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- PDB-8osn: GTPASE HRAS IN COMPLEX WITH ZN-CYCLEN AT AMBIENT PRESSURE -

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Basic information

Entry
Database: PDB / ID: 8osn
TitleGTPASE HRAS IN COMPLEX WITH ZN-CYCLEN AT AMBIENT PRESSURE
ComponentsGTPase HRasHRAS
KeywordsONCOPROTEIN / G PROTEIN / SIGNALING PROTEIN / HPMX
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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / TRIETHYLENE GLYCOL / GTPase HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsColloc'h, N. / Prange, T. / Girard, E. / Kalbitzer, H.R.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: Chemistry / Year: 2024
Title: High pressure promotes binding of the allosteric inhibitor Zn2+-cyclen in crystals of activated H-Ras.
Authors: Girard, E. / Lopes, P. / Spoerner, M. / Dhaussy, A.C. / Prange, T. / Kalbitzer, H.R. / Colloc'h, N.
#1: Journal: Chem Sci / Year: 2022
Title: Equilibria between conformational states of the Ras oncogene protein revealed by high pressure crystallography.
Authors: Girard, E. / Lopes, P. / Spoerner, M. / Dhaussy, A.C. / Prange, T. / Kalbitzer, H.R. / Colloc'h, N.
History
DepositionApr 19, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5724
Polymers18,8751
Non-polymers6973
Water1,40578
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: NMR Distance Restraints
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.511, 39.511, 160.840
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Space group name HallP322"

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Components

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


Mass: 18875.191 Da / Num. of mol.: 1 / Fragment: GTPase HRAS N-terminally processed
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Plasmid: pTac / Production host: Escherichia coli (E. coli) / Strain (production host): CK600K / References: UniProt: P01112, small monomeric GTPase
#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 / Feature type: SUBJECT OF INVESTIGATION
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-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 78 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.92 Å3/Da / Density % sol: 35.94 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5
Details: 40 MM TRIS HCL, 10 MM MGCL2, 2 MM DTE, 26-30 % PEG-400

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: CRISTAL / Wavelength: 0.51035 Å
DetectorType: RAYONIX SX-165mm / Detector: CCD / Date: Jul 22, 2015
RadiationMonochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.51035 Å / Relative weight: 1
ReflectionResolution: 1.8→34.22 Å / Num. obs: 13389 / % possible obs: 95.1 % / Redundancy: 4.3 % / Biso Wilson estimate: 22.57 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.049 / Rrim(I) all: 0.105 / Net I/σ(I): 9.6 / Num. measured all: 57558
Reflection shellResolution: 1.8→1.9 Å / % possible obs: 95.5 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.862 / Num. measured all: 8330 / Num. unique obs: 1912 / CC1/2: 0.616 / Rpim(I) all: 0.453 / Rrim(I) all: 0.978 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
SCALA3.3.22data scaling
XDSdata reduction
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→34.22 Å / SU ML: 0.2282 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.0091
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2154 662 4.95 %RANDOM
Rwork0.1757 12711 --
obs0.1778 13373 93.56 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.74 Å2
Refinement stepCycle: LAST / Resolution: 1.8→34.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1323 0 43 78 1444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00361448
X-RAY DIFFRACTIONf_angle_d0.57631971
X-RAY DIFFRACTIONf_chiral_restr0.0418215
X-RAY DIFFRACTIONf_plane_restr0.004258
X-RAY DIFFRACTIONf_dihedral_angle_d15.2523542
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.940.29731250.26822489X-RAY DIFFRACTION94.64
1.94-2.130.3211330.24312520X-RAY DIFFRACTION94.48
2.14-2.440.22521280.1912530X-RAY DIFFRACTION94.36
2.44-3.080.20791360.17772544X-RAY DIFFRACTION93.44
3.08-34.220.17861400.13782628X-RAY DIFFRACTION91.23
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0938011027318-0.0551210205138-0.1936792682530.3722929514970.01677692722770.338226207644-0.08323783561420.09187826939660.0588391237183-0.1374736078640.100206655121-0.04420768696880.1683981830480.0524493791804-0.006357397967630.18987533863-0.02801152503160.006967297925410.121732997967-0.02293086215240.123403479582-25.0499777221.659913566419.99216067719
20.2546201005080.00261057075305-0.2193031367070.03952355063290.03664275671150.2367753406340.03980381873370.0514934760774-0.0189451703774-0.128946887880.02141641885380.01163537344780.25220871642-0.0442292245127-8.68955289243E-60.233330396415-0.00633432790651-0.005687737774580.1745262302070.01814294409780.158529125485-21.19690937210.6268472716317.84193059079
30.3253036364440.380608448391-0.3061387627010.781413921147-0.3049520732210.311925735434-0.106724609194-0.5013964654190.0733607151969-0.2730019814470.155786408289-0.3866892097810.481235657851-0.349228448678-0.01193753183790.3212326504940.0511654403561-0.01494925816960.4275594506620.02870058569290.291997946269-14.67042022477.8682157900521.6485079709
40.2436066717520.191206542867-0.07358374907130.546842708658-0.02475862137330.073523636410.145511132301-0.1038944973230.296210296550.0431330274430.0272373172423-0.0261909539214-0.2671048085960.09394684896490.1268947247330.197137762735-0.0582105389482-0.001383616753660.15709111894-0.04357374686920.183244056631-21.912205827416.699476536115.9018692063
50.605113775527-0.06981319439510.08538034806360.3312264371240.2164300575080.570578875915-0.1381155740250.1869593133870.176618195448-0.2696403511690.09172672988350.330928109231-0.232614214903-0.283195231722-0.01242043584280.1818087758840.0115685835723-0.02351048929460.108735734996-0.01753814400040.182725093061-34.935228263513.298097859812.3382686139
60.265745669175-0.39747368209-0.2627700084230.6080891076320.407984961410.287686641176-0.1504222772120.2067002637510.2655668129240.0451676134622-0.1255980146250.0299645898718-0.2952617918010.166408223856-0.1096042978670.182119573009-0.0437481341837-0.08413981173230.1387067130150.04434412143440.190156269451-24.371033664212.98273094790.439970903824
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11(chain A and resid 1:29)1 - 291 - 29
22(chain A and resid 30:59)30 - 5930 - 59
33(chain A and resid 60:72)60 - 7260 - 72
44(chain A and resid 73:110)73 - 11073 - 110
55(chain A and resid 111:154)111 - 154111 - 154
66(chain A and resid 155:166)155 - 166155 - 166

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