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- PDB-3l8y: Complex of Ras with cyclen -

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Basic information

Entry
Database: PDB / ID: 3l8y
TitleComplex of Ras with cyclen
ComponentsGTPase HRas
KeywordsONCOPROTEIN / Ras-ligand complex / Cell membrane / Disease mutation / Golgi apparatus / GTP-binding / Lipoprotein / Methylation / Nucleotide-binding / Palmitate / Prenylation / Proto-oncogene / S-nitrosylation
Function / homology
Function and homology information


phospholipase C activator activity / GTPase complex / positive regulation of ruffle assembly / oncogene-induced cell senescence / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / defense response to protozoan ...phospholipase C activator activity / GTPase complex / positive regulation of ruffle assembly / oncogene-induced cell senescence / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / 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 / positive regulation of protein targeting to membrane / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Signalling to RAS / adipose tissue development / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Schwann cell development / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Erythropoietin activates RAS / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / protein-membrane adaptor activity / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EPHB-mediated forward signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / EGFR Transactivation by Gastrin / Signaling by FGFR1 in disease / myelination / positive regulation of GTPase activity / NCAM signaling for neurite out-growth / positive regulation of MAP kinase activity / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / Downstream signal transduction / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / small monomeric GTPase / animal organ morphogenesis / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / positive regulation of JNK cascade / RAF activation / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 TMD/JMD mutants / Signaling by high-kinase activity BRAF mutants / Signaling by SCF-KIT / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / cellular response to gamma radiation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / positive regulation of type II interferon production / positive regulation of fibroblast proliferation / endocytosis / Regulation of RAS by GAPs / RAS processing / chemotaxis / Signaling by RAF1 mutants / Negative regulation of MAPK pathway / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / GDP binding / cellular senescence / Signaling by BRAF and RAF1 fusions / MAPK cascade / insulin receptor signaling pathway / DAP12 signaling / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants
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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / 1,4,7,10-tetraazacyclododecane / GTPase HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.02 Å
AuthorsRosnizeck, I.C. / Graf, T. / Spoerner, M. / Traenkle, J. / Filchtinski, D. / Herrmann, C. / Gremer, L. / Vetter, I.R. / Wittinghofer, A. / Koenig, B. / Kalbitzer, H.R.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2010
Title: Stabilizing a weak binding state for effectors in the human ras protein by cyclen complexes
Authors: Rosnizeck, I.C. / Graf, T. / Spoerner, M. / Trankle, J. / Filchtinski, D. / Herrmann, C. / Gremer, L. / Vetter, I.R. / Wittinghofer, A. / Konig, B. / Kalbitzer, H.R.
History
DepositionJan 4, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Nov 1, 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)19,8209
Polymers18,8751
Non-polymers9448
Water2,558142
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)88.000, 88.000, 134.000
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-203-

CA

21A-205-

CA

31A-223-

HOH

41A-231-

HOH

51A-293-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 18875.191 Da / Num. of mol.: 1 / Fragment: residues 1-166
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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Non-polymers , 6 types, 150 molecules

#2: Chemical ChemComp-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-YCN / 1,4,7,10-tetraazacyclododecane / Cyclen


Mass: 172.271 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H20N4
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / 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: 2.65 Å3/Da / Density % sol: 53.5 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17% PEG6000, 200mM CaCl2, 30mM TRIS/HCL, 5mM MgCl2, 2mM DTE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1.27982 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 29, 2007 / Details: mirrors
RadiationMonochromator: FOCUSED SI(111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.27982 Å / Relative weight: 1
ReflectionResolution: 2.02→20 Å / Num. obs: 12483 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.16 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.046 / Rsym value: 0.047 / Net I/σ(I): 24.39
Reflection shellResolution: 2.02→2.15 Å / Redundancy: 4.11 % / Rmerge(I) obs: 0.118 / Mean I/σ(I) obs: 10.85 / Num. unique all: 6809 / Rsym value: 0.135 / % possible all: 97.9

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Processing

Software
NameVersionClassification
MAR345data collection
MOLREPphasing
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5p21

5p21


Resolution: 2.02→19.92 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.9 / SU B: 3.363 / SU ML: 0.098 / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.19 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.23806 654 5 %RANDOM
Rwork0.1889 ---
all0.19132 12483 --
obs0.19132 12423 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.046 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20.13 Å20 Å2
2--0.26 Å20 Å2
3----0.39 Å2
Refinement stepCycle: LAST / Resolution: 2.02→19.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1323 0 50 142 1515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221405
X-RAY DIFFRACTIONr_angle_refined_deg1.7092.0011913
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4615169
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.36624.58372
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.77615244
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.071511
X-RAY DIFFRACTIONr_chiral_restr0.0620.2213
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021052
X-RAY DIFFRACTIONr_nbd_refined0.1860.2697
X-RAY DIFFRACTIONr_nbtor_refined0.3010.2957
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2165
X-RAY DIFFRACTIONr_metal_ion_refined0.120.210
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2290.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1240.227
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1130.24
X-RAY DIFFRACTIONr_mcbond_it0.5211.5855
X-RAY DIFFRACTIONr_mcangle_it0.91521341
X-RAY DIFFRACTIONr_scbond_it1.0543626
X-RAY DIFFRACTIONr_scangle_it1.6314.5562
LS refinement shellResolution: 2.017→2.069 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 40 -
Rwork0.197 773 -
obs--100 %

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