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- PDB-1xcm: Crystal structure of the GppNHp-bound H-Ras G60A mutant -

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Entry
Database: PDB / ID: 1xcm
TitleCrystal structure of the GppNHp-bound H-Ras G60A mutant
ComponentsTransforming protein p21/H-Ras-1
KeywordsSIGNALING PROTEIN / GTP-binding protein / Ras
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
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / GTPase HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsFord, B. / Nassar, N.
CitationJournal: To be Published
Title: Crystal structure of the GppNHp-bound form of the RasG60A mutant
Authors: Ford, B. / Nassar, N.
History
DepositionSep 2, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 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 1.4Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.6Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transforming protein p21/H-Ras-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6054
Polymers19,0341
Non-polymers5713
Water2,036113
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.292, 81.419, 121.302
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-172-

MG

21A-263-

HOH

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Components

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


Mass: 19034.396 Da / Num. of mol.: 1 / Mutation: G60A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Plasmid: pProEX-HTb / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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-GNP / PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER


Mass: 522.196 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H17N6O13P3
Comment: GppNHp, GMPPNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / 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 Å3/Da / Density % sol: 37.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 2000 MME, magnesium sulfate, HEPES, hydrogen peroxide, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.84→50 Å / Num. all: 15050 / Num. obs: 14668 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 27.1 Å2 / Rsym value: 0.087 / Net I/σ(I): 15.5
Reflection shellResolution: 1.84→1.92 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 1469 / Rsym value: 0.573 / % possible all: 98.9

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 5P21

5p21


Resolution: 1.84→31.61 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.927 / SU B: 2.975 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.152 / ESU R Free: 0.152 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24356 739 5 %RANDOM
Rwork0.18279 ---
all0.18564 ---
obs0.18564 13925 96.55 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 13.592 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.02 Å2
Refine analyzeLuzzati coordinate error obs: 0.024 Å
Refinement stepCycle: LAST / Resolution: 1.84→31.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1368 0 34 113 1515
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221419
X-RAY DIFFRACTIONr_bond_other_d0.0020.021250
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.981918
X-RAY DIFFRACTIONr_angle_other_deg1.84432920
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8525166
X-RAY DIFFRACTIONr_chiral_restr0.0910.2209
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021550
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02282
X-RAY DIFFRACTIONr_nbd_refined0.1940.2292
X-RAY DIFFRACTIONr_nbd_other0.2410.21516
X-RAY DIFFRACTIONr_nbtor_other0.0870.2863
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.281
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2090.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2880.256
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1740.210
X-RAY DIFFRACTIONr_mcbond_it0.8351.5827
X-RAY DIFFRACTIONr_mcangle_it1.56321341
X-RAY DIFFRACTIONr_scbond_it2.4013592
X-RAY DIFFRACTIONr_scangle_it3.9354.5577
LS refinement shellResolution: 1.84→1.89 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.431 56
Rwork0.279 890
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)
110.63583.94166.66130.40892.64186.53420.3263-0.4375-1.02410.10870.0271-0.24430.4746-0.1145-0.35330.26460.0236-0.02210.2090.06190.2442.444213.807231.2941
23.4706-0.1665-2.64662.35281.44662.3015-0.13840.05620.2091-0.27220.1137-0.2596-0.00930.30440.02470.25090.01050.01650.270.03550.191218.307621.861638.7222
39.2018-0.041-2.1914-3.1867-1.52563.33590.14860.48890.39210.12610.0567-0.09740.2221-0.1848-0.20540.054-0.0531-0.00410.06860.02980.1375-2.391728.222739.969
48.7943-2.1119-3.37060.32562.24041.82390.27770.319-0.0603-0.4759-0.23880.0591-0.3751-0.0815-0.03890.17760.00460.00480.15490.07930.1752-1.319927.651939.0429
50.81160.45430.2082.7482-0.03621.262-0.00070.01690.0822-0.2684-0.02330.06170.0693-0.05620.02410.17570.0035-0.00650.18030.01290.14865.869419.822441.0332
60.88850.44120.04741.7637-0.25250.91060.0064-0.04740.0156-0.0091-0.0092-0.0330.0385-0.01010.00270.1451-0.0135-0.01080.1640.00920.16688.404817.768751.9301
73.03863.6398-6.54066.1549-5.683512.1737-0.36420.5719-0.2969-0.360.255-0.31020.5903-0.42470.10920.2255-0.04160.00090.1402-0.020.15267.21436.725941.2509
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA24 - 4024 - 40
2X-RAY DIFFRACTION2AA57 - 7657 - 76
3X-RAY DIFFRACTION3AA41 - 5641 - 56
4X-RAY DIFFRACTION4AA41 - 5641 - 56
5X-RAY DIFFRACTION5AA1 - 231 - 23
6X-RAY DIFFRACTION5AA1 - 231 - 23
7X-RAY DIFFRACTION6AA77 - 16777 - 167
8X-RAY DIFFRACTION6AA77 - 16777 - 167
9X-RAY DIFFRACTION7AD - B170 - 1711

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