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- PDB-4l9s: Crystal Structure of H-Ras G12C, GDP-bound -

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Basic information

Entry
Database: PDB / ID: 4l9s
TitleCrystal Structure of H-Ras G12C, GDP-bound
ComponentsGTPase HRas
KeywordsSIGNALING PROTEIN / GTPase / activating mutant
Function / homology
Function and homology information


phospholipase C activator activity / GTPase complex / oncogene-induced cell senescence / 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 ...phospholipase C activator activity / GTPase complex / oncogene-induced cell senescence / 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 / adipose tissue development / Signalling to RAS / Activated NTRK2 signals through FRS2 and FRS3 / SHC-related events triggered by IGF1R / Schwann cell development / Estrogen-stimulated signaling through PRKCZ / 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 / 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 / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / protein-membrane adaptor activity / Tie2 Signaling / Signaling by FGFR2 in disease / myelination / EPHB-mediated forward signaling / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / 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 / intrinsic apoptotic signaling pathway / Downstream signal transduction / Insulin receptor signalling cascade / SHC1 events in ERBB2 signaling / Ras activation upon Ca2+ influx through NMDA receptor / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / animal organ morphogenesis / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / small monomeric GTPase / regulation of actin cytoskeleton organization / positive regulation of JNK cascade / FCERI mediated MAPK activation / Signaling by ERBB2 TMD/JMD mutants / RAF activation / cellular response to gamma radiation / Signaling by SCF-KIT / Signaling by high-kinase activity BRAF mutants / Constitutive Signaling by EGFRvIII / regulation of long-term neuronal synaptic plasticity / 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 / chemotaxis / Regulation of RAS by GAPs / 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 / GDP binding / cellular senescence / Signaling by BRAF and RAF1 fusions / insulin receptor signaling pathway / DAP12 signaling / T cell receptor signaling pathway / MAPK cascade / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / regulation of cell population proliferation / G protein activity
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 / GTPase HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.606 Å
AuthorsOstrem, J.M. / Peters, U. / Sos, M.L. / Wells, J.A. / Shokat, K.M.
CitationJournal: Nature / Year: 2013
Title: K-Ras(G12C) inhibitors allosterically control GTP affinity and effector interactions.
Authors: Ostrem, J.M. / Peters, U. / Sos, M.L. / Wells, J.A. / Shokat, K.M.
History
DepositionJun 18, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Revision 1.3Sep 20, 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_alt_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_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_alt_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_ptnr1_label_alt_id / _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_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 HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9187
Polymers19,3251
Non-polymers5946
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)92.725, 92.725, 121.897
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-203-

CA

21A-204-

CA

31A-205-

NA

41A-369-

HOH

51A-375-

HOH

61A-376-

HOH

71A-391-

HOH

81A-394-

HOH

91A-448-

HOH

101A-449-

HOH

111A-461-

HOH

121A-466-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 19324.738 Da / Num. of mol.: 1 / Fragment: GTPase domain, UNP residues 1-166 / Mutation: G12C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Plasmid: ProEx HTb / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P01112, small monomeric GTPase

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Non-polymers , 5 types, 173 molecules

#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.61 Å3/Da / Density % sol: 52.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 17% PEG8000, 0.1M CaCl2, 0.1M TRIS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1159 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 16, 2010
RadiationMonochromator: Double crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1159 Å / Relative weight: 1
ReflectionResolution: 1.606→25 Å / Num. obs: 26379 / % possible obs: 99.7 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.05 / Χ2: 1.027 / Net I/σ(I): 19.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.606-1.646.40.38412981.0021100
1.64-1.676.50.35613031.0261100
1.67-1.76.50.29913111.0811100
1.7-1.736.50.23813201.0661100
1.73-1.776.50.21413231.091100
1.77-1.816.50.18312881.0941100
1.81-1.866.50.15413131.0721100
1.86-1.916.50.12613171.0831100
1.91-1.966.50.11313121.0571100
1.96-2.036.50.09513031.0391100
2.03-2.16.60.08413320.9151100
2.1-2.186.60.08113001.0181100
2.18-2.286.60.07213161.0661100
2.28-2.46.60.06213361.0861100
2.4-2.566.60.06113201.054199.9
2.56-2.756.50.06113100.9041100
2.75-3.036.50.06413421.0321100
3.03-3.476.40.05113420.9311100
3.47-4.366.30.03313451.001199.3
4.36-256.30.02513480.92195.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.5.4phasing
PHENIXdev_1402refinement
PDB_EXTRACT3.11data extraction
BOSdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3GFT

3gft


Resolution: 1.606→21.505 Å / Occupancy max: 1 / Occupancy min: 0.49 / FOM work R set: 0.8923 / SU ML: 0.1 / σ(F): 1.34 / Phase error: 17.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1729 1983 7.52 %
Rwork0.1547 --
obs0.1561 26375 99.5 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.87 Å2 / Biso mean: 34.2758 Å2 / Biso min: 14.26 Å2
Refinement stepCycle: LAST / Resolution: 1.606→21.505 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1259 0 33 167 1459
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011319
X-RAY DIFFRACTIONf_angle_d1.3031791
X-RAY DIFFRACTIONf_chiral_restr0.066203
X-RAY DIFFRACTIONf_plane_restr0.006230
X-RAY DIFFRACTIONf_dihedral_angle_d15.977497
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.606-1.64590.20891400.18831682182297
1.6459-1.69040.21361390.192517261865100
1.6904-1.74010.21621420.175517221864100
1.7401-1.79630.19381420.168317311873100
1.7963-1.86050.18081460.171117261872100
1.8605-1.93490.18711370.154417481885100
1.9349-2.02290.16111460.149817281874100
2.0229-2.12950.17741410.160917301871100
2.1295-2.26270.17041330.146717741907100
2.2627-2.43720.16521460.14817561902100
2.4372-2.68210.18561430.149717441887100
2.6821-3.06920.19241380.165917741912100
3.0692-3.86320.15411490.14817641913100
3.8632-21.50690.16221410.14921787192897
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)
14.3632-1.51490.27243.10580.05672.0748-0.0064-0.30680.35290.35320.00420.2294-0.204-0.2478-0.01240.23370.02780.0350.1757-0.03520.139827.9793-8.8043-4.6684
24.34582.5811-1.50348.8281-3.36924.4145-0.1647-0.77150.33850.57740.0989-0.0866-0.20160.26310.07510.45540.0551-0.05270.3504-0.1260.274237.6621-6.24760.8581
36.637-3.93876.14383.653-4.83677.4036-0.3828-0.71570.41180.34890.12890.0384-0.1377-0.82130.25310.3299-0.00090.01190.233-0.04830.235420.3768-2.2997-6.9743
43.7013-3.06464.40676.0888-2.09526.0376-0.0939-0.3984-0.14770.87370.23530.4063-0.0101-0.1455-0.25610.34890.02110.09560.2597-00.264624.5367-10.4705-0.9171
55.3508-1.64782.66183.1594-0.16084.808-0.1261-1.83-0.32271.6759-0.19560.63240.4093-0.8272-0.08790.6598-0.09980.18690.67280.13970.552818.8649-17.34141.0734
65.28380.9063-1.04132.1401-0.37692.0809-0.0778-0.1548-0.38180.14210.04640.24970.1826-0.16010.04170.1714-0.01220.02890.14550.01510.161129.2252-22.9006-8.0903
75.0609-0.5388-0.18722.7893-0.50081.3162-0.05930.29880.0605-0.07790.0730.0821-0.04960.0182-0.00990.1856-0.0096-0.00390.18120.00540.116831.726-14.8038-16.204
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 37 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 38 through 50 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 51 through 68 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 69 through 76 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 77 through 116 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 117 through 166 )A0

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