1RCV	Toxin	date	Nov 04, 2003
title	Cholera Toxin B-Pentamer Complexed With Bivalent Nitrophenol-Galactoside Ligand Bv1
authors	J.C.Pickens, D.D.Mitchell, J.Liu, X.Tan, Z.Zhang, C.L.Verlinde, W.G.Hol, E.Fan
compound		source
Molecule: Cholera Toxin B Protein (Ctb) Chain: D, E, F, G, H Engineered: Yes		Organism_scientific: Vibrio Cholerae Organism_common: Bacteria Gene: Ctxb Expression_system: Escherichia Coli Expression_system_common: Bacteria Expression_system_strain: Top10 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pbad
symmetry	Space Group: C 1 2 1	R_factor	0.164
crystal cell	length a length b length c angle alpha angle beta angle gamma 101.829 66.133 77.771 90.00 105.62 90.00
method	X-Ray Diffraction	resolution	1.60 Å
ligand	BV1	enzyme
similarity	Belongs to the Enterotoxin_b family.
subunit	The a subunit contains two chains, a1 and a2, linked by a disulfide bridge. The holotoxin (choleragen) consists of a pentameric ring of b subunits whose central pore is occupied by the a subunit.
gene	ctxB (V. cholerae)
function	It can bind five gm1 gangliosides. The b subunit pentameric ring directs the a subunit to its target by binding to the gm1 gangliosides present on the surface of the intestinal epithelial cells. It has no toxic activity by itself.
Gene Ontology	Chain Function Process Component H, F, D, G, E pathogenesis extracellular region membrane
Primary reference	Nonspanning bivalent ligands as improved surface receptor binding inhibitors of the cholera toxin B pentamer., Pickens JC, Mitchell DD, Liu J, Tan X, Zhang Z, Verlinde CL, Hol WG, Fan E, Chem Biol 2004 Sep;11(9):1205-15. PMID:15380181

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (110 Kb) [Save to disk] Biological Unit Coordinates (1rcv.pdb1.gz) 95 Kb CSU: Contacts of Structural Units for 1RCV Likely Quarternary Molecular Structure file(s) for 1RCV Structure Factors (653 Kb) Retrieve 1RCV in mmCIF format [Save to disk]

View 1RCV in 3D

On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

Visual 3D analysis of 1RCV

Protein Explorer, Easier to use and more powerful than RasMol. (Win and Mac only) Noncovalent Bond Finder displays the closest contacts to ligand or interface, reports distances, walks over water bridges. STING, shows the sequence and maps the locations of sequence residues or residue ranges onto the 3D structure. GRASS (Graphical Representation and Analysis of Structure Server) Cartoon representation from PDB Cartoon Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute Crystal Contacts, from CryCo at Weizmann Institute 3D motif for 1RCV, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1rcvd_, region D [Jmol] [rasmolscript] [script source]     - Domain d1rcve_, region E [Jmol] [rasmolscript] [script source]     - Domain d1rcvf_, region F [Jmol] [rasmolscript] [script source]     - Domain d1rcvg_, region G [Jmol] [rasmolscript] [script source]     - Domain d1rcvh_, region H [Jmol] [rasmolscript] [script source] Fold representative 1rcv from FSSP and Dali (Families of Structurally Similar Proteins) Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH Summaries and structural analyses of PDB data files from PDBSum Identification of Protein Pockets & Cavities at CASTp

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [1rcv_E] [1rcv_F] [1rcv_H] [1rcv_G] [1rcv_D]

Other resources with information on 1RCV

InterPro: IPR001835 MMDB (Entrez's Structure Database)

Movements, Movies and Images

Images from IMB Jena Image Library of Biological Macromolecules.

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2006
Bioinformatics and Biological Computing
Weizmann Institute of Science

---