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- PDB-5whe: KRas G12V/D38P, bound to GppNHp and miniprotein 225-11 -

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Basic information

Entry
Database: PDB / ID: 5whe
TitleKRas G12V/D38P, bound to GppNHp and miniprotein 225-11
Components
  • GTPase KRas
  • Miniprotein 225-11
KeywordsPROTEIN BINDING / Ras binder / 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 / cytoplasmic side of plasma membrane / Signaling by SCF-KIT / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 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 1.3Jan 29, 2020Group: Derived calculations
Category: pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase KRas
D: GTPase KRas
G: GTPase KRas
J: GTPase KRas
B: Miniprotein 225-11
C: Miniprotein 225-11
E: Miniprotein 225-11
F: Miniprotein 225-11
H: Miniprotein 225-11
I: Miniprotein 225-11
K: Miniprotein 225-11
L: Miniprotein 225-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,11230
Polymers108,52612
Non-polymers2,58718
Water7,044391
1
A: GTPase KRas
B: Miniprotein 225-11
C: Miniprotein 225-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8389
Polymers27,1313
Non-polymers7076
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-55 kcal/mol
Surface area11610 Å2
MethodPISA
2
D: GTPase KRas
E: Miniprotein 225-11
F: Miniprotein 225-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8389
Polymers27,1313
Non-polymers7076
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-48 kcal/mol
Surface area11110 Å2
MethodPISA
3
G: GTPase KRas
H: Miniprotein 225-11
I: Miniprotein 225-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7587
Polymers27,1313
Non-polymers6274
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint-47 kcal/mol
Surface area11060 Å2
MethodPISA
4
J: GTPase KRas
K: Miniprotein 225-11
L: Miniprotein 225-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6785
Polymers27,1313
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4260 Å2
ΔGint-55 kcal/mol
Surface area11190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.549, 232.525, 48.213
Angle α, β, γ (deg.)90.00, 90.16, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 12 molecules ADGJBCEFHIKL

#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: Protein/peptide
Miniprotein 225-11


Mass: 3997.395 Da / Num. of mol.: 8
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 , 4 types, 409 molecules

#3: Chemical
ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Ca
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 391 / 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: 2.15 Å3/Da / Density % sol: 42.88 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.25 M CALCIUM CHLORIDE, 21% PEG 3350,

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97911 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 19, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 1.91→19.54 Å / Num. obs: 65457 / % possible obs: 95.2 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.4
Reflection shellResolution: 1.91→1.94 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: 1.91→19.54 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 23.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2273 3314 5.07 %
Rwork0.1844 --
obs0.1866 65401 95.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.91→19.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7118 0 142 391 7651
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057418
X-RAY DIFFRACTIONf_angle_d0.87210074
X-RAY DIFFRACTIONf_dihedral_angle_d13.7252762
X-RAY DIFFRACTIONf_chiral_restr0.0321075
X-RAY DIFFRACTIONf_plane_restr0.0041286
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-1.93730.31591430.27392519X-RAY DIFFRACTION93
1.9373-1.96620.31341230.2562595X-RAY DIFFRACTION96
1.9662-1.99690.3261310.25882459X-RAY DIFFRACTION91
1.9969-2.02960.25891370.23512445X-RAY DIFFRACTION88
2.0296-2.06450.2681300.19782454X-RAY DIFFRACTION93
2.0645-2.1020.27551340.2092638X-RAY DIFFRACTION94
2.102-2.14240.22611280.19662529X-RAY DIFFRACTION94
2.1424-2.18610.26411290.19372668X-RAY DIFFRACTION98
2.1861-2.23360.25861220.19182553X-RAY DIFFRACTION94
2.2336-2.28540.23971300.18282614X-RAY DIFFRACTION96
2.2854-2.34250.21851500.18022647X-RAY DIFFRACTION98
2.3425-2.40570.21161290.18882596X-RAY DIFFRACTION95
2.4057-2.47640.25261430.19232633X-RAY DIFFRACTION99
2.4764-2.55610.28221300.19812634X-RAY DIFFRACTION95
2.5561-2.64730.25081450.1952641X-RAY DIFFRACTION99
2.6473-2.7530.25031280.20322593X-RAY DIFFRACTION95
2.753-2.87790.271400.20242593X-RAY DIFFRACTION94
2.8779-3.02910.23951610.19882505X-RAY DIFFRACTION94
3.0291-3.21810.21351650.18632623X-RAY DIFFRACTION97
3.2181-3.46530.25111460.18332654X-RAY DIFFRACTION98
3.4653-3.81170.18731510.16512584X-RAY DIFFRACTION97
3.8117-4.3580.16611360.1442675X-RAY DIFFRACTION97
4.358-5.47060.18941480.15372581X-RAY DIFFRACTION95
5.4706-19.54090.19091350.16482654X-RAY DIFFRACTION96
Refinement TLS params.Method: refined / Origin x: 91.0617 Å / Origin y: -9.5832 Å / Origin z: 49.6616 Å
111213212223313233
T0.0979 Å2-0.0116 Å20.019 Å2-0.1543 Å2-0.0142 Å2--0.172 Å2
L0.0967 °20.2351 °2-0.032 °2-0.9935 °2-0.269 °2--0.1474 °2
S0.011 Å °-0.0336 Å °-0.013 Å °-0.0459 Å °0.0121 Å °-0.031 Å °0.0052 Å °0.0182 Å °-0.0178 Å °
Refinement TLS groupSelection details: ALL

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