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- PDB-2a5g: Cholera toxin A1 subunit bound to ARF6(Q67L) -

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Basic information

Entry
Database: PDB / ID: 2a5g
TitleCholera toxin A1 subunit bound to ARF6(Q67L)
Components
  • ADP-ribosylation factor 6
  • Cholera enterotoxin, A chain
KeywordsPROTEIN TRANSPORT/TRANSFERASE / PROTEIN TRANSPORT-TRANSFERASE complex
Function / homology
Function and homology information


erythrocyte apoptotic process / protein localization to cleavage furrow / maintenance of postsynaptic density structure / positive regulation of mitotic cytokinetic process / regulation of dendritic spine development / galactose binding / establishment of epithelial cell polarity / protein localization to endosome / negative regulation of protein localization to cell surface / negative regulation of dendrite development ...erythrocyte apoptotic process / protein localization to cleavage furrow / maintenance of postsynaptic density structure / positive regulation of mitotic cytokinetic process / regulation of dendritic spine development / galactose binding / establishment of epithelial cell polarity / protein localization to endosome / negative regulation of protein localization to cell surface / negative regulation of dendrite development / negative regulation of receptor-mediated endocytosis / regulation of Rac protein signal transduction / ruffle assembly / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / regulation of filopodium assembly / MET receptor recycling / thioesterase binding / endocytic recycling / filopodium membrane / Flemming body / protein localization to cell surface / TBC/RABGAPs / cortical actin cytoskeleton organization / positive regulation of actin filament polymerization / glycosyltransferase activity / hepatocyte apoptotic process / cleavage furrow / regulation of presynapse assembly / synaptic vesicle endocytosis / catalytic complex / Transferases; Glycosyltransferases; Pentosyltransferases / endocytic vesicle / localization / signaling adaptor activity / vesicle-mediated transport / positive regulation of tyrosine phosphorylation of STAT protein / ruffle / nucleotidyltransferase activity / small monomeric GTPase / cellular response to nerve growth factor stimulus / G protein activity / liver development / protein localization to plasma membrane / positive regulation of protein secretion / positive regulation of protein localization to plasma membrane / intracellular protein transport / positive regulation of neuron projection development / recycling endosome membrane / GDP binding / presynapse / Clathrin-mediated endocytosis / nervous system development / cell cortex / midbody / early endosome membrane / toxin activity / postsynapse / periplasmic space / cell differentiation / cell adhesion / endosome / cell cycle / cell division / focal adhesion / GTPase activity / glutamatergic synapse / lipid binding / GTP binding / Golgi apparatus / extracellular space / extracellular exosome / membrane / plasma membrane / 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 Arf family 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 ...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 Arf family 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 / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 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: 2.66 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 1.4Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.5Apr 3, 2024Group: Refinement description / Category: 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)42,3765
Polymers41,8062
Non-polymers5703
Water1,18966
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2850 Å2
ΔGint-41 kcal/mol
Surface area15730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.067, 44.484, 56.045
Angle α, β, γ (deg.)107.38, 101.72, 102.94
Int Tables number1
Space group name H-MP1
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: 20095.195 Da / Num. of mol.: 1 / Mutation: Q67L
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


Mass: 21710.779 Da / Num. of mol.: 1 / Fragment: Cholera toxin 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 , 4 types, 69 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 66 / 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: 2.01 Å3/Da / Density % sol: 38.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: PEG 2000mme, cacodylate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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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: 2.66→50 Å / Num. all: 8923 / Num. obs: 8923 / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5
Reflection shellResolution: 2.66→2.8 Å / % possible all: 75.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CTA1:ARF6-GTP

Resolution: 2.66→18.52 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.874 / SU B: 26.611 / SU ML: 0.3 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.421 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26519 417 4.7 %RANDOM
Rwork0.19912 ---
obs0.20217 8477 94.87 %-
all-8477 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 4.094 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0.2 Å2-0.24 Å2
2--0.2 Å20.37 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2.66→18.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2717 0 34 66 2817
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0212822
X-RAY DIFFRACTIONr_bond_other_d0.0010.022448
X-RAY DIFFRACTIONr_angle_refined_deg0.7171.9563847
X-RAY DIFFRACTIONr_angle_other_deg0.55935656
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5065344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.73423.358137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.09915422
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8231521
X-RAY DIFFRACTIONr_chiral_restr0.0430.2404
X-RAY DIFFRACTIONr_gen_planes_refined0.0010.023183
X-RAY DIFFRACTIONr_gen_planes_other00.02595
X-RAY DIFFRACTIONr_nbd_refined0.1940.3579
X-RAY DIFFRACTIONr_nbd_other0.1850.32719
X-RAY DIFFRACTIONr_nbtor_refined0.1840.51407
X-RAY DIFFRACTIONr_nbtor_other0.0810.51635
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1940.5162
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1060.51
X-RAY DIFFRACTIONr_metal_ion_refined0.0660.53
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1050.318
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1510.346
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.57
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.28921715
X-RAY DIFFRACTIONr_mcbond_other0.0182710
X-RAY DIFFRACTIONr_mcangle_it0.5232745
X-RAY DIFFRACTIONr_scbond_it0.09921171
X-RAY DIFFRACTIONr_scangle_it0.17631102
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.66→2.728 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.425 15 -
Rwork0.364 435 -
obs--64.56 %
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)
12.1255-0.1570.04711.3169-0.00583.0928-0.08880.0199-0.00950.0480.0464-0.1086-0.02410.03820.04240.3250.10240.12090.4164-0.10360.36184.559-4.3212.451
21.2194-0.3906-0.08162.5861-0.0481.787-0.1036-0.0219-0.00160.09740.08260.0283-0.0406-0.02290.0210.3680.06650.09690.3767-0.10080.3253-4.3993.819-12.336
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA16 - 17316 - 173
2X-RAY DIFFRACTION2BB1 - 462 - 47
3X-RAY DIFFRACTION2BB57 - 18758 - 188

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