2WJQ

NanC porin structure in hexagonal crystal form.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Nanc Crystal Structure, a Model for Outer Membrane Channels of the Acidic Sugar-Specific Kdgm Porin Family.

Wirth, C.Condemine, G.Boiteux, C.Berneche, S.Schirmer, T.Peneff, C.M.

(2009) J.Mol.Biol. 394: 718

  • DOI: 10.1016/j.jmb.2009.09.054
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Sialic acids are acidic sugars present mostly on vertebrate cell surfaces, which can be metabolized by bacteria and act as an inflammation signal. N-Acetylneuraminic acid, the most abundant sialic acid, can enter into Escherichia coli K12 through Nan ...

    Sialic acids are acidic sugars present mostly on vertebrate cell surfaces, which can be metabolized by bacteria and act as an inflammation signal. N-Acetylneuraminic acid, the most abundant sialic acid, can enter into Escherichia coli K12 through NanC, an N-acetylneuraminic acid-inducible outer-membrane channel. With its 215 residues, NanC belongs to the family of small monomeric KdgM-related porins. KdgM homologues are found in gammaproteobacteria, including major plant and human pathogens, and together they define a large family of putative acidic sugar/oligosaccharide transporters, which are as yet poorly characterized. Here, we present the first high-resolution structure of a KdgM family member. NanC folds into a 28-A-high, 12-stranded beta-barrel, resembling the beta-domain of autotransporter NalP and defining an open pore with an average radius of 3.3 A. The channel is lined by two strings of basic residues facing each other across the pore, a feature that appears largely conserved within the KdgM family and is likely to facilitate the diffusion of acidic oligosaccharides.


    Organizational Affiliation

    Department of Structural Biology, Biozentrum, University of Basel, Klingelbergstrasse 70, CH-4056 Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROBABLE N-ACETYLNEURAMINIC ACID OUTER MEMBRANE CHANNEL PROTEIN NANC
A
215Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: nanC (yjhA)
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Beta-Barrel Membrane Proteins: Monomeric/Dimeric
Protein: 
NanC Porin, model for KdgM porin family
Find proteins for P69856 (Escherichia coli (strain K12))
Go to UniProtKB:  P69856
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OCT
Query on OCT

Download SDF File 
Download CCD File 
A
N-OCTANE
C8 H18
TVMXDCGIABBOFY-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
LDA
Query on LDA

Download SDF File 
Download CCD File 
A
LAURYL DIMETHYLAMINE-N-OXIDE
C14 H31 N O
SYELZBGXAIXKHU-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.191 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 96.823α = 90.00
b = 96.823β = 90.00
c = 121.253γ = 120.00
Software Package:
Software NamePurpose
SHELXDphasing
REFMACrefinement
SCALAdata scaling
MOSFLMdata reduction
SHARPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Advisory, Version format compliance