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- PDB-2n46: EC-NMR Structure of Human H-RasT35S mutant protein Determined by ... -

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Entry
Database: PDB / ID: 2n46
TitleEC-NMR Structure of Human H-RasT35S mutant protein Determined by Combining Evolutionary Couplings (EC) and Sparse NMR Data
ComponentsGTPase HRas
KeywordsSIGNALING PROTEIN / EC-NMR / NORTHEAST STRUCTURAL GENOMICS CONSORTIUM / NESG / Protein Structure Initiative / PSI-Biology / Structural Genomics
Function / homology
Function and homology information


phospholipase C activator activity / positive regulation of miRNA metabolic process / positive regulation of ruffle assembly / positive regulation of wound healing / adipose tissue development / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / 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 ...phospholipase C activator activity / positive regulation of miRNA metabolic process / positive regulation of ruffle assembly / positive regulation of wound healing / adipose tissue development / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / 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 / positive regulation of protein targeting to membrane / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / Schwann cell development / SHC1 events in ERBB4 signaling / Signalling to RAS / 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 / positive regulation of Ras protein signal transduction / myelination / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / Signaling by FGFR4 in disease / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / p38MAPK events / animal organ morphogenesis / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / Tie2 Signaling / EPHB-mediated forward signaling / Signaling by FGFR2 in disease / positive regulation of epithelial cell proliferation / protein-membrane adaptor activity / GRB2 events in EGFR signaling / Signaling by FLT3 fusion proteins / SHC1 events in EGFR signaling / FLT3 Signaling / EGFR Transactivation by Gastrin / Signaling by FGFR1 in disease / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / regulation of actin cytoskeleton organization / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / small monomeric GTPase / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Signaling by SCF-KIT / RAF activation / cellular response to gamma radiation / Signaling by high-kinase activity BRAF mutants / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / Signaling by ERBB2 KD Mutants / positive regulation of JNK cascade / cellular senescence / chemotaxis / insulin receptor signaling 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 / MAPK cascade / Negative regulation of MAPK pathway / Regulation of RAS by GAPs / RAS processing / Signaling by BRAF and RAF1 fusions / GDP binding / DAP12 signaling / regulation of cell population proliferation / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / RAF/MAP kinase cascade / G protein activity / positive regulation of MAPK cascade / regulation of cell cycle / Ras protein signal transduction / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / positive regulation of cell migration / negative regulation of cell population proliferation / negative regulation of gene expression
Similarity search - Function
Small GTPase, Ras-type / Small GTPase Ras domain 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 / Rossmann fold ...Small GTPase, Ras-type / Small GTPase Ras domain 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailslowest energy, model1
AuthorsTang, Y. / Huang, Y.J. / Hopf, T.A. / Sander, C. / Marks, D. / Montelione, G.T. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: J.Biol.Chem. / Year: 2011
Title: Solution structure of the state 1 conformer of GTP-bound H-Ras protein and distinct dynamic properties between the state 1 and state 2 conformers.
Authors: Araki, M. / Shima, F. / Yoshikawa, Y. / Muraoka, S. / Ijiri, Y. / Nagahara, Y. / Shirono, T. / Kataoka, T. / Tamura, A.
History
DepositionJun 17, 2015Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jul 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 0THIS ENTRY 2N46 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA IN 2LCF DETERMINED ...THIS ENTRY 2N46 REFLECTS AN ALTERNATIVE MODELING OF THE ORIGINAL STRUCTURAL DATA IN 2LCF DETERMINED BY AUTHORS: M.ARAKI,F.SHIMA,Y.YOSHIKAWA,S.MURAOKA,Y.IJIRI,Y.NAGAHARA,T.SHIRONO,T.KATAOKA,A.TAMURA

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Structure visualization

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Assembly

Deposited unit
A: GTPase HRas


Theoretical massNumber of molelcules
Total (without water)19,3881
Polymers19,3881
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein GTPase 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 / 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

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR detailsText: AUTHOR USED THE EXPERIMENTAL DATA FROM ENTRY 2LCF.

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Processing

NMR software
NameDeveloperClassification
RosettaD. Bakerrefinement
EVfold-plmdata analysis
ASDPdata analysis
CYANAGuntert, P., Mumenthaler, C. and Wuthrich, K.data analysis
EC-NMRdata analysis
TALOS+data analysis
ReduceJ. Richardson and D. Richardsonrefinement
CYANAGuntert, P., Mumenthaler, C. and Wuthrich, K.structure calculation
RefinementMethod: torsion angle dynamics / Software ordinal: 1
Details: ReDCat was used to simulate 2 RDC data set with 2 different alignment tensors from the reference structure.Protons from the Rosetta models were removed and added back using Reduce.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20 / Representative conformer: 1

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