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- PDB-5wha: KRas G12V, bound to GDP and miniprotein 225-11 -

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Basic information

Entry
Database: PDB / ID: 5wha
TitleKRas G12V, bound to GDP and miniprotein 225-11
Components
  • GTPase KRas
  • miniprotein 225-11
KeywordsPROTEIN BINDING / Ras binder / GTP BINDING PROTEIN
Function / homology
Function and homology information


response to mineralocorticoid / GMP binding / forebrain astrocyte development / 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 ...response to mineralocorticoid / GMP binding / forebrain astrocyte development / 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 / 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 / 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 / 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 / Regulation of RAS by GAPs / Signaling by CSF1 (M-CSF) in myeloid cells / RAS processing / Negative regulation of MAPK pathway / 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 / GDP binding / Signaling by BRAF and RAF1 fusions / positive regulation of cellular senescence / DAP12 signaling / MAPK cascade / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants
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 nucleotide triphosphate hydrolases ...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 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
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 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 ...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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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.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
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)110,78828
Polymers108,59712
Non-polymers2,19116
Water3,243180
1
A: GTPase KRas
B: miniprotein 225-11
C: miniprotein 225-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6977
Polymers27,1493
Non-polymers5484
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-56 kcal/mol
Surface area10880 Å2
MethodPISA
2
D: GTPase KRas
E: miniprotein 225-11
F: miniprotein 225-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6977
Polymers27,1493
Non-polymers5484
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-55 kcal/mol
Surface area11070 Å2
MethodPISA
3
G: GTPase KRas
H: miniprotein 225-11
I: miniprotein 225-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7779
Polymers27,1493
Non-polymers6286
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4360 Å2
ΔGint-54 kcal/mol
Surface area11400 Å2
MethodPISA
4
J: GTPase KRas
K: miniprotein 225-11
L: miniprotein 225-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6175
Polymers27,1493
Non-polymers4682
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4120 Å2
ΔGint-54 kcal/mol
Surface area10680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.003, 40.328, 230.939
Angle α, β, γ (deg.)90.00, 90.99, 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: 19154.572 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 1-166 / Mutation: G12V
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, 196 molecules

#3: Chemical
ChemComp-MG / MAGNESIUM ION


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


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 0.25 M CALCIUM CHLORIDE, 24% 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: 2.04→115.45 Å / Num. obs: 55395 / % possible obs: 97 % / Redundancy: 3 % / Rmerge(I) obs: 0.125 / Net I/σ(I): 7.7
Reflection shellHighest resolution: 2.04 Å

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Processing

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

3gft


Resolution: 2.04→115.45 Å / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 37.69
RfactorNum. reflection% reflection
Rfree0.277 2920 5.27 %
Rwork0.238 --
obs0.24 55386 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.04→115.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6974 0 124 180 7278
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027238
X-RAY DIFFRACTIONf_angle_d0.4619813
X-RAY DIFFRACTIONf_dihedral_angle_d10.42682
X-RAY DIFFRACTIONf_chiral_restr0.0171053
X-RAY DIFFRACTIONf_plane_restr0.0021253
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0402-2.07540.38251490.29682626X-RAY DIFFRACTION94
2.0754-2.11310.3761270.29282657X-RAY DIFFRACTION94
2.1131-2.15380.32041520.27692653X-RAY DIFFRACTION94
2.1538-2.19770.3281440.28052655X-RAY DIFFRACTION94
2.1977-2.24550.29241550.27452702X-RAY DIFFRACTION94
2.2455-2.29770.29731370.27142622X-RAY DIFFRACTION94
2.2977-2.35520.29791450.2692667X-RAY DIFFRACTION94
2.3552-2.41880.26841630.26872683X-RAY DIFFRACTION93
2.4188-2.490.31641400.26952659X-RAY DIFFRACTION94
2.49-2.57030.3131430.27632614X-RAY DIFFRACTION93
2.5703-2.66210.28021360.26672733X-RAY DIFFRACTION94
2.6621-2.76860.2971420.26972600X-RAY DIFFRACTION93
2.7686-2.89450.25751570.25062635X-RAY DIFFRACTION92
2.8945-3.0470.31011370.23872614X-RAY DIFFRACTION92
3.047-3.23770.26181190.232601X-RAY DIFFRACTION91
3.2377-3.48740.24161450.22142561X-RAY DIFFRACTION89
3.4874-3.83780.25891350.20662525X-RAY DIFFRACTION88
3.8378-4.39180.231240.19772539X-RAY DIFFRACTION87
4.3918-5.5280.25991200.20042565X-RAY DIFFRACTION88
5.528-30.87920.27121400.20652627X-RAY DIFFRACTION86
Refinement TLS params.Method: refined / Origin x: 1.6898 Å / Origin y: 9.782 Å / Origin z: -57.5237 Å
111213212223313233
T0.2698 Å20.0129 Å2-0.0181 Å2-0.1684 Å2-0.0179 Å2--0.1094 Å2
L0.2003 °20.0322 °2-0.0858 °2-0.0104 °2-0.0501 °2--0.5663 °2
S-0.029 Å °0.0142 Å °0.0143 Å °0.0337 Å °0.0494 Å °-0.0544 Å °0.0544 Å °-0.0872 Å °-0.0201 Å °
Refinement TLS groupSelection details: ALL

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