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- PDB-2a5f: Cholera toxin A1 subunit bound to its substrate, NAD+, and its hu... -

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Basic information

Entry
Database: PDB / ID: 2a5f
TitleCholera toxin A1 subunit bound to its substrate, NAD+, and its human protein activator, ARF6
Components
  • ADP-ribosylation factor 6ARF6
  • Cholera enterotoxin, A chain
KeywordsPROTEIN TRANSPORT/TRANSFERASE / PROTEIN TRANSPORT-TRANSFERASE complex
Function / homology
Function and homology information


erythrocyte apoptotic process / maintenance of postsynaptic density structure / regulation of dendritic spine development / establishment of epithelial cell polarity / galactose binding / negative regulation of receptor-mediated endocytosis / protein localization to endosome / negative regulation of dendrite development / ruffle assembly / negative regulation of protein localization to cell surface ...erythrocyte apoptotic process / maintenance of postsynaptic density structure / regulation of dendritic spine development / establishment of epithelial cell polarity / galactose binding / negative regulation of receptor-mediated endocytosis / protein localization to endosome / negative regulation of dendrite development / ruffle assembly / negative regulation of protein localization to cell surface / regulation of Rac protein signal transduction / positive regulation of keratinocyte migration / positive regulation of focal adhesion disassembly / regulation of filopodium assembly / endocytic recycling / thioesterase binding / MET receptor recycling / filopodium membrane / protein localization to cell surface / Flemming body / TBC/RABGAPs / cortical actin cytoskeleton organization / positive regulation of actin filament polymerization / hepatocyte apoptotic process / glycosyltransferase activity / cleavage furrow / regulation of presynapse assembly / synaptic vesicle endocytosis / endocytic vesicle / Transferases; Glycosyltransferases; Pentosyltransferases / catalytic complex / localization / signaling adaptor activity / positive regulation of tyrosine phosphorylation of STAT protein / vesicle-mediated transport / ruffle / nucleotidyltransferase activity / cellular response to nerve growth factor stimulus / small monomeric GTPase / 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 / toxin activity / early endosome membrane / postsynapse / cell differentiation / periplasmic space / 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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Cholera enterotoxin subunit A / ADP-ribosylation factor 6
Similarity search - Component
Biological speciesHomo sapiens (human)
Vibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Isomorphous replacement / Resolution: 2.02 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: Non-polymer description / Version format compliance
Revision 1.3Nov 30, 2016Group: Other
Revision 1.4Oct 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 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6Apr 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)43,1477
Polymers41,8212
Non-polymers1,3265
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4350 Å2
ΔGint-46 kcal/mol
Surface area15650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.905, 90.925, 98.001
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 / ARF6


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: 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 , 6 types, 174 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 / Guanosine 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-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 169 / 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: 2.38 Å3/Da / Density % sol: 47.9 %
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: APS / Beamline: 32-ID / Wavelength: 0.97943 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Nov 8, 2004
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97943 Å / Relative weight: 1
ReflectionResolution: 2.02→50 Å / Num. all: 25861 / Num. obs: 25861 / % possible obs: 97.5 % / Observed criterion σ(F): 1.5 / Observed criterion σ(I): 1.5
Reflection shellResolution: 2.02→2.09 Å / % possible all: 81.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
HKL-2000data reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: Isomorphous replacement
Starting model: CTA1:ARF6-GTP

Resolution: 2.02→43.15 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.622 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.181 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23075 1329 5.1 %RANDOM
Rwork0.18114 ---
all0.233 24930 --
obs0.18369 24930 96.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 36.241 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.04 Å20 Å2
3---0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.02→43.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2740 0 84 169 2993
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0212901
X-RAY DIFFRACTIONr_bond_other_d0.0010.022497
X-RAY DIFFRACTIONr_angle_refined_deg1.5611.9753963
X-RAY DIFFRACTIONr_angle_other_deg0.77335774
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5465345
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.04123.214140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16815427
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1621522
X-RAY DIFFRACTIONr_chiral_restr0.090.2416
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023231
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02609
X-RAY DIFFRACTIONr_nbd_refined0.2140.3575
X-RAY DIFFRACTIONr_nbd_other0.2060.32530
X-RAY DIFFRACTIONr_nbtor_refined0.1890.51404
X-RAY DIFFRACTIONr_nbtor_other0.090.51577
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.5269
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0750.51
X-RAY DIFFRACTIONr_metal_ion_refined0.0820.52
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1220.35
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2970.349
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2410.515
X-RAY DIFFRACTIONr_mcbond_it1.43821718
X-RAY DIFFRACTIONr_mcbond_other0.2852711
X-RAY DIFFRACTIONr_mcangle_it2.42132760
X-RAY DIFFRACTIONr_scbond_it1.39921250
X-RAY DIFFRACTIONr_scangle_it2.16931203
LS refinement shellResolution: 2.018→2.071 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.287 59 -
Rwork0.259 1354 -
obs--71.54 %

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