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- PDB-4rsg: Neutron crystal structure of Ras bound to the GTP analogue GppNHp -

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Basic information

Entry
Database: PDB / ID: 4rsg
TitleNeutron crystal structure of Ras bound to the GTP analogue GppNHp
ComponentsGTPase HRas
KeywordsSIGNALING PROTEIN / oncoprotein / nucleotide-binding protein / protein-nucleotide complex
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 / 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 / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / 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 / positive regulation of protein targeting to membrane / Signalling to RAS / 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 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / 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 / 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 / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / myelination / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by FGFR1 in disease / 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 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / G protein activity / positive regulation of GTPase activity / 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 / RAF activation / regulation of long-term neuronal synaptic plasticity / 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 / Regulation of RAS by GAPs / endocytosis / Negative regulation of MAPK pathway / RAS processing / 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 / chemotaxis / MAPK cascade / cellular senescence / Signaling by BRAF and RAF1 fusions / positive regulation of type II interferon production / positive regulation of fibroblast proliferation / insulin receptor signaling pathway / 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 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
DEUTERATED WATER / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / MOLECULAR REPLACEMENT / Resolution: 1.907 Å
AuthorsKnihtila, R.R. / Holzapfel, G. / Weiss, K.L. / Meilleur, F. / Mattos, C.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Neutron Crystal Structure of RAS GTPase Puts in Question the Protonation State of the GTP gamma-Phosphate.
Authors: Knihtila, R. / Holzapfel, G. / Weiss, K. / Meilleur, F. / Mattos, C.
History
DepositionNov 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2Jan 13, 2016Group: Database references
Revision 1.3Apr 25, 2018Group: Data collection / Category: diffrn_source
Item: _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site ..._diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type
Revision 1.4Jun 30, 2021Group: Data collection / Derived calculations
Category: diffrn_detector / diffrn_radiation ...diffrn_detector / diffrn_radiation / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _diffrn_detector.detector / _diffrn_detector.type ..._diffrn_detector.detector / _diffrn_detector.type / _diffrn_radiation.pdbx_monochromatic_or_laue_m_l / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)19,4223
Polymers18,8751
Non-polymers5472
Water1,35175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)40.084, 40.084, 160.785
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-354-

DOD

21A-356-

DOD

31A-374-

DOD

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Components

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


Mass: 18875.191 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P01112
#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-DOD / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 18mg/mL protein, 0.2M calcium acetate, 20% PEG 3350, 20mM HEPES, 50mM NaCl, 20mM MgCl2, 0.1% N-octy-B-D-glucopyranoside, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: ORNL High Flux Isotope Reactor / Beamline: CG4D / Wavelength: 3.3-4.5
DetectorType: FUJI / Detector: IMAGE PLATE / Date: May 9, 2014
RadiationMonochromator: neutron mirrors and neutron filters / Protocol: LAUE / Monochromatic (M) / Laue (L): L / Scattering type: neutron
Radiation wavelength
IDWavelength (Å)Relative weight
13.31
24.51
ReflectionResolution: 1.899→17.01 Å / Num. all: 9888 / Num. obs: 9888 / % possible obs: 82.1 % / Redundancy: 6.2 % / Biso Wilson estimate: 8.61 Å2 / Rmerge(I) obs: 0.262 / Rsym value: 0.262 / Net I/σ(I): 5.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsRsym valueDiffraction-ID% possible all
1.899-230.3791.90.379160.4
2-2.124.50.3871.80.387176
2.12-2.275.80.391.80.39179.7
2.27-2.456.40.3631.90.363183.9
2.45-2.696.80.33820.338186.4
2.69-36.80.3072.20.307189.8
3-3.477.20.2582.60.258191.3
3.47-4.2580.2242.90.224193.9
4.25-6.018.20.1883.10.188196.8
6.01-16.9546.50.1324.10.132192

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Processing

Software
NameVersionClassificationNB
SCALA3.2.25data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
Quasi-LaueDiffractometer v4.06data collection
LAUEGENdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.907→17.009 Å / SU ML: 0.31 / σ(F): 1.41 / Phase error: 28.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2875 1003 10.15 %
Rwork0.2492 --
obs0.253 9882 79.61 %
all-9882 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 16.4865 Å2
Refinement stepCycle: LAST / Resolution: 1.907→17.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1207 0 33 75 1315
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0142584
NEUTRON DIFFRACTIONf_angle_d0.8724511
NEUTRON DIFFRACTIONf_dihedral_angle_d18.327707
NEUTRON DIFFRACTIONf_chiral_restr0.036203
NEUTRON DIFFRACTIONf_plane_restr0.003442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9066-2.00690.3974990.3318894NEUTRON DIFFRACTION57
2.0069-2.13250.34671230.30181119NEUTRON DIFFRACTION73
2.1325-2.29670.29011450.26881208NEUTRON DIFFRACTION78
2.2967-2.52720.29551390.23121292NEUTRON DIFFRACTION81
2.5272-2.89130.28681550.2471342NEUTRON DIFFRACTION85
2.8913-3.63690.22721590.22151425NEUTRON DIFFRACTION88
3.6369-17.00960.27371830.2271599NEUTRON DIFFRACTION94

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