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- PDB-8bos: Transition state analogue complex of small G protein and its GAP ... -

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Basic information

Entry
Database: PDB / ID: 8bos
TitleTransition state analogue complex of small G protein and its GAP effector
Components
  • GTPase HRas
  • Ras GTPase-activating protein 1
KeywordsHYDROLASE / transition state analogue complex / metal fluoride complex / Ras / signalling protein / RasGAP / oncoprotein
Function / homology
Function and homology information


regulation of RNA metabolic process / regulation of actin filament polymerization / potassium channel inhibitor activity / negative regulation of cell adhesion / phospholipase C activator activity / GTPase complex / positive regulation of ruffle assembly / oncogene-induced cell senescence / negative regulation of GTPase activity / blood vessel morphogenesis ...regulation of RNA metabolic process / regulation of actin filament polymerization / potassium channel inhibitor activity / negative regulation of cell adhesion / phospholipase C activator activity / GTPase complex / positive regulation of ruffle assembly / oncogene-induced cell senescence / negative regulation of GTPase activity / blood vessel morphogenesis / positive regulation of miRNA metabolic process / T-helper 1 type immune response / positive regulation of wound healing / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / defense response to protozoan / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / mitotic cytokinesis / RAS signaling downstream of NF1 loss-of-function variants / SOS-mediated signalling / Activated NTRK3 signals through RAS / positive regulation of protein targeting to membrane / Activated NTRK2 signals through RAS / ephrin receptor signaling pathway / negative regulation of cell-matrix adhesion / 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 / SHC-mediated cascade:FGFR3 / MET activates RAS signaling / Schwann cell development / vasculogenesis / SHC-mediated cascade:FGFR2 / Signaling by PDGFRA transmembrane, juxtamembrane and kinase domain mutants / Signaling by PDGFRA extracellular domain mutants / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / SHC-mediated cascade:FGFR4 / Signaling by FGFR4 in disease / Erythropoietin activates RAS / SHC-mediated cascade:FGFR1 / FRS-mediated FGFR3 signaling / Signaling by FLT3 ITD and TKD mutants / protein-membrane adaptor activity / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / Signaling by FGFR3 in disease / p38MAPK events / ruffle / Tie2 Signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR2 in disease / GRB2 events in EGFR signaling / SHC1 events in EGFR signaling / EPHB-mediated forward signaling / Signaling by FLT3 fusion proteins / FLT3 Signaling / phosphotyrosine residue binding / Signaling by FGFR1 in disease / myelination / EGFR Transactivation by Gastrin / positive regulation of GTPase activity / NCAM signaling for neurite out-growth / CD209 (DC-SIGN) signaling / positive regulation of MAP kinase activity / GRB2 events in ERBB2 signaling / Downstream signal transduction / Ras activation upon Ca2+ influx through NMDA receptor / SHC1 events in ERBB2 signaling / Insulin receptor signalling cascade / intrinsic apoptotic signaling pathway / GTPase activator activity / Constitutive Signaling by Overexpressed ERBB2 / Signaling by phosphorylated juxtamembrane, extracellular and kinase domain KIT mutants / VEGFR2 mediated cell proliferation / positive regulation of epithelial cell proliferation / small monomeric GTPase / animal organ morphogenesis / regulation of actin cytoskeleton organization / FCERI mediated MAPK activation / positive regulation of JNK cascade / RAF activation / regulation of long-term neuronal synaptic plasticity / Signaling by ERBB2 TMD/JMD mutants / Signaling by high-kinase activity BRAF mutants / Signaling by SCF-KIT / Constitutive Signaling by EGFRvIII / MAP2K and MAPK activation / cellular response to gamma radiation / Signaling by ERBB2 ECD mutants / Signaling by ERBB2 KD Mutants / positive regulation of type II interferon production / positive regulation of fibroblast proliferation / endocytosis / Regulation of RAS by GAPs / RAS processing / chemotaxis
Similarity search - Function
Ras GTPase-activating protein 1, N-terminal SH2 domain / RasGAP, SH3 domain / Ras GTPase-activating protein 1, C-terminal SH2 domain / Ras GTPase-activating protein / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain ...Ras GTPase-activating protein 1, N-terminal SH2 domain / RasGAP, SH3 domain / Ras GTPase-activating protein 1, C-terminal SH2 domain / Ras GTPase-activating protein / Ras GTPase-activating protein, conserved site / Ras GTPase-activating proteins domain signature. / GTPase-activator protein for Ras-like GTPase / Ras GTPase-activating proteins profile. / GTPase-activator protein for Ras-like GTPases / Ras GTPase-activating domain / Rho GTPase activation protein / Protein kinase C conserved region 2 (CalB) / C2 domain / C2 domain / C2 domain profile. / Small GTPase, Ras-type / small GTPase Ras family profile. / PH domain / C2 domain superfamily / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / SH3 domain / Rho (Ras homology) subfamily of Ras-like small GTPases / Ras subfamily of RAS small GTPases / Small GTPase / Ras family / SH2 domain / Rab subfamily of small GTPases / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / SH2 domain superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Small GTP-binding protein domain / PH-like domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
GUANIDINE / GUANOSINE-5'-DIPHOSPHATE / TRIFLUOROMAGNESATE / GTPase HRas / Ras GTPase-activating protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBaumann, P. / Jin, Y.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome Trust218568/Z/19/Z United Kingdom
Wellcome Trust209057/Z/17/Z United Kingdom
CitationJournal: To Be Published
Title: A small G protein with MgF3 TSA complex
Authors: Baumann, P. / Jin, Y.
History
DepositionNov 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 29, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
R: GTPase HRas
G: Ras GTPase-activating protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2646
Polymers56,6562
Non-polymers6084
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-23 kcal/mol
Surface area20950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.832, 41.558, 89.674
Angle α, β, γ (deg.)90.00, 109.25, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules RG

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


Mass: 18875.191 Da / Num. of mol.: 1 / Fragment: GTPase HRAS N-terminally processed
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HRAS, HRAS1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01112, small monomeric GTPase
#2: Protein Ras GTPase-activating protein 1 / GAP / GTPase-activating protein / RasGAP / Ras p21 protein activator / p120GAP


Mass: 37780.793 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RASA1, GAP, RASA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P20936

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Non-polymers , 5 types, 62 molecules

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


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MGF / TRIFLUOROMAGNESATE


Mass: 81.300 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: F3Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-GAI / GUANIDINE


Mass: 59.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH5N3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
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: 2.26 Å3/Da / Density % sol: 45.54 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: precipitant: HEPES-Na 100 mM pH = 8.0, PEG3350 22% (w/v), (NH4)2SO4 20 mM, Gd-HCl 100 mM, NaF 20 mM protein buffer: HRas 0.400 mM, RasGAP 0.400 mM, HEPES-Na 20 mM, NaF 20 mM drop size: 5 uL, ...Details: precipitant: HEPES-Na 100 mM pH = 8.0, PEG3350 22% (w/v), (NH4)2SO4 20 mM, Gd-HCl 100 mM, NaF 20 mM protein buffer: HRas 0.400 mM, RasGAP 0.400 mM, HEPES-Na 20 mM, NaF 20 mM drop size: 5 uL, protein:precipitant ratio: 1:1.2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Mar 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.1→84.66 Å / Num. obs: 16248 / % possible obs: 54.1 % / Redundancy: 3.4 % / CC1/2: 0.981 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.112 / Rrim(I) all: 0.213 / Χ2: 1.51 / Net I/σ(I): 12.6
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.659 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 206 / CC1/2: 0.552 / Rpim(I) all: 0.478 / Rrim(I) all: 0.821

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Cootmodel building
Aimlessdata scaling
MOLREPphasing
xia2data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WQ1

1wq1


Resolution: 2.1→84.66 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.88 / SU B: 7.875 / SU ML: 0.21 / Cross valid method: THROUGHOUT / ESU R Free: 0.37 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27994 791 4.9 %RANDOM
Rwork0.19802 ---
obs0.20217 15452 54.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.913 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å20.04 Å2
2--0.02 Å20 Å2
3---0.18 Å2
Refinement stepCycle: 1 / Resolution: 2.1→84.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3914 0 1 58 3973
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123984
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163707
X-RAY DIFFRACTIONr_angle_refined_deg1.4371.6525376
X-RAY DIFFRACTIONr_angle_other_deg0.461.5618656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2995483
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.693525
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.39810745
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.060.2629
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024411
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02722
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2184.4281941
X-RAY DIFFRACTIONr_mcbond_other3.2054.4291941
X-RAY DIFFRACTIONr_mcangle_it4.9396.6292421
X-RAY DIFFRACTIONr_mcangle_other4.946.6312422
X-RAY DIFFRACTIONr_scbond_it3.5164.7762043
X-RAY DIFFRACTIONr_scbond_other3.5134.7782042
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3817.0312953
X-RAY DIFFRACTIONr_long_range_B_refined7.97156.5194605
X-RAY DIFFRACTIONr_long_range_B_other7.97156.514606
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.212 10 -
Rwork0.215 177 -
obs--8.69 %

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