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- PDB-8bwg: HRas (1-166) Y64 phosphorylation -

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Basic information

Entry
Database: PDB / ID: 8bwg
TitleHRas (1-166) Y64 phosphorylation
ComponentsGTPase HRasHRAS
KeywordsHYDROLASE / Small G protein / Ras / Post-translational modification / GTP binding protein / Signalling
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
GUANOSINE-5'-DIPHOSPHATE / GTPase HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.32 Å
AuthorsBaumann, P. / Jin, Y.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust218568/Z/19/Z 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
DepositionDec 6, 2022Deposition 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
R: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4394
Polymers18,8751
Non-polymers5643
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1080 Å2
ΔGint-33 kcal/mol
Surface area7670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.662, 92.662, 119.323
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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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-HRas / Production host: Escherichia coli BL21(DE3) (bacteria) / 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Using a commercial crystal screen (HAMPTON RESEARCH, HR2-130) yielded a hit for monophosphorylated HRas under sitting drop conditions (drop size 600 nL) with a 1:1 ratio of protein solution ...Details: Using a commercial crystal screen (HAMPTON RESEARCH, HR2-130) yielded a hit for monophosphorylated HRas under sitting drop conditions (drop size 600 nL) with a 1:1 ratio of protein solution (phospho-HRas 0.4 mM, RasGAP 0.4 mM, Na-HEPES 20 mM pH = 8.0, MgCl2 5 mM, NaF 20 mM) and precipitant (Na-citrate 100 mM pH = 5.6, Li2SO4 1.0 M, CaCl2 200 mM). After three rounds of microseeding well-formed single crystals were obtained using 2.0 uL sitting drops and a 1:1 ratio of protein buffer (HRas 400 uM, RasGAP 400 uM, MgCl2 5 mM, Na-HEPES 20 mM pH = 8.0, NaF 20 mM) and precipitant (Na-Citrate 100 mM pH = 5.6, Li2SO4 800 mM, CaCl2 200 mM). These were harvested using cryoprotectant (80% precipitant, 20% glycerol (v/v)) and sent for data collection.

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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 XE 16M / Detector: PIXEL / Date: Jan 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.32→47.925 Å / Num. obs: 45988 / % possible obs: 99.2 % / Redundancy: 17.6 % / CC1/2: 1 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.014 / Rrim(I) all: 0.043 / Net I/σ(I): 28.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
7.23-47.8817.40.0223140.9990.0080.023
1.32-1.347.81.3420730.5770.7231.535

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Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
Aimlessdata scaling
DIALSdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.32→47.925 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.972 / WRfactor Rfree: 0.171 / WRfactor Rwork: 0.131 / SU B: 1.86 / SU ML: 0.033 / Average fsc free: 0.9694 / Average fsc work: 0.9759 / Cross valid method: FREE R-VALUE / ESU R: 0.041 / ESU R Free: 0.043
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1739 2232 4.854 %
Rwork0.1354 43751 -
all0.137 --
obs-45983 99.176 %
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: 22.946 Å2
Baniso -1Baniso -2Baniso -3
1--0.796 Å2-0.398 Å2-0 Å2
2---0.796 Å2-0 Å2
3---2.583 Å2
Refinement stepCycle: LAST / Resolution: 1.32→47.925 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 34 128 1442
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0121392
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161244
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.6581895
X-RAY DIFFRACTIONr_angle_other_deg0.5921.5692903
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4655171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.675512
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.44810244
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.6481069
X-RAY DIFFRACTIONr_chiral_restr0.0890.2216
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021604
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02270
X-RAY DIFFRACTIONr_nbd_refined0.2660.2255
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2010.21157
X-RAY DIFFRACTIONr_nbtor_refined0.180.2662
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2727
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2220.292
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1630.220
X-RAY DIFFRACTIONr_nbd_other0.1470.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1740.254
X-RAY DIFFRACTIONr_mcbond_it3.2832.16672
X-RAY DIFFRACTIONr_mcbond_other3.1712.16671
X-RAY DIFFRACTIONr_mcangle_it3.6123.241844
X-RAY DIFFRACTIONr_mcangle_other3.613.243845
X-RAY DIFFRACTIONr_scbond_it7.6042.758720
X-RAY DIFFRACTIONr_scbond_other7.622.748714
X-RAY DIFFRACTIONr_scangle_it7.2023.961050
X-RAY DIFFRACTIONr_scangle_other7.1923.9421045
X-RAY DIFFRACTIONr_lrange_it5.36935.3271588
X-RAY DIFFRACTIONr_lrange_other5.07932.1241559
X-RAY DIFFRACTIONr_rigid_bond_restr15.68232636
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
1.32-1.3540.3131430.29629750.29733960.9040.89791.81390.293
1.354-1.3910.3171410.25831060.2633350.9150.92597.36130.248
1.391-1.4320.2261280.21530700.21632000.9510.95399.93750.201
1.432-1.4760.2091590.16729790.16931380.9620.9741000.147
1.476-1.5240.1811590.13528690.13830280.9730.9851000.116
1.524-1.5770.1641340.12428040.12629380.9790.9881000.105
1.577-1.6370.1741530.11226800.11528330.9820.9911000.096
1.637-1.7040.161070.10626310.10827380.9830.9931000.091
1.704-1.7790.171560.09224640.09726200.9820.9941000.081
1.779-1.8660.1541110.09524110.09725220.9850.9941000.085
1.866-1.9670.1731110.10822780.11123890.9840.9931000.099
1.967-2.0860.1631070.10321630.10522700.9850.9941000.096
2.086-2.230.1331220.10220080.10421300.9890.9941000.097
2.23-2.4080.151230.10718580.1119810.9870.9931000.103
2.408-2.6370.151780.12317610.12518390.9850.9911000.119
2.637-2.9470.2840.14615890.14916730.9750.9871000.143
2.947-3.4010.205660.1414110.14314770.9710.9871000.142
3.401-4.160.143500.13212220.13212720.9890.9891000.139
4.16-5.8610.182670.1469240.1489910.9820.9891000.16
5.861-47.9250.193330.2265480.2245940.9710.96897.81140.248

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