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- PDB-6mqt: HRAS G12S in complex with GDP -

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Basic information

Entry
Database: PDB / ID: 6mqt
TitleHRAS G12S in complex with GDP
ComponentsGTPase HRasHRAS
KeywordsHYDROLASE / GTPASE KRAS HYDROLYSIS
Function / homology
Function and homology information


GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / defense response to protozoan / Signaling by RAS GAP mutants ...GTPase complex / oncogene-induced cell senescence / positive regulation of ruffle assembly / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / negative regulation of GTPase activity / positive regulation of miRNA metabolic process / 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 / 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 / Signalling to RAS / SHC-related events triggered by IGF1R / Activated NTRK2 signals through FRS2 and FRS3 / adipose tissue development / Estrogen-stimulated signaling through PRKCZ / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / positive regulation of phospholipase C activity / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / Schwann cell development / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / protein-membrane adaptor activity / 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 / FRS-mediated FGFR1 signaling / Tie2 Signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / EPHB-mediated forward signaling / SHC1 events in EGFR signaling / myelination / EGFR Transactivation by Gastrin / Signaling by FLT3 fusion proteins / Ras activation upon Ca2+ influx through NMDA receptor / FLT3 Signaling / 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 / Insulin receptor signalling cascade / Constitutive Signaling by Overexpressed ERBB2 / intrinsic apoptotic signaling pathway / small monomeric GTPase / G protein activity / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / positive regulation of JNK cascade / regulation of long-term neuronal synaptic plasticity / animal organ morphogenesis / Signaling by ERBB2 TMD/JMD mutants / RAF activation / Signaling by high-kinase activity BRAF mutants / cellular response to gamma radiation / Constitutive Signaling by EGFRvIII / positive regulation of MAP kinase activity / MAP2K and MAPK activation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / Signaling by SCF-KIT / positive regulation of GTPase activity / endocytosis / Regulation of RAS by GAPs / Negative regulation of MAPK pathway / RAS processing / GDP binding / 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 / positive regulation of fibroblast proliferation / MAPK cascade / cellular senescence / Signaling by BRAF and RAF1 fusions / positive regulation of type II interferon production / Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants / DAP12 signaling
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 HRas
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.498 Å
AuthorsBera, A.K. / Westover, K.D.
CitationJournal: To Be Published
Title: HRAS G12S in complex with GDP
Authors: Bera, A.K. / Westover, K.D.
History
DepositionOct 10, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2020Group: Database references / Derived calculations / Structure summary
Category: citation / pdbx_struct_conn_angle ...citation / pdbx_struct_conn_angle / struct / struct_conn
Item: _citation.title / _pdbx_struct_conn_angle.ptnr1_auth_seq_id ..._citation.title / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct.title / _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
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GTPase HRas
B: GTPase HRas
C: GTPase HRas
D: GTPase HRas
E: GTPase HRas
F: GTPase HRas
G: GTPase HRas
H: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,55024
Polymers151,8108
Non-polymers3,74016
Water18,5011027
1
A: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4443
Polymers18,9761
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4443
Polymers18,9761
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4443
Polymers18,9761
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4443
Polymers18,9761
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4443
Polymers18,9761
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4443
Polymers18,9761
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4443
Polymers18,9761
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: GTPase HRas
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,4443
Polymers18,9761
Non-polymers4682
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)122.808, 79.773, 134.062
Angle α, β, γ (deg.)90.000, 101.940, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11D-440-

HOH

21E-447-

HOH

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Components

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


Mass: 18976.295 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli (E. coli) / References: UniProt: P01112
#2: Chemical
ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 8 / 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.: 8 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1027 / 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: 2.12 Å3/Da / Density % sol: 41.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M Sodium acetate trihydrate, 0.1 M TRIS hydrochloride pH 8.5, 30% w/v Polyethylene glycol 4,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.49→50 Å / Num. obs: 195200 / % possible obs: 96.6 % / Redundancy: 6.7 % / CC1/2: 0.99 / Rpim(I) all: 0.025 / Net I/σ(I): 39.7
Reflection shellResolution: 1.5→1.53 Å / Mean I/σ(I) obs: 6.39 / Num. unique obs: 9667 / CC1/2: 0.987 / Rpim(I) all: 95.5 / % possible all: 95.5

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Processing

Software
NameVersionClassification
PHENIXdev_2932refinement
PDB_EXTRACT3.22data extraction
HKL-3000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5b2z

5b2z


Resolution: 1.498→39.445 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 28.65
RfactorNum. reflection% reflection
Rfree0.1952 9706 4.99 %
Rwork0.1572 --
obs0.1591 194487 95.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.58 Å2 / Biso mean: 25.3437 Å2 / Biso min: 8.29 Å2
Refinement stepCycle: final / Resolution: 1.498→39.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10612 0 345 1027 11984
Biso mean--18.26 32.22 -
Num. residues----1332
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4979-1.51490.2182730.17575243551683
1.5149-1.53280.22943080.17086149645795
1.5328-1.55140.22143360.15596096643296
1.5514-1.57110.21193350.14756131646695
1.5711-1.59180.20813360.15026167650396
1.5918-1.61360.21253210.15146143646496
1.6136-1.63660.21063200.14666151647196
1.6366-1.6610.21093110.15096181649296
1.661-1.6870.20853150.14685903621893
1.687-1.71470.20073320.1435913624593
1.7147-1.74420.18313430.14026252659597
1.7442-1.77590.2263190.14936177649697
1.7759-1.81010.20223240.15566231655597
1.8101-1.8470.2113550.16066184653997
1.847-1.88720.21783070.1556278658597
1.8872-1.93110.2073420.14396223656597
1.9311-1.97940.18773500.13886214656497
1.9794-2.03290.1843200.14625842616291
2.0329-2.09270.21823250.16196250657597
2.0927-2.16030.21023350.15346273660898
2.1603-2.23750.20082930.14716352664598
2.2375-2.32710.18673190.14216300661998
2.3271-2.43290.17143120.14436351666398
2.4329-2.56120.19053330.14856218655197
2.5612-2.72160.20792970.16496107640494
2.7216-2.93170.2023470.17266374672199
2.9317-3.22660.19113330.16946362669599
3.2266-3.69320.18683210.16926355667698
3.6932-4.65190.16343040.14646212651695
4.6519-39.45860.19793400.18036149648993

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