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- PDB-5whd: Crystal structure of KRas G12V/D38P, bound to GDP -

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Basic information

Entry
Database: PDB / ID: 5whd
TitleCrystal structure of KRas G12V/D38P, bound to GDP
ComponentsGTPase KRas
KeywordsPROTEIN BINDING / Open conformation of Ras / GTP Binding Protein
Function / homology
Function and homology information


forebrain astrocyte development / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants ...forebrain astrocyte development / regulation of synaptic transmission, GABAergic / negative regulation of epithelial cell differentiation / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Rac protein signal transduction / skeletal muscle cell differentiation / positive regulation of Rac protein signal transduction / 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 / glial cell proliferation / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / 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:FGFR2 / SHC-mediated cascade:FGFR4 / protein-membrane adaptor activity / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / homeostasis of number of cells within a tissue / positive regulation of glial cell proliferation / FRS-mediated FGFR3 signaling / Signaling by CSF3 (G-CSF) / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / striated muscle cell differentiation / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Ras activation upon Ca2+ influx through NMDA receptor / FLT3 Signaling / Signaling by FGFR1 in disease / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / small monomeric GTPase / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / FCERI mediated MAPK activation / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / visual learning / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cytoplasmic side of plasma membrane / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / GDP binding / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by CSF1 (M-CSF) in myeloid cells / MAPK cascade / Signaling by BRAF and RAF1 fusions / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling / Ca2+ pathway / gene expression / actin cytoskeleton organization / RAF/MAP kinase cascade / neuron apoptotic process / Ras protein signal transduction / negative regulation of neuron apoptotic process / mitochondrial outer membrane / positive regulation of protein phosphorylation / Golgi membrane / focal adhesion
Similarity search - Function
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 ...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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.641 Å
AuthorsShim, S.Y. / McGee, J.H. / Lee, S.-J. / Verdine, G.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Lustgarten United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Exceptionally high-affinity Ras binders that remodel its effector domain.
Authors: McGee, J.H. / Shim, S.Y. / Lee, S.J. / Swanson, P.K. / Jiang, S.Y. / Durney, M.A. / Verdine, G.L.
History
DepositionJul 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year / _citation_author.name
Revision 1.3Oct 4, 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
B: GTPase KRas
C: GTPase KRas
D: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,3198
Polymers76,5464
Non-polymers1,7734
Water5,224290
1
A: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5802
Polymers19,1371
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5802
Polymers19,1371
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5802
Polymers19,1371
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5802
Polymers19,1371
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: GTPase KRas
hetero molecules

C: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1604
Polymers38,2732
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y+1/2,-z+11
Buried area2840 Å2
ΔGint-17 kcal/mol
Surface area14180 Å2
MethodPISA
6
B: GTPase KRas
D: GTPase KRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1604
Polymers38,2732
Non-polymers8862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2810 Å2
ΔGint-16 kcal/mol
Surface area13980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.239, 80.912, 108.041
Angle α, β, γ (deg.)90.00, 90.62, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 19136.600 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 1-166 / Mutation: G12V D38P
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
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.2 M SODIUM FLUORIDE, 23% PEG 3350,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 22, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.64→64.762 Å / Num. obs: 74937 / % possible obs: 95.8 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.067 / Net I/σ(I): 11.5
Reflection shellResolution: 1.64→1.67 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GFT

3gft


Resolution: 1.641→64.762 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2246 3774 5.04 %
Rwork0.1923 --
obs0.194 74864 95.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.641→64.762 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5086 0 112 290 5488
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0055287
X-RAY DIFFRACTIONf_angle_d0.9167159
X-RAY DIFFRACTIONf_dihedral_angle_d14.8371999
X-RAY DIFFRACTIONf_chiral_restr0.035810
X-RAY DIFFRACTIONf_plane_restr0.003907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6411-1.66190.3962590.40121084X-RAY DIFFRACTION40
1.6619-1.68380.33261300.3332288X-RAY DIFFRACTION83
1.6838-1.70680.36281470.30192632X-RAY DIFFRACTION96
1.7068-1.73120.29751500.28372663X-RAY DIFFRACTION99
1.7312-1.7570.32061500.26412773X-RAY DIFFRACTION100
1.757-1.78450.26951380.23412760X-RAY DIFFRACTION100
1.7845-1.81380.23521520.23092702X-RAY DIFFRACTION100
1.8138-1.8450.27371580.22732728X-RAY DIFFRACTION100
1.845-1.87860.27991420.21592742X-RAY DIFFRACTION100
1.8786-1.91470.21911530.21562702X-RAY DIFFRACTION100
1.9147-1.95380.27091370.20912781X-RAY DIFFRACTION100
1.9538-1.99630.28791290.20812745X-RAY DIFFRACTION100
1.9963-2.04270.23931310.21092756X-RAY DIFFRACTION100
2.0427-2.09380.24661470.20372757X-RAY DIFFRACTION100
2.0938-2.15040.23321410.19312738X-RAY DIFFRACTION100
2.1504-2.21370.26261340.19282754X-RAY DIFFRACTION100
2.2137-2.28520.24571160.19352795X-RAY DIFFRACTION100
2.2852-2.36690.20611390.18582723X-RAY DIFFRACTION100
2.3669-2.46160.21511440.19972767X-RAY DIFFRACTION100
2.4616-2.57370.21871450.20242702X-RAY DIFFRACTION99
2.5737-2.70940.27241380.20322763X-RAY DIFFRACTION99
2.7094-2.87910.2421760.20662690X-RAY DIFFRACTION99
2.8791-3.10140.22371330.20022699X-RAY DIFFRACTION97
3.1014-3.41350.23661450.18382642X-RAY DIFFRACTION96
3.4135-3.90740.18671450.16522588X-RAY DIFFRACTION94
3.9074-4.92260.16351450.1382617X-RAY DIFFRACTION94
4.9226-64.81280.18191500.16622499X-RAY DIFFRACTION88
Refinement TLS params.Method: refined / Origin x: 33.6375 Å / Origin y: 77.843 Å / Origin z: 27.2269 Å
111213212223313233
T0.1842 Å20.0179 Å20.0007 Å2-0.1781 Å2-0.0002 Å2--0.1807 Å2
L0.0442 °20.0313 °20.0134 °2-0.0532 °20.0042 °2--0.4583 °2
S-0.0272 Å °0.0277 Å °-0.0092 Å °-0.0003 Å °0.0294 Å °0.011 Å °-0.0465 Å °-0.0352 Å °-0.0002 Å °
Refinement TLS groupSelection details: ALL

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