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- PDB-3con: Crystal structure of the human NRAS GTPase bound with GDP -

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Basic information

Entry
Database: PDB / ID: 3con
TitleCrystal structure of the human NRAS GTPase bound with GDP
ComponentsGTPase NRas
KeywordsHYDROLASE / Structural Genomics Consortium / SGC / gtpase / gdp / oncogene / Disease mutation / Golgi apparatus / GTP-binding / Lipoprotein / Membrane / Methylation / Nucleotide-binding / Palmitate / Prenylation / Proto-oncogene
Function / homology
Function and homology information


myoblast differentiation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / tertiary granule membrane / 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 ...myoblast differentiation / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / tertiary granule membrane / 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 / 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 / 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 / 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 / positive regulation of endothelial cell proliferation / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / FLT3 Signaling / 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 / small monomeric GTPase / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / G protein activity / VEGFR2 mediated cell proliferation / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / 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 / Regulation of RAS by GAPs / 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 / MAPK cascade / Signaling by BRAF and RAF1 fusions / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling / RAF/MAP kinase cascade / Ras protein signal transduction / Golgi membrane / GTPase activity / Neutrophil degranulation / protein-containing complex binding / endoplasmic reticulum membrane / GTP binding / Golgi apparatus / extracellular exosome / membrane / plasma membrane / cytosol
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
GUANOSINE-5'-DIPHOSPHATE / GTPase NRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.649 Å
AuthorsNedyalkova, L. / Tong, Y. / Tempel, W. / Shen, L. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. ...Nedyalkova, L. / Tong, Y. / Tempel, W. / Shen, L. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the human NRAS GTPase bound with GDP.
Authors: Nedyalkova, L. / Tong, Y. / Tempel, W. / Shen, L. / Loppnau, P. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionMar 28, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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.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.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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase NRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,31214
Polymers21,7721
Non-polymers54013
Water1,51384
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.061, 83.061, 38.907
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-205-

MG

DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS POLYPEPTIDE IS UNKNOWN.

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Components

#1: Protein GTPase NRas / Transforming protein N-Ras


Mass: 21771.615 Da / Num. of mol.: 1 / Fragment: Residues 1-172
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NRAS, HRAS1 / Plasmid: pET28-mhl / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P01111
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / 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-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 8 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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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: 1.78 Å3/Da / Density % sol: 30.89 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30.0% PEG 3350, 0.2M Magnesium chloride, 0.1 M Tris-HCl, GDP was added to the concentrated protein to a final concentration of 5mM. Crystallization were set up with 1:100 chymotrypsin, pH 8. ...Details: 30.0% PEG 3350, 0.2M Magnesium chloride, 0.1 M Tris-HCl, GDP was added to the concentrated protein to a final concentration of 5mM. Crystallization were set up with 1:100 chymotrypsin, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Mar 13, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.649→40 Å / Num. obs: 18539 / % possible obs: 99.2 % / Redundancy: 9.7 % / Rmerge(I) obs: 0.065 / Χ2: 1.843 / Net I/σ(I): 13.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.649-1.714.60.46917100.75492.8
1.71-1.787.10.35618650.83899.6
1.78-1.8610.40.27418460.97199.9
1.86-1.9610.60.19118371.183100
1.96-2.0810.60.13718701.477100
2.08-2.2410.70.10418641.662100
2.24-2.4610.70.08118581.791100
2.46-2.8210.80.06518691.87100
2.82-3.5510.70.0518932.236100
3.55-40100.05419274.60999.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.3.0037refinement
PDB_EXTRACT3.005data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 4Q21

4q21


Resolution: 1.649→35.967 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.945 / WRfactor Rfree: 0.212 / WRfactor Rwork: 0.182 / SU B: 1.746 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.102 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. Programs arp/warp, coot, molprobity have also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.219 949 5.122 %RANDOM
Rwork0.185 ---
obs0.186 18528 99.16 %-
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: 19.437 Å2
Baniso -1Baniso -2Baniso -3
1--0.056 Å2-0.028 Å20 Å2
2---0.056 Å20 Å2
3---0.083 Å2
Refinement stepCycle: LAST / Resolution: 1.649→35.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1216 0 40 84 1340
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221267
X-RAY DIFFRACTIONr_bond_other_d0.0020.02827
X-RAY DIFFRACTIONr_angle_refined_deg1.531.9911726
X-RAY DIFFRACTIONr_angle_other_deg0.94332029
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7225160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.80824.44454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.59415215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.187157
X-RAY DIFFRACTIONr_chiral_restr0.0910.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021392
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02251
X-RAY DIFFRACTIONr_nbd_refined0.2110.2246
X-RAY DIFFRACTIONr_nbd_other0.2040.2906
X-RAY DIFFRACTIONr_nbtor_refined0.1760.2634
X-RAY DIFFRACTIONr_nbtor_other0.0830.2632
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.259
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1280.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.260.232
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.214
X-RAY DIFFRACTIONr_mcbond_it2.3962846
X-RAY DIFFRACTIONr_mcbond_other0.6932321
X-RAY DIFFRACTIONr_mcangle_it3.02131264
X-RAY DIFFRACTIONr_scbond_it2.8462544
X-RAY DIFFRACTIONr_scangle_it3.8793459
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.649-1.6920.347730.2661175139289.655
1.692-1.7380.33560.21612531309100
1.738-1.7880.24700.1951212129099.38
1.788-1.8430.177750.17512011276100
1.843-1.9030.201720.17111341206100
1.903-1.970.178750.15711161191100
1.97-2.0440.201560.1610941150100
2.044-2.1270.224550.16210461101100
2.127-2.2220.206390.16610041043100
2.222-2.330.189360.1629771013100
2.33-2.4550.26490.183916965100
2.455-2.6030.22520.177869921100
2.603-2.7820.193500.195814864100
2.782-3.0030.22460.211745791100
3.003-3.2880.291420.193700742100
3.288-3.6720.233260.179652678100
3.672-4.2330.139240.1657359899.833
4.233-5.1660.226200.16548951099.804
5.166-7.2320.223240.241373397100
7.232-35.9670.22290.24623624898.79

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