Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 46.49 kDa 
• Atom Count: 3278 
• Modelled Residue Count: 377 
• Deposited Residue Count: 410 
• Unique protein chains: 2

2A9K

Crystal structure of the C3bot-NAD-RalA complex reveals a novel type of action of a bacterial exoenzyme

• PDB DOI: 10.2210/pdb2A9K/pdb

• Classification: PROTEIN BINDING/TRANSFERASE
• Organism(s): Homo sapiens, Clostridium botulinum D phage
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2005-07-12 Released: 2005-10-11 
• Deposition Author(s): Pautsch, A., Vogelsgesang, M., Trankle, J., Herrmann, C., Aktories, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.225 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Literature

Crystal structure of the C3bot-RalA complex reveals a novel type of action of a bacterial exoenzyme.

Pautsch, A., Vogelsgesang, M., Trankle, J., Herrmann, C., Aktories, K.

(2005) EMBO J 24: 3670-3680

• PubMed: 16177825 
• DOI: 10.1038/sj.emboj.7600813
• Primary Citation of Related Structures:  
  2A78, 2A9K


• PubMed Abstract: 
  

C3 exoenzymes from bacterial pathogens ADP-ribosylate and inactivate low-molecular-mass GTPases of the Rho subfamily. Ral, a Ras subfamily GTPase, binds the C3 exoenzymes from Clostridium botulinum and C. limosum with high affinity without being a substrate for ADP ribosylation. In the complex, the ADP-ribosyltransferase activity of C3 is blocked, while binding of NAD and NAD-glycohydrolase activity remain. Here we report the crystal structure of C3 from C. botulinum in a complex with GDP-bound RalA at 1.8 A resolution. C3 binds RalA with a helix-loop-helix motif that is adjacent to the active site. A quaternary complex with NAD suggests a mode for ADP-ribosyltransferase inhibition. Interaction of C3 with RalA occurs at a unique interface formed by the switch-II region, helix alpha3 and the P loop of the GTPase. C3-binding stabilizes the GDP-bound conformation of RalA and blocks nucleotide release. Our data indicate that C. botulinum exoenzyme C3 is a single-domain toxin with bifunctional properties targeting Rho GTPases by ADP ribosylation and Ral by a guanine nucleotide dissociation inhibitor-like effect, which blocks nucleotide exchange.

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Related Citations: 

• Molecular recognition of an ADP-ribosylating Clostridium botulinum C3 exoenzyme by RalA GTPase.
  Holbourn, K.P., Sutton, J.M., Evans, H.R., Shone, C.C., Acharya, K.R.
  (2005) Proc Natl Acad Sci U S A 102: 5357

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Organizational Affiliation: 

Structural Research, Department of Integrated Lead Discovery, Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ras-related protein Ral-A	A	187	Homo sapiens	Mutation(s): 0  Gene Names: RALA, RAL EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P11233 (Homo sapiens) Explore P11233  Go to UniProtKB:  P11233
PHAROS:  P11233 GTEx:  ENSG00000006451

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mono-ADP-ribosyltransferase C3	B	223	Clostridium botulinum D phage	Mutation(s): 0  Gene Names: C3 EC: 2.4.2
UniProt
Find proteins for P15879 (Clostridium botulinum D phage) Explore P15879  Go to UniProtKB:  P15879

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth B]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
GDP	D [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.73 Å
• R-Value Free: 0.225 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.26	α = 90
b = 113.85	β = 106.4
c = 56.31	γ = 90

Software Package:

Software Name	Purpose
MAR345	data collection
XDS	data reduction
MOLREP	phasing
REFMAC	refinement
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-07-12 
• Released Date: 2005-10-11 
Deposition Author(s): Pautsch, A., Vogelsgesang, M., Trankle, J., Herrmann, C., Aktories, K.

Revision History  

• Version 1.0: 2005-10-11
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description