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- PDB-2bov: Molecular recognition of an ADP-ribosylating Clostridium botulinu... -

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Basic information

Entry
Database: PDB / ID: 2bov
TitleMolecular recognition of an ADP-ribosylating Clostridium botulinum C3 exoenzyme by RalA GTPase
Components
  • MONO-ADP-RIBOSYLTRANSFERASE C3
  • RAS-RELATED PROTEIN RAL-A
KeywordsTRANSFERASE / C3BOT / EXOENZYME / RALA / GTPASE / ADP / RIBOSYLATING TOXIN / GTP-BINDING / LIPOPROTEIN / PRENYLATION / GLYCOSYLTRANSFERASE / NAD
Function / homology
Function and homology information


membrane raft localization / Edg-2 lysophosphatidic acid receptor binding / establishment of protein localization to mitochondrion / regulation of exocytosis / Flemming body / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of filopodium assembly / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of mitochondrial fission / myosin binding ...membrane raft localization / Edg-2 lysophosphatidic acid receptor binding / establishment of protein localization to mitochondrion / regulation of exocytosis / Flemming body / regulation of postsynaptic neurotransmitter receptor internalization / positive regulation of filopodium assembly / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of mitochondrial fission / myosin binding / exocytosis / NAD+-protein ADP-ribosyltransferase activity / cleavage furrow / Transferases; Glycosyltransferases; Pentosyltransferases / p38MAPK events / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / nucleotidyltransferase activity / small monomeric GTPase / G protein activity / synaptic membrane / neural tube closure / Translocation of SLC2A4 (GLUT4) to the plasma membrane / regulation of actin cytoskeleton organization / Schaffer collateral - CA1 synapse / cytoplasmic vesicle membrane / receptor internalization / GDP binding / chemotaxis / ATPase binding / Ras protein signal transduction / cell cycle / cell division / focal adhesion / GTPase activity / ubiquitin protein ligase binding / GTP binding / cell surface / signal transduction / mitochondrion / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Mono-ADP-ribosyltransferase C3/Edin / Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / Rho (Ras homology) subfamily of Ras-like small GTPases ...Mono-ADP-ribosyltransferase C3/Edin / Toxin ADP-ribosyltransferase; Chain A, domain 1 / Toxin ADP-ribosyltransferase; Chain A, domain 1 / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / Small GTPase, Ras-type / small GTPase Ras family profile. / Ran (Ras-related nuclear proteins) /TC4 subfamily of small GTPases / 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 / Alpha-Beta Complex / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / Ras-related protein Ral-A / Mono-ADP-ribosyltransferase C3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
CLOSTRIDIUM BOTULINUM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.66 Å
AuthorsHolbourn, K.P. / Sutton, J.M. / Evans, H.R. / Shone, C.C. / Acharya, K.R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Molecular Recognition of an Adp-Ribosylating Clostridium Botulinum C3 Exoenzyme by Rala Gtpase
Authors: Holbourn, K.P. / Sutton, J.M. / Evans, H.R. / Shone, C.C. / Acharya, K.R.
History
DepositionApr 14, 2005Deposition site: PDBE / Processing site: PDBE
SupersessionApr 15, 2005ID: 1WCA
Revision 1.0Apr 15, 2005Provider: 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 / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RAS-RELATED PROTEIN RAL-A
B: MONO-ADP-RIBOSYLTRANSFERASE C3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9494
Polymers51,4812
Non-polymers4682
Water4,702261
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)56.629, 90.836, 100.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RAS-RELATED PROTEIN RAL-A / RALA


Mass: 23603.846 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-2T / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109 / References: UniProt: P11233
#2: Protein MONO-ADP-RIBOSYLTRANSFERASE C3 / C3BOT1 EXOENZYME / EXOENZYME C3


Mass: 27877.172 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CLOSTRIDIUM BOTULINUM (bacteria) / Plasmid: PMAL / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): JM109
References: UniProt: P15879, Transferases; Glycosyltransferases; Pentosyltransferases
#3: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 261 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: ADP-RIBOSYLATION IN EUKARYOTIC RHO AND RAC PROTEINS ON AN ASPARAGINE RESIDUE

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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: 2.7 Å3/Da / Density % sol: 54 %
Crystal growpH: 7.3
Details: 0.1M HEPES PH 7.3 12-15% ETHYLENE GLYCOL 14-18% PEG 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 22, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 2.66→50 Å / Num. obs: 15556 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 15.6 % / Biso Wilson estimate: 27.2 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 14.6
Reflection shellResolution: 2.66→2.76 Å / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 5.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
CNS1refinement
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1G24 AND 1UAD

1g24

1uad


Resolution: 2.66→50 Å / Rfactor Rfree error: 0.009 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.274 915 5.9 %RANDOM
Rwork0.206 ---
obs0.206 15430 99.8 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.3303 Å2 / ksol: 0.375286 e/Å3
Displacement parametersBiso mean: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å20 Å20 Å2
2---1.44 Å20 Å2
3---2.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.31 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.66→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3024 0 29 261 3314
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.66→2.83 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.312 151 6 %
Rwork0.213 2385 -
obs--100 %

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