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- PDB-2a5d: Structural basis for the activation of cholera toxin by human ARF6-GTP -

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Basic information

Entry
Database: PDB / ID: 2a5d
TitleStructural basis for the activation of cholera toxin by human ARF6-GTP
Components
  • ADP-ribosylation factor 6
  • Cholera enterotoxin, A chain
KeywordsPROTEIN TRANSPORT/TRANSFERASE / PROTEIN TRANSPORT-TRANSFERASE complex
Function / homology
Function and homology information


symbiont-mediated activation of host G protein-coupled receptor signal transduction / erythrocyte apoptotic process / maintenance of postsynaptic density structure / protein localization to cleavage furrow / positive regulation of mitotic cytokinetic process / negative regulation of dendrite development / establishment of epithelial cell polarity / regulation of dendritic spine development / regulation of Rac protein signal transduction / protein localization to endosome ...symbiont-mediated activation of host G protein-coupled receptor signal transduction / erythrocyte apoptotic process / maintenance of postsynaptic density structure / protein localization to cleavage furrow / positive regulation of mitotic cytokinetic process / negative regulation of dendrite development / establishment of epithelial cell polarity / regulation of dendritic spine development / regulation of Rac protein signal transduction / protein localization to endosome / negative regulation of protein localization to cell surface / galactose binding / negative regulation of receptor-mediated endocytosis / ruffle assembly / positive regulation of keratinocyte migration / regulation of filopodium assembly / positive regulation of focal adhesion disassembly / MET receptor recycling / endocytic recycling / thioesterase binding / Flemming body / filopodium membrane / TBC/RABGAPs / protein localization to cell surface / cortical actin cytoskeleton organization / positive regulation of tyrosine phosphorylation of STAT protein / hepatocyte apoptotic process / glycosyltransferase activity / positive regulation of actin filament polymerization / cleavage furrow / Transferases; Glycosyltransferases; Pentosyltransferases / endocytic vesicle / synaptic vesicle endocytosis / catalytic complex / regulation of presynapse assembly / vesicle-mediated transport / ruffle / signaling adaptor activity / nucleotidyltransferase activity / small monomeric GTPase / positive regulation of protein secretion / protein localization to plasma membrane / positive regulation of protein localization to plasma membrane / intracellular protein transport / liver development / positive regulation of neuron projection development / cellular response to nerve growth factor stimulus / recycling endosome membrane / GDP binding / nervous system development / presynapse / Clathrin-mediated endocytosis / G protein activity / toxin activity / midbody / early endosome membrane / cell cortex / cell differentiation / periplasmic space / postsynapse / cell adhesion / endosome / cell division / focal adhesion / GTPase activity / lipid binding / GTP binding / glutamatergic synapse / Golgi apparatus / extracellular space / extracellular exosome / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Heat-labile enterotoxin, A chain / Heat-labile enterotoxin alpha chain / ADP-ribosylation factor 6 / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / Small GTPase superfamily, ARF type / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family ...Heat-labile enterotoxin, A chain / Heat-labile enterotoxin alpha chain / ADP-ribosylation factor 6 / Heat-Labile Enterotoxin; Chain A / Heat-Labile Enterotoxin, subunit A / Small GTPase superfamily, ARF type / Small GTPase Arf domain profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleotide triphosphate hydrolases / Alpha-Beta Complex / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-TRIPHOSPHATE / Cholera enterotoxin subunit A / ADP-ribosylation factor 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Vibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsO'Neal, C.J. / Jobling, M.G. / Holmes, R.K. / Hol, W.G.J.
CitationJournal: Science / Year: 2005
Title: Structural basis for the activation of cholera toxin by human ARF6-GTP.
Authors: O'Neal, C.J. / Jobling, M.G. / Holmes, R.K. / Hol, W.G.
History
DepositionJun 30, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / 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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ADP-ribosylation factor 6
B: Cholera enterotoxin, A chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4846
Polymers41,8212
Non-polymers6634
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3310 Å2
ΔGint-40 kcal/mol
Surface area15760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.915, 91.446, 98.547
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is the heterodimer present in the asymmetric unit.

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein ADP-ribosylation factor 6


Mass: 20110.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ARF6 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P62330
#2: Protein Cholera enterotoxin, A chain / NAD(+)--diphthamide ADP-ribosyltransferase / Cholera enterotoxin A subunit


Mass: 21710.779 Da / Num. of mol.: 1 / Fragment: A1 subunit / Mutation: E110D, E112D, C187S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Gene: ctxA, toxA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P01555, NAD+-diphthamide ADP-ribosyltransferase

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Non-polymers , 5 types, 295 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 2.41 Å3/Da / Density % sol: 48.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG2000mme, cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 1, 2004
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 36064 / Num. obs: 36064 / % possible obs: 93.3 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5
Reflection shellResolution: 1.8→1.86 Å / % possible all: 56.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1. mouse ARF1 (1O3Y) 2. CTA1 (1S5E)

1o3y

1s5e


Resolution: 1.8→45.74 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.958 / SU B: 5.246 / SU ML: 0.089 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.118 / ESU R Free: 0.112 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19939 1798 5 %RANDOM
Rwork0.16686 ---
obs0.16855 34206 93.34 %-
all-34206 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 21.063 Å2
Baniso -1Baniso -2Baniso -3
1-0.3 Å20 Å20 Å2
2---0.05 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 1.8→45.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2762 0 40 291 3093
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0212884
X-RAY DIFFRACTIONr_bond_other_d0.0010.022507
X-RAY DIFFRACTIONr_angle_refined_deg2.0251.9553927
X-RAY DIFFRACTIONr_angle_other_deg0.86935800
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1285348
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.83723.217143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.12815439
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0441523
X-RAY DIFFRACTIONr_chiral_restr0.1150.2408
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023244
X-RAY DIFFRACTIONr_gen_planes_other00.02616
X-RAY DIFFRACTIONr_nbd_refined0.2350.3600
X-RAY DIFFRACTIONr_nbd_other0.2190.32638
X-RAY DIFFRACTIONr_nbtor_refined0.190.51425
X-RAY DIFFRACTIONr_nbtor_other0.1010.51562
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2310.5407
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1650.51
X-RAY DIFFRACTIONr_metal_ion_refined0.090.52
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1610.315
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3570.348
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.529
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.57821731
X-RAY DIFFRACTIONr_mcbond_other0.4492718
X-RAY DIFFRACTIONr_mcangle_it2.49532777
X-RAY DIFFRACTIONr_scbond_it1.8721215
X-RAY DIFFRACTIONr_scangle_it2.70831150
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.797→1.844 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 81 -
Rwork0.194 1422 -
obs--54.38 %
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)
11.34661.10260.44583.50061.78252.05540.0515-0.0522-0.14040.19530.0969-0.14610.390.0602-0.1484-0.34780.0183-0.0367-0.23420.0187-0.09837.8833.51729.276
22.52150.54221.12741.01430.55840.73040.1245-0.1701-0.17710.09070.0192-0.21660.04110.0085-0.1438-0.42740.0161-0.0021-0.1555-0.0285-0.053918.42854.91144.185
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA20 - 17420 - 174
2X-RAY DIFFRACTION2BB5 - 1806 - 181

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