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- PDB-2a9k: Crystal structure of the C3bot-NAD-RalA complex reveals a novel t... -

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Basic information

Entry
Database: PDB / ID: 2a9k
TitleCrystal structure of the C3bot-NAD-RalA complex reveals a novel type of action of a bacterial exoenzyme
Components
  • Mono-ADP-ribosyltransferase C3
  • Ras-related protein Ral-A
KeywordsPROTEIN BINDING/TRANSFERASE / Exoenzyme C3 / bacterial ADP-ribosyltransferase / RAL / RHO / GDP-binding / PROTEIN BINDING-TRANSFERASE COMPLEX
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 / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Ras-related protein Ral-A / Mono-ADP-ribosyltransferase C3
Similarity search - Component
Biological speciesHomo sapiens (human)
Clostridium botulinum D phage (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.73 Å
AuthorsPautsch, A. / Vogelsgesang, M. / Trankle, J. / Herrmann, C. / Aktories, K.
Citation
Journal: Embo J. / Year: 2005
Title: Crystal structure of the C3bot-RalA complex reveals a novel type of action of a bacterial exoenzyme.
Authors: Pautsch, A. / Vogelsgesang, M. / Trankle, J. / Herrmann, C. / Aktories, K.
#1: Journal: 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
DepositionJul 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 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 11, 2017Group: Refinement description / Category: software
Revision 1.4Aug 23, 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 / 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 / _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

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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)46,4895
Polymers45,3582
Non-polymers1,1313
Water3,783210
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)35.260, 113.850, 56.310
Angle α, β, γ (deg.)90.00, 106.40, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Ras-related protein Ral-A


Mass: 20895.238 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RALA, RAL / Plasmid: PGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P11233
#2: Protein Mono-ADP-ribosyltransferase C3 / Exoenzyme C3


Mass: 24462.840 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium botulinum D phage (virus) / Species: Clostridium phage c-st / Gene: C3 / Plasmid: PGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
References: UniProt: P15879, Transferases; Glycosyltransferases; Pentosyltransferases

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Non-polymers , 4 types, 213 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: 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
#5: 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
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / 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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 M ammonium citrate pH 7.0, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 30, 2004 / Details: OSMIC BLUE
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.73→20 Å / Num. all: 40078 / Num. obs: 40078 / % possible obs: 90.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.9 % / Rsym value: 0.049 / Net I/σ(I): 13.2
Reflection shellResolution: 1.73→1.83 Å / Mean I/σ(I) obs: 3.6 / Rsym value: 0.239 / % possible all: 62.6

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Processing

Software
NameVersionClassification
MAR345data collection
XDSdata reduction
MOLREPphasing
REFMAC5.2.0005refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G24, 1UAD

1g24

1uad


Resolution: 1.73→19.03 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.808 / SU ML: 0.082 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22465 2004 5 %RANDOM
Rwork0.18648 ---
all0.18834 40077 --
obs0.18834 38073 100 %-
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: 21.023 Å2
Baniso -1Baniso -2Baniso -3
1--0.79 Å20 Å20.42 Å2
2---0.42 Å20 Å2
3---1.45 Å2
Refinement stepCycle: LAST / Resolution: 1.73→19.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2995 0 73 210 3278
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0223122
X-RAY DIFFRACTIONr_angle_refined_deg1.111.994211
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2025375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.0924.966147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.67715572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5031517
X-RAY DIFFRACTIONr_chiral_restr0.0770.2459
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022316
X-RAY DIFFRACTIONr_nbd_refined0.1910.21430
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22142
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1860.2229
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.234
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1050.214
X-RAY DIFFRACTIONr_mcbond_it0.4851.51935
X-RAY DIFFRACTIONr_mcangle_it0.81623004
X-RAY DIFFRACTIONr_scbond_it1.29131358
X-RAY DIFFRACTIONr_scangle_it2.084.51207
LS refinement shellResolution: 1.73→1.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 87 -
Rwork0.287 1652 -
obs--100 %
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)
10.882-0.107-0.01511.2407-0.0860.6421-0.00390.0656-0.0862-0.0198-0.02430.0138-0.026-0.00090.0282-0.03690.0053-0.0086-0.0114-0.0015-0.059212.45130.1977.2727
20.41980.0034-0.05850.560.14150.79830.018-0.04390.0304-0.0168-0.03560.0336-0.01340.01590.0176-0.031-0.0043-0.0081-0.0221-0.0035-0.045.111725.254727.9962
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA13 - 18017 - 184
2X-RAY DIFFRACTION2BB45 - 25117 - 223

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