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Entry
Database: PDB / ID: 2evw
TitleCrystal structure analysis of a fluorescent form of H-Ras p21 in complex with R-caged GTP
ComponentsGTPase HRas
KeywordsSIGNALING PROTEIN / guanine nucleotide binding protein / fluorescence / caged GTP
Function / homology
Function and homology information


phospholipase C activator activity / GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan ...phospholipase C activator activity / GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / T-helper 1 type immune response / positive regulation of wound healing / 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 / adipose tissue development / SHC-mediated cascade:FGFR2 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Schwann cell development / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR2 signaling / protein-membrane adaptor activity / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / Signaling by FGFR2 in disease / FRS-mediated FGFR4 signaling / p38MAPK events / Signaling by FGFR3 in disease / Tie2 Signaling / FRS-mediated FGFR1 signaling / GRB2 events in EGFR signaling / FLT3 Signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / EPHB-mediated forward signaling / Signaling by FGFR1 in disease / myelination / GRB2 events in ERBB2 signaling / intrinsic apoptotic signaling pathway / CD209 (DC-SIGN) signaling / Ras activation upon Ca2+ influx through NMDA receptor / NCAM signaling for neurite out-growth / SHC1 events in ERBB2 signaling / Downstream signal transduction / Constitutive Signaling by Overexpressed ERBB2 / Insulin receptor signalling cascade / positive regulation of epithelial cell proliferation / positive regulation of GTPase activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / small monomeric GTPase / VEGFR2 mediated cell proliferation / regulation of actin cytoskeleton organization / animal organ morphogenesis / FCERI mediated MAPK activation / positive regulation of JNK cascade / Signaling by ERBB2 TMD/JMD mutants / RAF activation / positive regulation of MAP kinase activity / Constitutive Signaling by EGFRvIII / regulation of long-term neuronal synaptic plasticity / Signaling by high-kinase activity BRAF mutants / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / cellular response to gamma radiation / G protein activity / Regulation of RAS by GAPs / positive regulation of type II interferon production / endocytosis / 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 / chemotaxis / GDP binding / cellular senescence / positive regulation of fibroblast proliferation / Signaling by BRAF and RAF1 fusions / MAPK cascade / DAP12 signaling / insulin receptor signaling pathway
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 / Rossmann fold ...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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-CAG / Chem-XY2 / GTPase HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.05 Å
AuthorsKlink, B.U.
CitationJournal: Biophys.J. / Year: 2006
Title: A newly designed microspectrofluorometer for kinetic studies on protein crystals in combination with x-ray diffraction.
Authors: Klink, B.U. / Goody, R.S. / Scheidig, A.J.
History
DepositionNov 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.6Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,7894
Polymers18,7991
Non-polymers9903
Water4,306239
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.300, 69.300, 35.510
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Number of models2
DetailsThe biological assembly is a monomer

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Components

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


Mass: 18799.096 Da / Num. of mol.: 1 / Fragment: truncated form residues 1-166 / Mutation: Y32C,C118S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Plasmid: ptac ras / Production host: Escherichia coli (E. coli) / Strain (production host): CK600K / References: UniProt: P01112
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CAG / GUANOSINE 5'-TRIPHOSPHATE P3-[1-(2-NITROPHENYL)ETHYL ESTER]


Mass: 672.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H23N6O16P3
#4: Chemical ChemComp-XY2 / N,N'-DIMETHYL-N-(ACETYL)-N'-(7-NITROBENZ-2-OXA-1,3-DIAZOL-4-YL)ETHYLENEDIAMINE


Mass: 293.279 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H15N5O4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.27 Å3/Da / Density % sol: 45.76 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: protein solution: 64 mM TRIS pH 7.6, 20 mM magnesium chloride, 10 mM DTT, 0,1 mM sodium azide; reservoir solution: 100 mM HEPES pH 7.2, 200 mM magnesium acetate, 16% PEG 8000 (freshly ...Details: protein solution: 64 mM TRIS pH 7.6, 20 mM magnesium chloride, 10 mM DTT, 0,1 mM sodium azide; reservoir solution: 100 mM HEPES pH 7.2, 200 mM magnesium acetate, 16% PEG 8000 (freshly prepared) mixture of equal volumes of protein and reservoir solution, VAPOR DIFFUSION, HANGING DROP, temperature 291.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 1, 2004 / Details: mirrors
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 1→69.34 Å / Num. all: 536019 / Num. obs: 78838 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.052 / Rsym value: 0.052 / Net I/σ(I): 13.82
Reflection shellResolution: 1→1.05 Å / Redundancy: 4 % / Rmerge(I) obs: 0.679 / Mean I/σ(I) obs: 2.43 / Num. unique all: 12300 / Num. unique obs: 11588 / Rsym value: 0.679 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT1.701data extraction
ProDCdata collection
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 5p21

5p21


Resolution: 1.05→69.34 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.971 / SU B: 1.682 / SU ML: 0.037 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.036 / ESU R Free: 0.039 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: An IANBD Fluorophore was attached to Cys-32. The structure was refined using two alternative conformations for the whole protein chain. Hydrogens have been added in the riding positions. The ...Details: An IANBD Fluorophore was attached to Cys-32. The structure was refined using two alternative conformations for the whole protein chain. Hydrogens have been added in the riding positions. The close contacts with water molecules are caused by the treatment of the whole protein chain with two alternative conformations, but only one position per water molecule.
RfactorNum. reflection% reflectionSelection details
Rfree0.181 3909 5 %RANDOM
Rwork0.156 ---
all0.157 78796 --
obs0.157 78796 99.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 6.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2---0.68 Å20 Å2
3---1.36 Å2
Refinement stepCycle: LAST / Resolution: 1.05→69.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1317 0 65 239 1621
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222808
X-RAY DIFFRACTIONr_bond_other_d0.0010.022472
X-RAY DIFFRACTIONr_angle_refined_deg1.8552.0173812
X-RAY DIFFRACTIONr_angle_other_deg0.8635740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2285330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.7324.493138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.09115480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6071522
X-RAY DIFFRACTIONr_chiral_restr0.0950.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023102
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02562
X-RAY DIFFRACTIONr_nbd_refined0.240.2178
X-RAY DIFFRACTIONr_nbd_other0.1930.21314
X-RAY DIFFRACTIONr_nbtor_refined0.1910.2650
X-RAY DIFFRACTIONr_nbtor_other0.090.2899
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2550.2238
X-RAY DIFFRACTIONr_metal_ion_refined0.020.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1950.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2850.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.270.234
X-RAY DIFFRACTIONr_symmetry_hbond_other0.110.21
X-RAY DIFFRACTIONr_mcbond_it1.1831.52152
X-RAY DIFFRACTIONr_mcbond_other0.2351.5684
X-RAY DIFFRACTIONr_mcangle_it1.28722658
X-RAY DIFFRACTIONr_scbond_it2.20931399
X-RAY DIFFRACTIONr_scangle_it2.8454.51154
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.279 290 -
Rwork0.265 5519 -
obs-5809 99.97 %
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)
11.2835-0.1116-0.24011.2006-0.00420.50340.0080.0622-0.0077-0.00290.0094-0.1168-0.0252-0.0384-0.01740.01230.0008-0.01470.0190.0063-0.051118.94855.359-2.274
22.75260.88530.05851.13212.45797.0211-0.00170.23730.4164-0.16330.0317-0.2185-0.32340.0878-0.030.042-0.00280.004-0.02110.01410.015421.22468.161-2.135
31.99870.1178-0.19172.18190.52880.75080.0002-0.0094-0.06280.16270.0834-0.19320.0015-0.0206-0.08360.01140.0006-0.03270.01360.0114-0.090918.44754.590.886
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: X

IDRefine TLS-IDLabel asym-IDAuth seq-IDLabel seq-ID
11A1 - 1661 - 166
22C - B367 - 3681
33E369 - 6071 - 239

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