPK pathway / 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 / MAPK cascade / DAP12 signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / G protein activity / actin cytoskeleton organization / Ca2+ pathway / RAF/MAP kinase cascade / neuron apoptotic process / gene expression / negative regulation of neuron apoptotic process / mitochondrial outer membrane / Ras protein signal transduction / Golgi membrane / focal adhesion / GTPase activity
Similarity search - Function
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 / TRIETHYLENE GLYCOL / S,R MESO-TARTARIC ACID / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsKapp, J.N. / Verdurmen, W. / Schaefer, J.V. / Kopra, K. / Nagy-Davidescu, G. / Richard, E. / Nokin, M.J. / Ernst, P. / Tamaskovic, R. / Schwill, M. ...Kapp, J.N. / Verdurmen, W. / Schaefer, J.V. / Kopra, K. / Nagy-Davidescu, G. / Richard, E. / Nokin, M.J. / Ernst, P. / Tamaskovic, R. / Schwill, M. / Degen, R. / Scholl, C. / Santamaria, D. / Plueckthun, A.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss Cancer LeagueKFS-4147-02-2017 Switzerland
CitationJournal: Mol Oncol / Year: 2025
Title: A nucleotide-independent, pan-RAS-targeted DARPin elicits anti-tumor activity in a multimodal manner.
Authors: Kapp, J.N. / Verdurmen, W.P.R. / Schaefer, J.V. / Kopra, K. / Nagy-Davidescu, G. / Richard, E. / Nokin, M.J. / Ernst, P. / Tamaskovic, R. / Schwill, M. / Degen, R. / Scholl, C. / Santamaria, D. / Pluckthun, A.
History
DepositionSep 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: 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: DARPin 784_F5
C: Isoform 2B of GTPase KRas
D: Isoform 2B of GTPase KRas
H: DARPin 784_F5
I: DARPin 784_F5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,75151
Polymers121,1876
Non-polymers4,56445
Water10,160564
1
A: Isoform 2B of GTPase KRas
B: DARPin 784_F5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,47225
Polymers40,3962
Non-polymers2,07623
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Isoform 2B of GTPase KRas
I: DARPin 784_F5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,88717
Polymers40,3962
Non-polymers1,49215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Isoform 2B of GTPase KRas
H: DARPin 784_F5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3919
Polymers40,3962
Non-polymers9957
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.320, 152.830, 149.150
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 6 molecules ACDBHI

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


Mass: 22225.311 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: Protein DARPin 784_F5


Mass: 18170.434 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 7 types, 609 molecules

#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


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
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#8: Chemical ChemComp-SRT / S,R MESO-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 564 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.74 Å3/Da / Density % sol: 55.15 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: Crystals grew within 25 days in 0.2 M potassium sodium tartrate, 20% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→48 Å / Num. obs: 173930 / % possible obs: 100 % / Redundancy: 7.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.082 / Rrim(I) all: 0.088 / Net I/σ(I): 14.28
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2-2.052.242128660.3612.4131
2.05-2.111.866125460.4812.0091
2.11-2.171.436122160.5941.5461
2.17-2.241.171118560.6641.2621
2.24-2.310.886114390.770.9551
2.31-2.390.68110990.8540.7341
2.39-2.480.507107290.910.5481
2.48-2.580.362103120.9480.3931
2.58-2.70.25799040.9670.281
2.7-2.830.20594530.9830.221
2.83-2.980.14189960.9910.1521
2.98-3.160.10885030.9950.1161
3.16-3.380.07580170.9970.0811
3.38-3.650.05574360.9980.0591
3.65-40.04268450.9990.0461
4-4.470.03461720.9990.0371
4.47-5.160.03154440.9990.0331
5.16-6.320.03346160.9990.0361
6.32-8.940.023354410.0241
8.94-480.017193710.0181

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XSCALEdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→47.28 Å / Cor.coef. Fo:Fc: 0.973 / Cor.coef. Fo:Fc free: 0.965 / SU B: 7.932 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.131 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20063 4544 5 %RANDOM
Rwork0.17101 ---
obs0.17249 86336 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 63.756 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2--0.22 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: 1 / Resolution: 2→47.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7825 0 288 564 8677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0128456
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168107
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.84511395
X-RAY DIFFRACTIONr_angle_other_deg0.5951.78418729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08651056
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.52542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.028101490
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0850.21282
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.029786
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021751
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5393.0334167
X-RAY DIFFRACTIONr_mcbond_other2.5393.0334167
X-RAY DIFFRACTIONr_mcangle_it3.6795.4345242
X-RAY DIFFRACTIONr_mcangle_other3.6795.4355243
X-RAY DIFFRACTIONr_scbond_it4.1023.624289
X-RAY DIFFRACTIONr_scbond_other4.0953.6184288
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6046.3356153
X-RAY DIFFRACTIONr_long_range_B_refined9.35230.899370
X-RAY DIFFRACTIONr_long_range_B_other9.31430.679278
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 330 -
Rwork0.318 6284 -
obs--99.91 %
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)
15.27731.1951-0.21924.3201-0.29083.556-0.04730.39720.0454-0.52750.1013-0.2566-0.1080.1229-0.0540.072-0.01050.03630.0517-0.01280.0293-10.3075-0.1101-52.0866
25.5119-2.04990.21625.1619-0.32652.28620.107-0.3167-0.79420.15490.00040.31760.3903-0.1677-0.10740.0808-0.0408-0.03490.03540.06740.234-28.0176-16.5583-39.7806
33.85810.0295-0.6433.4356-0.41725.78290.1281-0.4065-0.1950.2141-0.0998-0.02020.3704-0.1718-0.02830.1392-0.0423-0.02940.23420.04720.0201-9.7282-1.9807-18.6658
44.0986-0.14450.49785.1657-0.46562.8886-0.0065-0.43320.47210.30980.0128-0.1383-0.43950.1323-0.00630.1372-0.0459-0.01180.0736-0.08990.23551.859725.1645-34.6546
55.8654-0.2934-0.67943.67760.52816.0218-0.13411.16430.3222-0.79750.05060.3991-0.3511-0.32770.08350.4936-0.0403-0.11410.25730.08480.4805-8.367932.4978-58.718
64.5798-0.43290.04415.93021.14165.548-0.0901-0.49171.01690.31630.0687-0.2295-1.5325-0.09510.02140.7662-0.01080.02210.5543-0.14780.2842-10.658920.4143-3.3325
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 176
2X-RAY DIFFRACTION2B11 - 174
3X-RAY DIFFRACTION3C1 - 175
4X-RAY DIFFRACTION4D1 - 173
5X-RAY DIFFRACTION5H12 - 174
6X-RAY DIFFRACTION6I13 - 172

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