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- PDB-2x1v: Crystal Structure of the activating H-Ras I163F mutant in Costell... -

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Basic information

Entry
Database: PDB / ID: 2x1v
TitleCrystal Structure of the activating H-Ras I163F mutant in Costello Syndrome, bound to MG-GDP
ComponentsGTPASE HRASHRAS
KeywordsHYDROLASE / S-NITROSYLATION / DISEASE MUTATION / PALMITATE / METHYLATION / PRENYLATION / CELL MEMBRANE / PROTO-ONCOGENE / GTPASE PROTEIN / GOLGI APPARATUS
Function / homology
Function and homology information


GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / Signaling by RAS GAP mutants ...GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / 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 / positive regulation of protein targeting to membrane / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / adipose tissue development / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / positive regulation of phospholipase C activity / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Schwann cell development / 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 / myelination / Signaling by FLT3 fusion proteins / FLT3 Signaling / Ras activation upon Ca2+ influx through NMDA receptor / GRB2 events in ERBB2 signaling / Signaling by FGFR1 in disease / 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 / regulation of long-term neuronal synaptic plasticity / positive regulation of JNK cascade / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / cellular response to gamma radiation / positive regulation of MAP kinase activity / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / positive regulation of GTPase activity / endocytosis / 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 / chemotaxis / positive regulation of fibroblast proliferation / MAPK cascade / cellular senescence / Signaling by BRAF and RAF1 fusions / positive regulation of type II interferon production / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling
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
GUANOSINE-5'-DIPHOSPHATE / GTPase HRas
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsAnand, K.
CitationJournal: To be Published
Title: Crystal Structure of the Activating H-Ras I163F Mutant in Costello Syndrome, Bound to Mg-Gdp
Authors: Anand, K. / Parret, A. / Denayer, E. / Petrova, B. / Legius, E. / Scheffzek, K.
History
DepositionJan 4, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)19,3522
Polymers18,9091
Non-polymers4431
Water2,090116
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)73.140, 73.140, 62.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein GTPASE HRAS / HRAS / TRANSFORMING PROTEIN P21 / P21RAS / H-RAS-1 / C-H-RAS / HA-RAS


Mass: 18909.207 Da / Num. of mol.: 1 / Fragment: G-DOMAIN, RESIDUES 1-166 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P01112, small monomeric GTPase
#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ILE 163 TO PHE

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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: 2.82 Å3/Da / Density % sol: 56.07 %
Description: DATA WERE TWINNED AND REFINED USING PHENIX.XTRIAGE
Crystal growpH: 7.6
Details: 18% POLYETHYLENE GLYCOL (PEG) 6000, 100 MM HEPES PH 7.4, 150 MM MGCL2.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.482
ReflectionResolution: 1.7→20 Å / Num. obs: 1054 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 15 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 46.14
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 6.85 % / Rmerge(I) obs: 0.09 / Mean I/σ(I) obs: 5.73 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4Q21

4q21


Resolution: 1.7→28.285 Å / SU ML: 0.05 / σ(F): 1.99 / Phase error: 29.13 / Stereochemistry target values: TWIN_LSQ_F
Details: HRAS ILE163PHE PATIENT MUTANT LACK BOTH LOOPS THAT ARE INVOLVED IN THE (DISORDERED RESIDUE 30-38 AND 58-69) SWITCH I AND II.
RfactorNum. reflection% reflection
Rfree0.2272 1054 5 %
Rwork0.1899 --
obs0.1907 21075 99.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.55 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 96.88 Å2 / ksol: 0.413 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.1443 Å2-0 Å20 Å2
2---3.1443 Å2-0 Å2
3---6.2886 Å2
Refinement stepCycle: LAST / Resolution: 1.7→28.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1085 0 28 116 1229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061128
X-RAY DIFFRACTIONf_angle_d1.0891529
X-RAY DIFFRACTIONf_dihedral_angle_d19.677405
X-RAY DIFFRACTIONf_chiral_restr0.066177
X-RAY DIFFRACTIONf_plane_restr0.003193
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7002-1.78980.31161510.27872856X-RAY DIFFRACTION95
1.7898-1.90190.31131480.28592817X-RAY DIFFRACTION95
1.9019-2.04870.2631510.24372861X-RAY DIFFRACTION95
2.0487-2.25480.25791490.23842846X-RAY DIFFRACTION95
2.2548-2.58090.25971510.22812869X-RAY DIFFRACTION95
2.5809-3.25080.241520.19052871X-RAY DIFFRACTION95
3.2508-28.16550.17791520.13282888X-RAY DIFFRACTION94
Refinement TLS params.Method: refined / Origin x: 16.9216 Å / Origin y: -28.123 Å / Origin z: -0.8268 Å
111213212223313233
T0.1095 Å20.0011 Å2-0.0115 Å2-0.1362 Å20.0064 Å2--0.1837 Å2
L0.1671 °20.0522 °20.0949 °2-0.9188 °2-0.0048 °2--0.2546 °2
S-0.0464 Å °-0.0769 Å °0.09 Å °-0.0268 Å °0.0401 Å °-0.1261 Å °0.0032 Å °-0.017 Å °0.0111 Å °
Refinement TLS groupSelection details: CHAIN A

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