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- PDB-2lwi: Solution structure of H-RasT35S mutant protein in complex with Ko... -

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Basic information

Entry
Database: PDB / ID: 2lwi
TitleSolution structure of H-RasT35S mutant protein in complex with Kobe2601
ComponentsGTPase HRasHRAS
KeywordsSIGNALING PROTEIN/INHIBITOR / Ras / GTP-Bound Form / SIGNALING PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / negative regulation of GTPase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / T-helper 1 type immune response / positive regulation of wound healing / positive regulation of miRNA metabolic process / defense response to protozoan / Signaling by RAS GAP mutants ...GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / negative regulation of GTPase activity / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / T-helper 1 type immune response / positive regulation of wound healing / positive regulation of miRNA metabolic process / defense response to protozoan / 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 / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / positive regulation of protein targeting to membrane / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / adipose tissue development / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / : / Schwann cell development / 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 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / Erythropoietin activates RAS / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / p38MAPK events / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / EPHB-mediated forward signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / myelination / Signaling by FGFR1 in disease / Ras activation upon Ca2+ influx through NMDA receptor / GRB2 events in ERBB2 signaling / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / small monomeric GTPase / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / animal organ morphogenesis / positive regulation of JNK cascade / Signaling by ERBB2 TMD/JMD mutants / regulation of long-term neuronal synaptic plasticity / RAF activation / positive regulation of MAP kinase activity / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cellular response to gamma radiation / positive regulation of GTPase activity / endocytosis / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / Signaling by RAF1 mutants / GDP binding / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / chemotaxis / MAPK cascade / positive regulation of type II interferon production / cellular senescence / positive regulation of fibroblast proliferation / Signaling by BRAF and RAF1 fusions / DAP12 signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants
Similarity search - Function
Small GTPase, Ras-type / small GTPase Ras family profile. / 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 ...Small GTPase, Ras-type / small GTPase Ras family profile. / 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 / Chem-KOB / GTPase HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsAraki, M. / Tamura, A. / Shima, F. / Kataoka, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: In silico discovery of small-molecule Ras inhibitors that display antitumor activity by blocking the Ras-effector interaction.
Authors: Shima, F. / Yoshikawa, Y. / Ye, M. / Araki, M. / Matsumoto, S. / Liao, J. / Hu, L. / Sugimoto, T. / Ijiri, Y. / Takeda, A. / Nishiyama, Y. / Sato, C. / Muraoka, S. / Tamura, A. / Osoda, T. / ...Authors: Shima, F. / Yoshikawa, Y. / Ye, M. / Araki, M. / Matsumoto, S. / Liao, J. / Hu, L. / Sugimoto, T. / Ijiri, Y. / Takeda, A. / Nishiyama, Y. / Sato, C. / Muraoka, S. / Tamura, A. / Osoda, T. / Tsuda, K. / Miyakawa, T. / Fukunishi, H. / Shimada, J. / Kumasaka, T. / Yamamoto, M. / Kataoka, T.
History
DepositionAug 1, 2012Deposition site: BMRB / Processing site: PDBJ
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Data collection / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _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.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_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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2864
Polymers19,3881
Non-polymers8983
Water543
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein GTPase HRas / HRAS / H-Ras-1 / Ha-Ras / Transforming protein p21 / c-H-ras / p21ras / GTPase HRas / N-terminally processed


Mass: 19387.707 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-166 / Mutation: T35S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01112
#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 5'-Guanylyl imidodiphosphate


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-KOB / 2-(2,4-dinitrophenyl)-N-(4-fluorophenyl)hydrazinecarbothioamide


Mass: 351.313 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H10FN5O4S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-13C HSQC
1213D 1H-13C NOESY
1322D 1H-1H NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM [U-98% 13C; U-98% 15N] entity_1-1, 1 mM PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-2, 8 mM MAGNESIUM ION-3, 120 mM sodium chloride-4, 20 mM sodium phosphate-5, 3.8 mM KOB-6, 80% D2O/20% DMSO_d680% D2O/20% DMSO_d6
21 mM entity_1-7, 1 mM PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-8, 8 mM MAGNESIUM ION-9, 120 mM sodium chloride-10, 20 mM sodium phosphate-11, 3.8 mM KOB-12, 80% D2O/20% DMSO_d680% D2O/20% DMSO_d6
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMentity_1-1[U-98% 13C; U-98% 15N]1
1 mMPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-21
8 mMMAGNESIUM ION-31
120 mMsodium chloride-41
20 mMsodium phosphate-51
3.8 mMKOB-61
1 mMentity_1-72
1 mMPHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER-82
8 mMMAGNESIUM ION-92
120 mMsodium chloride-102
20 mMsodium phosphate-112
3.8 mMKOB-122
Sample conditionsIonic strength: 0.22 / pH: 6.8 / Pressure: ambient / Temperature: 278 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX7501
Bruker AvanceBrukerAVANCE6002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA2.1Guntert, Mumenthaler and Wuthrichstructure solution
CNS1.2refinement
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardpeak picking
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: anneal.inp
NMR constraintsNOE constraints total: 3138 / NOE intraresidue total count: 815 / NOE long range total count: 1023 / NOE medium range total count: 532 / NOE sequential total count: 749 / Protein phi angle constraints total count: 114 / Protein psi angle constraints total count: 116
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 15 / Representative conformer: 1
NMR ensemble rmsDistance rms dev: 0.0075 Å / Distance rms dev error: 0.0009 Å

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