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- PDB-2a78: Crystal structure of the C3bot-RalA complex reveals a novel type ... -

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Basic information

Entry
Database: PDB / ID: 2a78
TitleCrystal structure of the C3bot-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 / positive regulation of filopodium assembly / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of mitochondrial fission / regulation of postsynaptic neurotransmitter receptor internalization / myosin binding ...membrane raft localization / Edg-2 lysophosphatidic acid receptor binding / establishment of protein localization to mitochondrion / regulation of exocytosis / Flemming body / positive regulation of filopodium assembly / positive regulation of epidermal growth factor receptor signaling pathway / positive regulation of mitochondrial fission / regulation of postsynaptic neurotransmitter receptor internalization / myosin binding / NAD+-protein mono-ADP-ribosyltransferase activity / exocytosis / cleavage furrow / Transferases; Glycosyltransferases; Pentosyltransferases / p38MAPK events / nucleotidyltransferase activity / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / cytoplasmic vesicle membrane / synaptic membrane / small monomeric GTPase / regulation of actin cytoskeleton organization / neural tube closure / Translocation of SLC2A4 (GLUT4) to the plasma membrane / receptor internalization / Schaffer collateral - CA1 synapse / chemotaxis / GDP binding / G protein activity / ATPase binding / Ras protein signal transduction / 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 domain 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 domain 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 / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 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 D phage (virus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.81 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 5, 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 / Item: _software.classification / _software.name
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 / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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)45,8264
Polymers45,3582
Non-polymers4682
Water5,945330
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.940, 112.830, 56.350
Angle α, β, γ (deg.)90.00, 105.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#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
#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


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 330 / 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: 5.5
Details: 0.2 M ammonium sulfate, 0.1 M bis-Tris, 25% w/v polyethylene glycol 3350, pH 5.5, 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 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 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: 1.8→20 Å / Num. all: 39025 / Num. obs: 35816 / % possible obs: 91.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 22.3 Å2 / Rsym value: 0.059 / Net I/σ(I): 11.8
Reflection shellResolution: 1.8→1.91 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 3978 / Rsym value: 0.345 / % possible all: 62.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
PDB_EXTRACT1.601data extraction
MAR345data collection
XDSdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1G24, 1UAD

1g24

1uad


Resolution: 1.81→19.57 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 5.338 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.134 / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.217 1791 5 %RANDOM
Rwork0.18 ---
all0.182 35815 --
obs0.182 34024 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: 17.49 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20.46 Å2
2--0.09 Å20 Å2
3---0.7 Å2
Refinement stepCycle: LAST / Resolution: 1.81→19.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2995 0 29 330 3354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0223074
X-RAY DIFFRACTIONr_angle_refined_deg1.0481.9724138
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7695375
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.53324.966147
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.99515572
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0841517
X-RAY DIFFRACTIONr_chiral_restr0.0730.2451
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022295
X-RAY DIFFRACTIONr_nbd_refined0.1930.21693
X-RAY DIFFRACTIONr_nbtor_refined0.3050.22131
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2363
X-RAY DIFFRACTIONr_metal_ion_refined0.0160.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.253
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1060.220
X-RAY DIFFRACTIONr_mcbond_it0.4991.51922
X-RAY DIFFRACTIONr_mcangle_it0.88623004
X-RAY DIFFRACTIONr_scbond_it1.39831306
X-RAY DIFFRACTIONr_scangle_it2.2574.51134
LS refinement shellResolution: 1.806→1.852 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 79 -
Rwork0.313 1509 -
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)
10.9027-0.1757-0.03731.2677-0.13610.75160.01680.04-0.086-0.0334-0.02840.0158-0.0027-0.0070.0116-0.05150.0025-0.003-0.0309-0.009-0.031512.91420.22297.6387
20.4038-0.0821-0.0170.59920.31281.10390.0141-0.04950.0228-0.0102-0.03810.0539-0.0140.01310.024-0.0506-0.0045-0.0014-0.0304-0.0009-0.02225.665425.053628.3452
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA13 - 18017 - 184
22BB45 - 25117 - 223

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