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- PDB-6dzh: HRAS G13D bound to GDP (H13GDP) -

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Basic information

Entry
Database: PDB / ID: 6dzh
TitleHRAS G13D bound to GDP (H13GDP)
ComponentsGTPase HRas
KeywordsSIGNALING PROTEIN / Oncogene / RAS / p21
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 / Signalling to RAS / adipose tissue development / 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 / 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 / GRB2 events in EGFR signaling / EPHB-mediated forward 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 / Downstream signal transduction / intrinsic apoptotic signaling pathway / Insulin receptor signalling cascade / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / 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 / RAF activation / Signaling by ERBB2 TMD/JMD mutants / 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 / Signaling by BRAF and RAF1 fusions / cellular senescence / 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
2,3-DIHYDROXY-1,4-DITHIOBUTANE / GUANOSINE-5'-DIPHOSPHATE / GTPase HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsJohnson, C.W. / Mattos, C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)MCB-1517295 United States
CitationJournal: Cell Rep / Year: 2019
Title: Isoform-Specific Destabilization of the Active Site Reveals a Molecular Mechanism of Intrinsic Activation of KRas G13D.
Authors: Johnson, C.W. / Lin, Y.J. / Reid, D. / Parker, J. / Pavlopoulos, S. / Dischinger, P. / Graveel, C. / Aguirre, A.J. / Steensma, M. / Haigis, K.M. / Mattos, C.
History
DepositionJul 4, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / pdbx_database_related / refine / reflns
Item: _audit_author.identifier_ORCID / _citation.country ..._audit_author.identifier_ORCID / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_obs / _reflns.number_all / _reflns.number_obs / _reflns.percent_possible_obs
Revision 1.2Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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 / refine_hist / struct_conn
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_asym_id / _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_asym_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 / _refine_hist.d_res_low / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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_asym_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GTPase HRas
B: GTPase HRas
C: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,55314
Polymers56,8003
Non-polymers1,75311
Water4,432246
1
A: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4934
Polymers18,9331
Non-polymers5603
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6196
Polymers18,9331
Non-polymers6865
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4414
Polymers18,9331
Non-polymers5083
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)60.571, 71.410, 94.861
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 3 molecules ABC

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


Mass: 18933.227 Da / Num. of mol.: 3 / Fragment: residues 1-166 / Mutation: G13D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Plasmid: pET21 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01112

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Non-polymers , 6 types, 257 molecules

#2: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 3 / 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.: 4 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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

Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 5.9% stabilization buffer (20 mM HEPES, 50 mM NaCl, 20 mM MgCl2, pH 7.5) 188.2 mM Calcium Acetate 18.8% PEG 3350 Crystals were grown in 2uL by 2uL drops of mother liquor to protein (7.7mg/mL) ...Details: 5.9% stabilization buffer (20 mM HEPES, 50 mM NaCl, 20 mM MgCl2, pH 7.5) 188.2 mM Calcium Acetate 18.8% PEG 3350 Crystals were grown in 2uL by 2uL drops of mother liquor to protein (7.7mg/mL) Cryoprotectant for crystal diffraction: 70% mother liquor and 30% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 175532 / Num. obs: 25256 / % possible obs: 82 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.037 / Rrim(I) all: 0.1 / Χ2: 0.944 / Net I/σ(I): 8.1 / Num. measured all: 175531
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.95-1.983.20.5967130.6890.3450.6950.87447.3
1.98-2.023.80.6548390.7140.3520.7480.85654.8
2.02-2.064.20.5598660.7780.2910.6340.91758.9
2.06-2.14.50.54310000.7640.2730.6110.96865.4
2.1-2.154.70.52211010.8310.2520.5820.8372.9
2.15-2.25.20.46411720.8840.2160.5140.83877.3
2.2-2.255.30.40912780.9250.1880.4520.93182.7
2.25-2.315.90.42213470.9380.1820.4620.92689.5
2.31-2.386.20.3914900.9450.1640.4250.87197.6
2.38-2.466.70.38815110.9570.1580.420.86499.9
2.46-2.5470.3315310.9670.1310.3550.879100
2.54-2.657.10.28915370.9770.1140.3110.924100
2.65-2.777.20.22915360.9860.0890.2460.92199.9
2.77-2.917.30.1715170.9910.0670.1830.89699.9
2.91-3.17.40.13515450.9930.0520.1450.94599.9
3.1-3.337.70.08715560.9970.0330.0930.95999.9
3.33-3.677.80.06815490.9970.0260.0731.066100
3.67-4.27.90.04815700.9980.0180.0521.044100
4.2-5.297.80.03915940.9990.0150.0421.01899.9
5.29-507.40.03616960.9990.0140.0391.02499.7

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-3000data scaling
PDB_EXTRACT3.24data extraction
HKL-3000data reduction
PHENIX1.11.1_2575phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6E6P

6e6p


Resolution: 1.95→35.7 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.218 2000 -
Rwork0.163 --
obs-25252 87.5 %
Displacement parametersBiso max: 70.97 Å2 / Biso mean: 25.6642 Å2 / Biso min: 6.96 Å2
Refinement stepCycle: LAST / Resolution: 1.95→35.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3668 0 104 246 4018

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