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

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Entry
Database: PDB / ID: 2clc
TitleCRYSTAL STRUCTURE ANALYSIS OF A FLUORESCENT FORM OF H-RAS P21 IN COMPLEX WITH GTP (2)
ComponentsGTPASE HRAS
KeywordsNUCLEOTIDE-BINDING PROTEIN / GOLGI APPARATUS / PROTO-ONCOGENE / R-CAGED GTP / PRENYLATION / LIPOPROTEIN / GTP-BINDING / PALMITATE / METHYLATION
Function / homology
Function and homology information


phospholipase C activator activity / positive regulation of miRNA metabolic process / positive regulation of ruffle assembly / positive regulation of wound healing / adipose tissue development / 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 ...phospholipase C activator activity / positive regulation of miRNA metabolic process / positive regulation of ruffle assembly / positive regulation of wound healing / adipose tissue development / 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 / positive regulation of protein targeting to membrane / SOS-mediated signalling / Activated NTRK3 signals through RAS / Activated NTRK2 signals through RAS / SHC1 events in ERBB4 signaling / Schwann cell development / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / positive regulation of Ras protein signal transduction / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / myelination / 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 / Signaling by FGFR3 in disease / FRS-mediated FGFR1 signaling / Tie2 Signaling / animal organ morphogenesis / protein-membrane adaptor activity / Signaling by FGFR2 in disease / EPHB-mediated forward signaling / positive regulation of epithelial cell proliferation / Signaling by FLT3 fusion proteins / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / 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 / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Constitutive Signaling by Overexpressed ERBB2 / Ras activation upon Ca2+ influx through NMDA receptor / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / regulation of actin cytoskeleton organization / small monomeric GTPase / FCERI mediated MAPK activation / cellular response to gamma radiation / Signaling by ERBB2 TMD/JMD mutants / Constitutive Signaling by EGFRvIII / Signaling by SCF-KIT / RAF activation / Signaling by high-kinase activity BRAF mutants / Signaling by ERBB2 ECD mutants / MAP2K and MAPK activation / Signaling by ERBB2 KD Mutants / cellular senescence / positive regulation of JNK cascade / insulin receptor signaling pathway / chemotaxis / 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 / MAPK cascade / Negative regulation of MAPK pathway / RAS processing / Regulation of RAS by GAPs / Signaling by BRAF and RAF1 fusions / GDP binding / DAP12 signaling / regulation of cell population proliferation / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / RAF/MAP kinase cascade / G protein activity / positive regulation of MAPK cascade / Ras protein signal transduction / regulation of cell cycle / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / positive regulation of cell migration / negative regulation of cell population proliferation / negative regulation of gene expression
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'-TRIPHOSPHATE / Chem-XY2 / GTPase HRas
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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
DepositionApr 27, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 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 1.3Jan 30, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval
Revision 1.4Feb 6, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Dec 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 / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Nov 20, 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)19,6645
Polymers18,7991
Non-polymers8654
Water3,585199
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)69.320, 69.320, 35.010
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41
Number of models2

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Components

#1: Protein GTPASE HRAS / H-RAS P21 / TRANSFORMING PROTEIN P21 / P21RAS / H-RAS-1 / C-H-RAS


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.: 2 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRAS PROTEINS BIND GDP/GTP AND POSSESS INTRINSIC GTPASE ACTIVITY ENGINEERED RESIDUE IN CHAIN X, TYR ...RAS PROTEINS BIND GDP/GTP AND POSSESS INTRINSIC GTPASE ACTIVITY ENGINEERED 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: 2.2 Å3/Da / Density % sol: 43.8 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: PROTEIN SOLUTION: 13.35 MG/ML PROTEIN, 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 ...Details: PROTEIN SOLUTION: 13.35 MG/ML PROTEIN, 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: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 7, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.3→69.34 Å / Num. obs: 41195 / % possible obs: 100 % / Redundancy: 6.27 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.05
Reflection shellResolution: 1.3→1.4 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3.14 / % possible all: 100

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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 5P21

5p21


Resolution: 1.3→69.34 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.301 / SU ML: 0.06 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.064 / ESU R Free: 0.065 / 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
Rfree0.18 2055 5 %RANDOM
Rwork0.149 ---
obs0.15 39138 100 %-
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: 13.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.99 Å20 Å20 Å2
2---0.99 Å20 Å2
3---1.98 Å2
Refinement stepCycle: LAST / Resolution: 1.3→69.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1317 0 55 199 1571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222784
X-RAY DIFFRACTIONr_bond_other_d0.0020.022452
X-RAY DIFFRACTIONr_angle_refined_deg1.7532.0083778
X-RAY DIFFRACTIONr_angle_other_deg0.83235700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8075330
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.89424.493138
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.57215480
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6821522
X-RAY DIFFRACTIONr_chiral_restr0.0920.2414
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023074
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02542
X-RAY DIFFRACTIONr_nbd_refined0.2280.2157
X-RAY DIFFRACTIONr_nbd_other0.1920.21206
X-RAY DIFFRACTIONr_nbtor_refined0.1880.2645
X-RAY DIFFRACTIONr_nbtor_other0.090.2861
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.240.2193
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3750.215
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3730.222
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4010.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2371.52154
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.30622658
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.02831363
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.8084.51120
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: 1.3→1.33 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.309 146
Rwork0.272 2871
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)
12.2879-0.9779-0.41252.22930.20650.85770.05570.14410.1094-0.151-0.0218-0.1128-0.0259-0.0182-0.0339-0.0603-0.0003-0.0211-0.06250.0191-0.131919.07755.41-2.264
22.09272.60130.98024.2511.508517.18720.00670.16110.4985-0.22160.3069-0.3956-0.46730.2758-0.3135-0.07390.0142-0.0166-0.07610.01560.076222.13867.479-0.761
33.2986-1.2026-0.30223.15850.61951.2443-0.0172-0.0428-0.02350.040.08-0.12310.04660.0342-0.06280.1136-0.0215-0.03890.08750.01650.022619.62654.2520.957
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X1 - 169
2X-RAY DIFFRACTION2X1167
3X-RAY DIFFRACTION3X2001 - 2321

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