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- PDB-9kfl: KRAS G12V and peptide complex -

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Basic information

Entry
Database: PDB / ID: 9kfl
TitleKRAS G12V and peptide complex
Components
  • Isoform 2B of GTPase KRas
  • TIG3 peptide
KeywordsONCOPROTEIN / KRAS / mutant / G12V / TIG3 / STRUCTURAL PROTEIN
Function / homology
Function and homology information


positive regulation of protein-glutamine gamma-glutamyltransferase activity / phosphatidylethanolamine acyl-chain remodeling / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / Acyl chain remodelling of PE / phospholipase A1 activity / N-acyltransferase activity / phospholipase A2 activity / positive regulation of keratinocyte differentiation / phospholipase A2 ...positive regulation of protein-glutamine gamma-glutamyltransferase activity / phosphatidylethanolamine acyl-chain remodeling / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / Acyl chain remodelling of PE / phospholipase A1 activity / N-acyltransferase activity / phospholipase A2 activity / positive regulation of keratinocyte differentiation / phospholipase A2 / response to mineralocorticoid / GMP binding / forebrain astrocyte development / acyltransferase activity / 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 / type I pneumocyte differentiation / Rac protein signal transduction / 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 / SHC1 events in ERBB4 signaling / cardiac muscle cell proliferation / Signalling to RAS / 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 / 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 / lipid catabolic process / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / 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 / phospholipid metabolic process / striated muscle cell differentiation / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / homeostasis of number of cells within a tissue / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Ras activation upon Ca2+ influx through NMDA receptor / 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 / FCERI mediated MAPK activation / liver development / Signaling by ERBB2 TMD/JMD mutants / female pregnancy / RAF activation / 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 / Signaling by ERBB2 KD Mutants / visual learning / cytoplasmic side of plasma membrane / cytokine-mediated signaling pathway
Similarity search - Function
: / Lecithin retinol acyltransferase / LRAT domain / LRAT domain profile. / 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 ...: / Lecithin retinol acyltransferase / LRAT domain / LRAT domain profile. / 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
GUANOSINE-5'-DIPHOSPHATE / GTPase KRas / Phospholipase A and acyltransferase 4
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.45 Å
AuthorsHa, M.S. / Jang, S.B. / Han, C.W.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea) Korea, Republic Of
CitationJournal: To Be Published
Title: KRAS G12V and TIG3 peptide complex
Authors: Ha, M.S. / Jang, S.B. / Han, C.W.
History
DepositionNov 6, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 12, 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
D: Isoform 2B of GTPase KRas
E: Isoform 2B of GTPase KRas
H: Isoform 2B of GTPase KRas
K: Isoform 2B of GTPase KRas
P: TIG3 peptide
Y: TIG3 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,82317
Polymers97,4857
Non-polymers2,33810
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.840, 83.416, 83.492
Angle α, β, γ (deg.)120.06, 90.07, 89.96
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
22
33
44
55
66
77
88
99
1010
/ NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

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Components

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


Mass: 19184.656 Da / Num. of mol.: 5 / Mutation: G12V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KRAS, KRAS2, RASK2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P01116, small monomeric GTPase
#2: Protein/peptide TIG3 peptide / HRAS-like suppressor 4 / HRSL4 / RAR-responsive protein TIG3 / Retinoic acid receptor responder ...HRAS-like suppressor 4 / HRSL4 / RAR-responsive protein TIG3 / Retinoic acid receptor responder protein 3 / Retinoid-inducible gene 1 protein / Tazarotene-induced gene 3 protein / Phospholipase A and acyltransferase 4


Mass: 780.868 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9UL19
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: Polyethylene glycol 3350, 0.2M potassium nitrate (pH 6.8)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.45→29.57 Å / Num. obs: 12300 / % possible obs: 95.46 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 97.5
Reflection shellResolution: 3.45→3.539 Å / Rmerge(I) obs: 0.105 / Num. unique obs: 12300 / % possible all: 70.63

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.45→29.57 Å / Cor.coef. Fo:Fc: 0.865 / Cor.coef. Fo:Fc free: 0.793 / SU B: 31.102 / SU ML: 0.477 / Cross valid method: THROUGHOUT / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23342 667 5.4 %RANDOM
Rwork0.18886 ---
obs0.19111 11625 95.46 %-
Solvent computationIon probe radii: 1.1 Å / Shrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.034 Å2
Baniso -1Baniso -2Baniso -3
1--27.82 Å2-2.11 Å26.33 Å2
2--22.61 Å293.96 Å2
3---5.21 Å2
Refinement stepCycle: 1 / Resolution: 3.45→29.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6787 0 145 0 6932
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0127040
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6641.6769532
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8835849
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.06322.969384
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.648151244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9741545
X-RAY DIFFRACTIONr_chiral_restr0.0960.2937
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025227
X-RAY DIFFRACTIONr_gen_planes_other
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_it6.1236.4843417
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it10.6699.7124259
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it6.3676.773623
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined30.13130599
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A56470.1
12D56470.1
21A56560.1
22E56560.1
31A57160.09
32H57160.09
41A57310.09
42K57310.09
51D57630.09
52E57630.09
61D56800.1
62H56800.1
71D56690.1
72K56690.1
81E56880.1
82H56880.1
91E57030.1
92K57030.1
101H57700.08
102K57700.08
LS refinement shellResolution: 3.45→3.539 Å
RfactorNum. reflection% reflection
Rfree0.208 38 -
Rwork0.214 621 -
obs--70.63 %

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