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- PDB-1he1: Crystal structure of the complex between the GAP domain of the Ps... -

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Basic information

Entry
Database: PDB / ID: 1he1
TitleCrystal structure of the complex between the GAP domain of the Pseudomonas aeruginosa ExoS toxin and human Rac
Components
  • EXOENZYME S
  • RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
KeywordsSIGNALING PROTEIN / SIGNALLING COMPLEX / EXOS / RAC / PSEUDOMONAS AERUGINOSA / GAP / TOXIN / VIRULENCE FACTOR / TRANSITION STATE / PROTEIN-PROTEIN COMPLEX / GTPASE / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


regulation of respiratory burst / regulation of neutrophil migration / localization within membrane / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / engulfment of apoptotic cell ...regulation of respiratory burst / regulation of neutrophil migration / localization within membrane / negative regulation of interleukin-23 production / Activated NTRK2 signals through CDK5 / negative regulation of receptor-mediated endocytosis / regulation of hydrogen peroxide metabolic process / ruffle assembly / NTRK2 activates RAC1 / engulfment of apoptotic cell / Inactivation of CDC42 and RAC1 / NADPH oxidase complex / respiratory burst / cortical cytoskeleton organization / WNT5:FZD7-mediated leishmania damping / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / hepatocyte growth factor receptor signaling pathway / ruffle organization / Nef and signal transduction / regulation of stress fiber assembly / thioesterase binding / cell projection assembly / negative regulation of fibroblast migration / RHO GTPases activate CIT / sphingosine-1-phosphate receptor signaling pathway / RHO GTPases activate KTN1 / regulation of nitric oxide biosynthetic process / motor neuron axon guidance / PCP/CE pathway / Activation of RAC1 / positive regulation of neutrophil chemotaxis / regulation of lamellipodium assembly / Azathioprine ADME / MET activates RAP1 and RAC1 / DCC mediated attractive signaling / positive regulation of cell-substrate adhesion / Sema4D mediated inhibition of cell attachment and migration / CD28 dependent Vav1 pathway / Ephrin signaling / Wnt signaling pathway, planar cell polarity pathway / lamellipodium assembly / NRAGE signals death through JNK / positive regulation of Rho protein signal transduction / small GTPase-mediated signal transduction / regulation of cell size / Rho GDP-dissociation inhibitor binding / Activation of RAC1 downstream of NMDARs / establishment or maintenance of cell polarity / Rac protein signal transduction / glycosyltransferase activity / RHO GTPases activate PAKs / positive regulation of focal adhesion assembly / Sema3A PAK dependent Axon repulsion / semaphorin-plexin signaling pathway / ficolin-1-rich granule membrane / RHO GTPases Activate NADPH Oxidases / EPH-ephrin mediated repulsion of cells / anatomical structure morphogenesis / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / positive regulation of lamellipodium assembly / PTK6 Regulates RHO GTPases, RAS GTPase and MAP kinases / positive regulation of substrate adhesion-dependent cell spreading / RHO GTPases activate PKNs / GPVI-mediated activation cascade / positive regulation of stress fiber assembly / positive regulation of microtubule polymerization / EPHB-mediated forward signaling / RAC1 GTPase cycle / regulation of cell migration / actin filament polymerization / nucleotidyltransferase activity / positive regulation of endothelial cell migration / cell-matrix adhesion / GTPase activator activity / substrate adhesion-dependent cell spreading / cell chemotaxis / secretory granule membrane / small monomeric GTPase / VEGFR2 mediated vascular permeability / Signal transduction by L1 / cell projection / actin filament organization / cell motility / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of actin cytoskeleton organization / RHO GTPases Activate Formins / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / neuron migration / trans-Golgi network / MAPK6/MAPK4 signaling / Signaling by SCF-KIT / G protein activity / Regulation of actin dynamics for phagocytic cup formation / VEGFA-VEGFR2 Pathway / ruffle membrane / response to wounding / cytoplasmic ribonucleoprotein granule / recycling endosome membrane
Similarity search - Function
Virulence factor YopE uncharacterised domain / Type III secretion system effector protein YopE-like / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) / : / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Small GTPase Rho ...Virulence factor YopE uncharacterised domain / Type III secretion system effector protein YopE-like / Virulence factor YopE, GAP domain / Virulence factor YopE, GAP domain superfamily / Yersinia virulence determinant (YopE) / : / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Small GTPase Rho / small GTPase Rho family profile. / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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 / Up-down Bundle / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / NICKEL (II) ION / Ras-related C3 botulinum toxin substrate 1 / Ras-related C3 botulinum toxin substrate 1 / Exoenzyme S
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsWurtele, M. / Wolf, E. / Pederson, K.J. / Buchwald, G. / Ahmadian, M.R. / Barbieri, J.T. / Wittinghofer, A.
CitationJournal: Nat.Struct.Biol. / Year: 2001
Title: How the Pseudomonas Aeruginosa Exos Toxin Downregulates Rac
Authors: Wurtele, M. / Wolf, E. / Pederson, K.J. / Buchwald, G. / Ahmadian, M.R. / Barbieri, J.T. / Wittinghofer, A.
History
DepositionNov 18, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 2, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 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_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.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_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.pdbx_ptnr2_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_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 / _struct_conn.ptnr2_label_seq_id / _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: EXOENZYME S
B: EXOENZYME S
C: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
D: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,98714
Polymers67,6494
Non-polymers1,33810
Water12,827712
1
A: EXOENZYME S
C: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5528
Polymers33,8252
Non-polymers7286
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2640 Å2
ΔGint-14.3 kcal/mol
Surface area17000 Å2
MethodPQS
2
B: EXOENZYME S
D: RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4356
Polymers33,8252
Non-polymers6104
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2550 Å2
ΔGint-12.8 kcal/mol
Surface area16540 Å2
MethodPQS
Unit cell
Length a, b, c (Å)46.025, 125.087, 136.284
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.117, 0.8492, 0.5149), (0.8602, -0.1725, 0.48), (0.4964, 0.499, -0.7103)
Vector: -49.9088, 25.6622, 43.1668)

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein EXOENZYME S / EXOS


Mass: 14261.152 Da / Num. of mol.: 2 / Fragment: 96-234, GTPASE-ACTIVATING PROTEIN (GAP-DOMAIN)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Gene: EXOS / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q51451
#2: Protein RAS-RELATED C3 BOTULINUM TOXIN SUBSTRATE 1 / P21-RAC1 / RAS-LIKE PROTEIN TC25


Mass: 19563.525 Da / Num. of mol.: 2 / Fragment: 2-184
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P15154, UniProt: P63000*PLUS

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Non-polymers , 5 types, 722 molecules

#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE


Mass: 83.977 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: AlF3
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 712 / 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: 2.65 Å3/Da / Density % sol: 40 %
Crystal growpH: 8.5
Details: 8% PEG 6000, 3MM NICL2, 100 MM TRIS/HCL PH8.5, pH 8.50
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion, hanging drop / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
11 mM1dropMgCl2
220 mM1dropNaF
33 mMDTE1drop
430 mMTris-HCl1drop
520 mg/mlprotain1drop
68 %(w/v)PEG60001reservoir
73 mM1reservoirNiCl2
8100 mMTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 527331 / % possible obs: 99.5 % / Observed criterion σ(I): 3 / Redundancy: 9.8 % / Biso Wilson estimate: 15.7 Å2 / Rsym value: 0.065 / Net I/σ(I): 21.3
Reflection shellResolution: 2→2.07 Å / Mean I/σ(I) obs: 4.9 / Rsym value: 0.285 / % possible all: 99.9
Reflection
*PLUS
Num. obs: 53976 / Num. measured all: 527331 / Rmerge(I) obs: 0.065
Reflection shell
*PLUS
% possible obs: 99.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.285

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DS6 CHAIN A

1ds6


Resolution: 2→29.92 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 2288865.96 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.224 2739 5.1 %RANDOM
Rwork0.175 ---
obs0.175 53886 99.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.2816 Å2 / ksol: 0.372576 e/Å3
Displacement parametersBiso mean: 26.5 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20 Å20 Å2
2--0.68 Å20 Å2
3----2.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.11 Å
Refinement stepCycle: LAST / Resolution: 2→29.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4742 0 70 712 5524
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d21.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it1.962
X-RAY DIFFRACTIONc_scbond_it2.292
X-RAY DIFFRACTIONc_scangle_it3.432.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.252 439 5 %
Rwork0.195 8396 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GDP.PARGDP.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 30 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0077
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91

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