Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 28599.89 
• Atom Count: 1860 
• Residue Count: 246 
• Unique protein chains: 1

3C1Q

The three-dimensional structure of the cytoplasmic domains of EpsF from the Type 2 Secretion System of Vibrio cholerae

• DOI: 10.2210/pdb3C1Q/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)
• Expression System: Escherichia coli


• Deposited: 2008-01-24 Released: 2009-02-03 
• Deposition Author(s): Abendroth, J., Mitchell, D.D., Korotkov, K.V., Kreeger, A., Hol, W.G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.208 
• R-Value Work: 0.156 

Literature

The three-dimensional structure of the cytoplasmic domains of EpsF from the type 2 secretion system of Vibrio cholerae

Abendroth, J., Mitchell, D.D., Korotkov, K.V., Johnson, T.L., Kreger, A., Sandkvist, M., Hol, W.G.

(2009) J.Struct.Biol. 166: 303-315

• PubMed: 19324092 
• DOI: 10.1016/j.jsb.2009.03.009
• Primary Citation of Related Structures:  
  2VMB, 2VMA


• PubMed Abstract: 
  

The type 2 secretion system (T2SS), a multi-protein machinery that spans both the inner and the outer membranes of Gram-negative bacteria, is used for the secretion of several critically important proteins across the outer membrane. Here we report the crystal structure of the N-terminal cytoplasmic domain of EpsF, an inner membrane spanning T2SS protein from Vibrio cholerae. This domain consists of a bundle of six anti-parallel helices and adopts a fold that has not been described before. The long C-terminal helix alpha6 protrudes from the body of the domain and most likely continues as the first transmembrane helix of EpsF. Two N-terminal EpsF domains form a tight dimer with a conserved interface, suggesting that the observed dimer occurs in the T2SS of many bacteria. Two calcium binding sites are present in the dimer interface with ligands provided for each site by both subunits. Based on this new structure, sequence comparisons of EpsF homologs and localization studies of GFP fused with EpsF, we propose that the second cytoplasmic domain of EpsF adopts a similar fold as the first cytoplasmic domain and that full-length EpsF, and its T2SS homologs, have a three-transmembrane helix topology.

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Organizational Affiliation: 

Department of Biochemistry, Biomolecular Structure Center, University of Washington, 1959 Pacific Ave. NE, Box 357742, Seattle, WA 98195, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
General secretion pathway protein F	A, B	123	Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)	Mutation(s): 0  Gene Names: epsF
Find proteins for P45780 (Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961)) Go to UniProtKB:  P45780

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
PE5	A	3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL 2-(2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL, POLYETHYLENE GLYCOL PEG400 C18 H38 O9 CUDPPTPIUWYGFI-UHFFFAOYSA-N
CL	A	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
CA	A, B	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.7 Å
• R-Value Free: 0.208 
• R-Value Work: 0.156 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 46.988	α = 90.00
b = 52.122	β = 90.00
c = 89.470	γ = 90.00

Software Package:

Software Name	Purpose
CrystalClear	data collection
REFMAC	refinement
CrystalClear	data scaling
CrystalClear	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-01-24 
• Released Date: 2009-02-03 
• Deposition Author(s): Abendroth, J., Mitchell, D.D., Korotkov, K.V., Kreeger, A., Hol, W.G.J.

Revision History 

• Version 1.0: 2009-02-03
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Advisory, Version format compliance