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- PDB-2ce2: CRYSTAL STRUCTURE ANALYSIS OF A FLUORESCENT FORM OF H-RAS P21 IN ... -

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Entry
Database: PDB / ID: 2ce2
TitleCRYSTAL STRUCTURE ANALYSIS OF A FLUORESCENT FORM OF H-RAS P21 IN COMPLEX WITH GDP
ComponentsGTPASE HRAS
KeywordsSIGNALING PROTEIN / GUANINE NUCLEOTIDE BINDING PROTEIN / FLUORESCENCE / MEMBRANE / LIPOPROTEIN / PALMITATE / PRENYLATION
Function / homology
Function and homology information


phospholipase C activator activity / GTPase complex / oncogene-induced cell senescence / negative regulation of GTPase activity / 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 ...phospholipase C activator activity / GTPase complex / oncogene-induced cell senescence / negative regulation of GTPase activity / 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 / Signalling to RAS / adipose tissue development / positive regulation of MAP kinase activity / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Estrogen-stimulated signaling through PRKCZ / Schwann cell development / 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 / Signaling by FGFR4 in disease / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / protein-membrane adaptor activity / Signaling by FGFR3 in disease / p38MAPK events / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / positive regulation of GTPase activity / EPHB-mediated forward signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / myelination / 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 / Downstream signal transduction / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / intrinsic apoptotic signaling pathway / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / positive regulation of epithelial cell proliferation / VEGFR2 mediated cell proliferation / animal organ morphogenesis / small monomeric GTPase / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / positive regulation of JNK cascade / RAF activation / Signaling by ERBB2 TMD/JMD mutants / regulation of long-term neuronal synaptic plasticity / Signaling by high-kinase activity BRAF mutants / Signaling by SCF-KIT / cellular response to gamma radiation / Constitutive Signaling by EGFRvIII / 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 / Regulation of RAS by GAPs / chemotaxis / RAS processing / Signaling by RAF1 mutants / Negative regulation of MAPK pathway / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / GDP binding / Signaling by BRAF and RAF1 fusions / cellular senescence / MAPK cascade / insulin receptor signaling pathway / DAP12 signaling / T cell receptor signaling pathway
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 nucleotide triphosphate hydrolases / Rossmann fold ...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 nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Chem-XY2 / GTPase HRas
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1 Å
AuthorsKlink, B.U. / Goody, R.S. / Scheidig, A.J.
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
DepositionFeb 2, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Apr 22, 2015Group: Atomic model / Derived calculations ...Atomic model / Derived calculations / Non-polymer description / Other / Refinement description
Revision 1.3Jun 28, 2017Group: Database references / Category: citation / citation_author
Revision 1.4Jan 30, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / pdbx_struct_special_symmetry / Item: _exptl_crystal_grow.method
Revision 1.5Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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 / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.7Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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)19,5604
Polymers18,7991
Non-polymers7613
Water4,738263
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.000, 53.900, 116.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Number of models2
Components on special symmetry positions
IDModelComponents
11X-2230-

HOH

22X-2230-

HOH

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Components

#1: Protein GTPASE HRAS / H-RAS P21 / TRANSFORMING PROTEIN P21 / C-H-RAS-1


Mass: 18799.096 Da / Num. of mol.: 1 / Fragment: RESIDUES 1-166 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: AN IANBD FLUOROPHORE WAS ATTACHED TO CYS-32 / Source: (gene. exp.) HOMO SAPIENS (human) / 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-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#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.: 263 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN X, TYR 32 TO CYS ENGINEERED RESIDUE IN CHAIN X, CYS 118 TO SER
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: 2.1 Å3/Da / Density % sol: 39.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: PROTEIN SOLUTION: 17.22 MG/ML PROTEIN, 64 MM TRIS PH 7.6, 20 MM MAGNESIUM CHLORIDE, 10 MM DTT, 0,1 MM SODIUM AZIDE; RESERVOIR SOLUTION: 64 MM TRIS PH 7.6, 20 MM MAGNESIUM CHLORIDE, 10 MM ...Details: PROTEIN SOLUTION: 17.22 MG/ML PROTEIN, 64 MM TRIS PH 7.6, 20 MM MAGNESIUM CHLORIDE, 10 MM DTT, 0,1 MM SODIUM AZIDE; RESERVOIR SOLUTION: 64 MM TRIS PH 7.6, 20 MM MAGNESIUM CHLORIDE, 10 MM DTT, 0,1 MM SODIUM AZIDE, 35% PEG 400 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: SLS / Beamline: X06SA / Wavelength: 0.82655
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 20, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82655 Å / Relative weight: 1
ReflectionResolution: 0.99→50 Å / Num. obs: 82821 / % possible obs: 97 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 14.96
Reflection shellResolution: 0.99→1 Å / Redundancy: 4 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.33 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4Q21

4q21


Resolution: 1→50 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.969 / SU B: 1.202 / SU ML: 0.029 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.033 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AN IANBD FLUOROPHORE WAS ATTACHED TO CYS-32. THE STRUCTURE WAS REFINED USING TWO ALTERNATIVE CONFORMATIONS FOR THE WHOLE PROTEIN CHAIN. THE ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. AN IANBD FLUOROPHORE WAS ATTACHED TO CYS-32. THE STRUCTURE WAS REFINED USING TWO ALTERNATIVE CONFORMATIONS FOR THE WHOLE PROTEIN CHAIN. 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
Rfree0.163 4021 5 %RANDOM
Rwork0.144 ---
obs0.145 76394 97 %-
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: 8.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.53 Å20 Å20 Å2
2---0.17 Å20 Å2
3----0.36 Å2
Refinement stepCycle: LAST / Resolution: 1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1317 0 50 263 1630
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222776
X-RAY DIFFRACTIONr_bond_other_d0.0010.022456
X-RAY DIFFRACTIONr_angle_refined_deg1.7192.0043764
X-RAY DIFFRACTIONr_angle_other_deg0.80235706
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1425330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.1824.493138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.82515480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.9231522
X-RAY DIFFRACTIONr_chiral_restr0.0850.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023078
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02554
X-RAY DIFFRACTIONr_nbd_refined0.2410.2176
X-RAY DIFFRACTIONr_nbd_other0.1960.21305
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2673
X-RAY DIFFRACTIONr_nbtor_other0.0910.2875
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2140.2288
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3010.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3470.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1880.250
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9681.52142
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.04222658
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.73431360
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.4244.51106
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1→1.03 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.277 290
Rwork0.27 5493
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)
10.52130.2442-0.1480.8820.15230.9431-0.0065-0.0462-0.04160.0125-0.008-0.03930.07580.03240.0145-0.0559-0.01620.0084-0.0608-0.0085-0.038310.49836.98815.146
21.08880.8576-0.34511.55740.03481.306-0.05460.0211-0.013-0.07170.02290.0240.05290.03270.0318-0.006-0.0063-0.0048-0.0066-0.01180.0239.83438.17413.4
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X1 - 190
2X-RAY DIFFRACTION2X2001 - 2434

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