5FVN

X-ray crystal structure of Enterobacter cloacae OmpE36 porin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Gram-negative trimeric porins have specific LPS binding sites that are essential for porin biogenesis.

Arunmanee, W.Pathania, M.Solovyova, A.S.Le Brun, A.P.Ridley, H.Basle, A.van den Berg, B.Lakey, J.H.

(2016) Proc. Natl. Acad. Sci. U.S.A. 113: E5034-E5043

  • DOI: 10.1073/pnas.1602382113

  • PubMed Abstract: 
  • The outer membrane (OM) of gram-negative bacteria is an unusual asymmetric bilayer with an external monolayer of lipopolysaccharide (LPS) and an inner layer of phospholipids. The LPS layer is rigid and stabilized by divalent cation cross-links betwee ...

    The outer membrane (OM) of gram-negative bacteria is an unusual asymmetric bilayer with an external monolayer of lipopolysaccharide (LPS) and an inner layer of phospholipids. The LPS layer is rigid and stabilized by divalent cation cross-links between phosphate groups on the core oligosaccharide regions. This means that the OM is robust and highly impermeable to toxins and antibiotics. During their biogenesis, OM proteins (OMPs), which function as transporters and receptors, must integrate into this ordered monolayer while preserving its impermeability. Here we reveal the specific interactions between the trimeric porins of Enterobacteriaceae and LPS. Isolated porins form complexes with variable numbers of LPS molecules, which are stabilized by calcium ions. In earlier studies, two high-affinity sites were predicted to contain groups of positively charged side chains. Mutation of these residues led to the loss of LPS binding and, in one site, also prevented trimerization of the porin, explaining the previously observed effect of LPS mutants on porin folding. The high-resolution X-ray crystal structure of a trimeric porin-LPS complex not only helps to explain the mutagenesis results but also reveals more complex, subtle porin-LPS interactions and a bridging calcium ion.


    Organizational Affiliation

    Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
OMPC PORIN
A, B, C, D, E, F
342Enterobacter cloacaeMutation(s): 0 
Gene Names: ompC
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: BETA-BARREL
Sub Group: 
Beta-Barrel Membrane Proteins: Porins and Relatives
Protein: 
OmpC homolog (OmpE36) with bound lipopolysaccharide (LPS)
Find proteins for Q93K99 (Enterobacter cloacae)
Go to UniProtKB:  Q93K99
Small Molecules
Ligands 11 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYR
Query on MYR

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A, B, C, D, E, F
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

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A, B, C, D, E, F
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
L1L
Query on L1L

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A, B, C, D, E, F
[(2R,3R,4R,5S,6R)-3-azanyl-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl] dihydrogen phosphate
C6 H14 N O8 P
YMJBYRVFGYXULK-QZABAPFNSA-N
 Ligand Interaction
SO4
Query on SO4

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A, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
C8E
Query on C8E

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A, B, C, D, E, F
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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C, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Z9M
Query on Z9M

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A, B, C, D, E, F
2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose
C6 H14 N O8 P
QWDBGVNDGYUIAC-QZABAPFNSA-N
 Ligand Interaction
FTT
Query on FTT

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A, B, C, D, E, F
3-HYDROXY-TETRADECANOIC ACID
3-HYDROXY-MYRISTIC ACID
C14 H28 O3
ATRNZOYKSNPPBF-CYBMUJFWSA-N
 Ligand Interaction
KDO
Query on KDO

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A, B, C, D, E, F
3-DEOXY-D-MANNO-OCT-2-ULOSONIC ACID
C8 H14 O8
NNLZBVFSCVTSLA-HXUQBWEZSA-N
 Ligand Interaction
DAO
Query on DAO

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A, B, C, D, E, F
LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
 Ligand Interaction
GMH
Query on GMH

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B, C, F
L-GLYCERO-D-MANNO-HEPTOPYRANOSE
C7 H14 O7
BGWQRWREUZVRGI-QQABCQGCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.155 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 109.749α = 90.00
b = 123.260β = 91.01
c = 116.010γ = 90.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
XDSdata reduction
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-08-17
    Type: Database references
  • Version 1.2: 2016-09-28
    Type: Database references
  • Version 1.3: 2018-02-21
    Type: Advisory, Database references, Structure summary