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- PDB-5wlb: KRas G12V, bound to GppNHp and miniprotein 225-15a/b -

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Basic information

Entry
Database: PDB / ID: 5wlb
TitleKRas G12V, bound to GppNHp and miniprotein 225-15a/b
Components
  • 225-15 a
  • 225-15 b
  • GTPase KRas
KeywordsPROTEIN BINDING / Ras binders / 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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase KRas
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.72 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 26, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase KRas
B: 225-15 a
C: 225-15 b
D: GTPase KRas
E: 225-15 a
F: 225-15 b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,31513
Polymers53,8366
Non-polymers1,4797
Water3,243180
1
A: GTPase KRas
B: 225-15 a
C: 225-15 b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8518
Polymers26,9183
Non-polymers9335
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: GTPase KRas
E: 225-15 a
F: 225-15 b
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4655
Polymers26,9183
Non-polymers5472
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.145, 86.843, 71.038
Angle α, β, γ (deg.)90.00, 103.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AD

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


Mass: 18926.363 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 1-166
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

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Protein/peptide , 2 types, 4 molecules BECF

#2: Protein/peptide 225-15 a


Mass: 4181.517 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide 225-15 b


Mass: 3810.192 Da / Num. of mol.: 2
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 , 5 types, 187 molecules

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


Mass: 522.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 41.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M AMMONIUM SULFATE, 26% PEG 3350, 0.1M HEPES PH 7.5

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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: Nov 8, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.72→69.1 Å / Num. obs: 47613 / % possible obs: 99.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 13.9
Reflection shellResolution: 1.72→1.81 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: 1.72→69.1 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.27
RfactorNum. reflection% reflectionSelection details
Rfree0.2332 2406 5.06 %RANDOM
Rwork0.1921 ---
obs0.1942 47530 99.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.72→69.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3644 0 89 180 3913
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013813
X-RAY DIFFRACTIONf_angle_d1.1915167
X-RAY DIFFRACTIONf_dihedral_angle_d15.0011424
X-RAY DIFFRACTIONf_chiral_restr0.049551
X-RAY DIFFRACTIONf_plane_restr0.005657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7182-1.75330.38121410.34132571X-RAY DIFFRACTION97
1.7533-1.79140.35841290.31422650X-RAY DIFFRACTION100
1.7914-1.83310.35231560.28412642X-RAY DIFFRACTION100
1.8331-1.87890.32521250.25232666X-RAY DIFFRACTION100
1.8789-1.92970.28261360.25812702X-RAY DIFFRACTION100
1.9297-1.98650.32991590.22312617X-RAY DIFFRACTION100
1.9865-2.05060.25591420.21322640X-RAY DIFFRACTION100
2.0506-2.12390.2761480.20212703X-RAY DIFFRACTION100
2.1239-2.2090.24051520.19412644X-RAY DIFFRACTION100
2.209-2.30950.26741330.20572668X-RAY DIFFRACTION100
2.3095-2.43130.26821270.19352678X-RAY DIFFRACTION100
2.4313-2.58360.23451460.20032662X-RAY DIFFRACTION100
2.5836-2.78310.25921380.212674X-RAY DIFFRACTION100
2.7831-3.06320.24811420.19792666X-RAY DIFFRACTION99
3.0632-3.50640.21470.17812652X-RAY DIFFRACTION98
3.5064-4.41760.18281390.14762613X-RAY DIFFRACTION98
4.4176-69.11010.18111460.16042676X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: -13.0146 Å / Origin y: -4.5756 Å / Origin z: -25.6331 Å
111213212223313233
T0.1696 Å20.0009 Å2-0.0045 Å2-0.1606 Å2-0.0153 Å2--0.1696 Å2
L0.0698 °20.0128 °2-0.113 °2-0.029 °2-0.074 °2--0.3969 °2
S0.024 Å °-0.0032 Å °0.0059 Å °-0.0172 Å °0.0202 Å °0.0103 Å °-0.0502 Å °0.0019 Å °-0 Å °
Refinement TLS groupSelection details: all

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