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- PDB-7c41: KRAS G12V and H-REV107 peptide complex -

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Basic information

Entry
Database: PDB / ID: 7c41
TitleKRAS G12V and H-REV107 peptide complex
Components
  • GTPase KRas
  • HRAS-like suppressor 3
KeywordsONCOPROTEIN/HYDROLASE / KRAS G12V / H-REV107 / inhibitor / STRUCTURAL PROTEIN / ONCOPROTEIN-HYDROLASE complex
Function / homology
Function and homology information


membrane disassembly / regulation of adipose tissue development / ether lipid metabolic process / organelle disassembly / phosphatidylethanolamine acyl-chain remodeling / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS ...membrane disassembly / regulation of adipose tissue development / ether lipid metabolic process / organelle disassembly / phosphatidylethanolamine acyl-chain remodeling / N-acylphosphatidylethanolamine metabolic process / phospholipase A1 / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / phospholipase A1 activity / peroxisome organization / N-acyltransferase activity / phospholipase A2 activity / lens fiber cell differentiation / phospholipid biosynthetic process / phospholipase A2 / peroxisomal membrane / forebrain astrocyte development / triglyceride metabolic process / acyltransferase activity / 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) / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / lipid catabolic process / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / protein-membrane adaptor activity / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / phospholipid metabolic process / Signaling by FGFR3 in disease / p38MAPK events / Tie2 Signaling / positive regulation of glial cell proliferation / 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 / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / 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 / response to bacterium / RAF activation / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 TMD/JMD mutants / Signaling by high-kinase activity BRAF mutants / mitochondrial membrane / Signaling by SCF-KIT / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / visual learning / Signaling by ERBB2 KD Mutants
Similarity search - Function
: / Lecithin retinol acyltransferase / LRAT domain / LRAT domain profile. / 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 ...: / Lecithin retinol acyltransferase / LRAT domain / LRAT domain profile. / 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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GTPase KRas / Phospholipase A and acyltransferase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.276 Å
AuthorsHan, C.W. / Jeong, M.S. / Jang, S.B.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2018R1D1A1B07043701 Korea, Republic Of
CitationJournal: Cancers (Basel) / Year: 2020
Title: A H-REV107 Peptide Inhibits Tumor Growth and Interacts Directly with Oncogenic KRAS Mutants.
Authors: Han, C.W. / Jeong, M.S. / Ha, S.C. / Jang, S.B.
History
DepositionMay 14, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 19, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase KRas
D: HRAS-like suppressor 3
J: GTPase KRas
M: GTPase KRas
G: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,05513
Polymers81,1855
Non-polymers1,8708
Water1,49583
1
A: GTPase KRas
D: HRAS-like suppressor 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6124
Polymers21,1452
Non-polymers4682
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-23 kcal/mol
Surface area8290 Å2
MethodPISA
2
J: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4813
Polymers20,0141
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area900 Å2
ΔGint-18 kcal/mol
Surface area8110 Å2
MethodPISA
3
M: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4813
Polymers20,0141
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-19 kcal/mol
Surface area8380 Å2
MethodPISA
4
G: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,4813
Polymers20,0141
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area860 Å2
ΔGint-20 kcal/mol
Surface area8310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.907, 84.339, 84.335
Angle α, β, γ (deg.)59.98, 89.96, 89.97
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 20013.539 Da / Num. of mol.: 4 / 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
#2: Protein/peptide HRAS-like suppressor 3 / Phospholipase A and acyltransferase 3 / Adipose-specific phospholipase A2 / AdPLA / Group XVI ...Phospholipase A and acyltransferase 3 / Adipose-specific phospholipase A2 / AdPLA / Group XVI phospholipase A1/A2 / H-rev 107 protein homolog / HREV107-1 / HRAS-like suppressor 1 / HRSL3 / HREV107-3 / Renal carcinoma antigen NY-REN-65


Mass: 1131.214 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
References: UniProt: P53816, phospholipase A1, phospholipase A2
#3: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 3.18 Å3/Da / Density % sol: 61.31 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop
Details: polyethylene glycol 3350, 0.2 M potassium nitrate at 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: Dec 27, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.27→50 Å / Num. obs: 45859 / % possible obs: 97.7 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.102 / Net I/σ(I): 16.5
Reflection shellResolution: 2.27→2.3284 Å / Rmerge(I) obs: 0.2 / Num. unique obs: 2465

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data collection
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UQW

5uqw


Resolution: 2.276→36.522 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.46 / Phase error: 29.35
RfactorNum. reflection% reflection
Rfree0.2834 2143 4.67 %
Rwork0.2603 --
obs0.2613 45859 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.276→36.522 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5427 0 116 83 5626
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095632
X-RAY DIFFRACTIONf_angle_d1.167627
X-RAY DIFFRACTIONf_dihedral_angle_d6.6193397
X-RAY DIFFRACTIONf_chiral_restr0.058859
X-RAY DIFFRACTIONf_plane_restr0.005969
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.276-2.32840.28841160.22452996X-RAY DIFFRACTION99
2.3284-2.38670.28781710.21622797X-RAY DIFFRACTION100
2.3867-2.45120.30751040.20912985X-RAY DIFFRACTION100
2.4512-2.52330.24882060.19152850X-RAY DIFFRACTION100
2.5233-2.60470.2567920.19593012X-RAY DIFFRACTION100
2.6047-2.69780.27641770.21732865X-RAY DIFFRACTION100
2.6978-2.80570.34471500.23652952X-RAY DIFFRACTION100
2.8057-2.93340.26941500.22992834X-RAY DIFFRACTION100
2.9334-3.0880.28121540.23732884X-RAY DIFFRACTION100
3.088-3.28130.2381810.25562938X-RAY DIFFRACTION100
3.2813-3.53450.3893880.2782956X-RAY DIFFRACTION100
3.5345-3.88980.28291520.28232887X-RAY DIFFRACTION100
3.8898-4.45180.29651260.27532948X-RAY DIFFRACTION100
4.4518-5.60560.2639960.28922946X-RAY DIFFRACTION100
5.6056-36.5220.28121800.32032866X-RAY DIFFRACTION99

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