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- PDB-8cnj: HRas(1-166) in complex with GDP and BeF3- -

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Basic information

Entry
Database: PDB / ID: 8cnj
TitleHRas(1-166) in complex with GDP and BeF3-
ComponentsGTPase HRas
KeywordsHYDROLASE / small G protein / cellular signalling / metal fluorides / Ras superfamily
Function / homology
Function and homology information


phospholipase C activator activity / GTPase complex / oncogene-induced cell senescence / positive regulation of miRNA metabolic process / positive regulation of ruffle assembly / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / Signaling by RAS GAP mutants ...phospholipase C activator activity / GTPase complex / oncogene-induced cell senescence / positive regulation of miRNA metabolic process / positive regulation of ruffle assembly / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / 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 / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / positive regulation of protein targeting to membrane / SHC1 events in ERBB4 signaling / adipose tissue development / Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Schwann cell development / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / SHC-mediated cascade:FGFR2 / 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:FGFR4 / 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 / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / protein-membrane adaptor activity / Tie2 Signaling / Signaling by FGFR2 in disease / myelination / EPHB-mediated forward signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / Signaling by FGFR1 in disease / EGFR Transactivation by Gastrin / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / GRB2 events in ERBB2 signaling / intrinsic apoptotic signaling pathway / Downstream signal transduction / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Ras activation upon Ca2+ influx through NMDA receptor / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / animal organ morphogenesis / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / small monomeric GTPase / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / cellular response to gamma radiation / Signaling by SCF-KIT / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / regulation of long-term neuronal synaptic plasticity / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / positive regulation of type II interferon production / endocytosis / positive regulation of fibroblast proliferation / chemotaxis / Regulation of RAS by GAPs / RAS processing / Negative regulation of MAPK 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 / GDP binding / cellular senescence / Signaling by BRAF and RAF1 fusions / insulin receptor signaling pathway / DAP12 signaling / T cell receptor signaling pathway / MAPK cascade / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / regulation of cell population proliferation / G protein activity
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 nucleoside triphosphate hydrolase
Similarity search - Domain/homology
BERYLLIUM TRIFLUORIDE ION / GUANOSINE-5'-DIPHOSPHATE / GTPase HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBaumann, P. / Jin, Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Commun Chem / Year: 2024
Title: Far-reaching effects of tyrosine64 phosphorylation on Ras revealed with BeF 3 - complexes.
Authors: Baumann, P. / Jin, Y.
History
DepositionFeb 23, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2024Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase HRas
B: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9369
Polymers37,7502
Non-polymers1,1857
Water4,594255
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-52 kcal/mol
Surface area14000 Å2
Unit cell
Length a, b, c (Å)45.433, 51.957, 136.149
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

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


Mass: 18875.191 Da / Num. of mol.: 2 / Fragment: GTPase HRAS N-terminally processed
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01112, small monomeric GTPase

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Non-polymers , 5 types, 262 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: BeF3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 255 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.13 Å3/Da / Density % sol: 42.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: BeF3- GSA complexes were obtained under vapour diffusion sitting drop conditions. Protein buffer (HRas pY64 or HRas 0.4 mM, Na-HEPES 20 mM pH = 8.0, MgCl2 5 mM, NaF 20 mM) were mixed with ...Details: BeF3- GSA complexes were obtained under vapour diffusion sitting drop conditions. Protein buffer (HRas pY64 or HRas 0.4 mM, Na-HEPES 20 mM pH = 8.0, MgCl2 5 mM, NaF 20 mM) were mixed with precipitant in a 1:1 ratio with a total drop size of 600 nL. The precipitant solution consited of: (30 % (v/v) MPD, 100 mM imidazole, pH = 7.0). Protein crystals were soaked in their respective precipitant solutions containing 50 mM BeCl2 and subsequently flash-frozen using 20% glycerol as cryoprotectant.
PH range: 7.0-8.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.35→51.96 Å / Num. obs: 69077 / % possible obs: 96.2 % / Redundancy: 12.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.093 / Rpim(I) all: 0.038 / Rrim(I) all: 0.1 / Net I/σ(I): 13.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
7.39-51.9611.80.0355330.9990.0140.037
1.35-1.378.61.53223870.5980.7431.712

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→48.589 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.969 / WRfactor Rfree: 0.18 / WRfactor Rwork: 0.143 / SU B: 2.286 / SU ML: 0.04 / Average fsc free: 0.9763 / Average fsc work: 0.9837 / Cross valid method: THROUGHOUT / ESU R: 0.056 / ESU R Free: 0.054
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.1791 3548 5.143 %RANDOM
Rwork0.1432 65445 --
all0.145 ---
obs-68993 96.222 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.638 Å2
Baniso -1Baniso -2Baniso -3
1-1.751 Å2-0 Å20 Å2
2--0.154 Å2-0 Å2
3----1.905 Å2
Refinement stepCycle: LAST / Resolution: 1.35→48.589 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2644 0 74 255 2973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0122843
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162629
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.6613845
X-RAY DIFFRACTIONr_angle_other_deg0.471.5776052
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.235349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.076523
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg0.0652
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42110501
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.51110144
X-RAY DIFFRACTIONr_chiral_restr0.2190.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023357
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02655
X-RAY DIFFRACTIONr_nbd_refined0.2250.2526
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.22459
X-RAY DIFFRACTIONr_nbtor_refined0.1780.21378
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21534
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1350.2240
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1230.213
X-RAY DIFFRACTIONr_nbd_other0.1540.255
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.130.231
X-RAY DIFFRACTIONr_mcbond_it0.841.7811361
X-RAY DIFFRACTIONr_mcbond_other0.8391.7811361
X-RAY DIFFRACTIONr_mcangle_it1.2673.2021708
X-RAY DIFFRACTIONr_mcangle_other1.2673.2041709
X-RAY DIFFRACTIONr_scbond_it0.9972.1161482
X-RAY DIFFRACTIONr_scbond_other0.9982.1181479
X-RAY DIFFRACTIONr_scangle_it1.4173.7562132
X-RAY DIFFRACTIONr_scangle_other1.4173.7562133
X-RAY DIFFRACTIONr_lrange_it2.52622.2963285
X-RAY DIFFRACTIONr_lrange_other2.19620.3873216
X-RAY DIFFRACTIONr_rigid_bond_restr2.67435472
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.35-1.3850.2921900.26134480.26352170.9280.94969.73360.255
1.385-1.4230.2292210.23139360.23150820.9620.96181.79850.215
1.423-1.4640.2362640.20445020.20649690.9710.97195.91470.184
1.464-1.5090.2092550.17545470.17748020.9740.9791000.153
1.509-1.5590.2032270.15244790.15447060.9760.9861000.132
1.559-1.6130.1932390.14342780.14545170.9740.9871000.122
1.613-1.6740.1612080.12941980.13144060.9830.991000.111
1.674-1.7420.1442130.1139930.11142060.9880.9931000.096
1.742-1.820.1632060.11338530.11540600.9830.99399.97540.099
1.82-1.9080.1511840.11336940.11538780.9860.9931000.102
1.908-2.0120.171850.11535020.11736870.9830.9921000.106
2.012-2.1330.1661870.11633210.11935080.9840.9921000.111
2.133-2.280.1611560.11731870.11933430.9850.9921000.114
2.28-2.4630.1621710.12829050.1330760.9840.991000.128
2.463-2.6970.1911410.14227100.14428510.980.9881000.146
2.697-3.0140.181410.14224590.14426000.980.9881000.153
3.014-3.4780.1741290.1421860.14223150.9810.9881000.157
3.478-4.2540.1421090.14818490.14719580.9880.9871000.176
4.254-5.9940.224760.1614980.16315740.9790.9851000.206
5.994-48.5890.232460.2059000.2069460.9640.971000.253

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