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 
  • R-Value Observed: 0.156 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 4.2 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: https://doi.org/10.1073/pnas.1602382113
  • Primary Citation of Related Structures:  
    5FVN

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
OMPC PORIN
A, B, C, D, E
A, B, C, D, E, F
342Enterobacter cloacaeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q93K99 (Enterobacter cloacae)
Explore Q93K99 
Go to UniProtKB:  Q93K99
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ93K99
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose
G, K, L, M
3N/A
Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-[L-glycero-alpha-D-manno-heptopyranose-(1-5)]3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose
H, I, N
5N/A
Entity ID: 4
MoleculeChains Length2D Diagram Glycosylation3D Interactions
3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose
J, O
4N/A
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C8E
Query on C8E

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AB [auth C]
AC [auth D]
BB [auth C]
BC [auth D]
CB [auth C]
AB [auth C],
AC [auth D],
BB [auth C],
BC [auth D],
CB [auth C],
CC [auth D],
DB [auth C],
DC [auth D],
DD [auth F],
ED [auth F],
FD [auth F],
IA [auth B],
JA [auth B],
KA [auth B],
LA [auth B],
MA [auth B],
Q [auth A],
R [auth A],
S [auth A],
T [auth A],
TC [auth E],
U [auth A],
UA [auth C],
V [auth A],
VA [auth C],
VB [auth D],
W [auth A],
WA [auth C],
WB [auth D],
X [auth A],
XA [auth C],
XB [auth D],
Y [auth A],
YA [auth C],
YB [auth D],
ZA [auth C],
ZB [auth D]
(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
C16 H34 O5
FEOZZFHAVXYAMB-UHFFFAOYSA-N
FTT
Query on FTT

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AD [auth E]
BA [auth A]
CA [auth A]
DA [auth A]
GA [auth A]
AD [auth E],
BA [auth A],
CA [auth A],
DA [auth A],
GA [auth A],
GB [auth C],
HC [auth D],
IB [auth C],
IC [auth D],
ID [auth F],
JB [auth C],
JC [auth D],
JD [auth F],
KB [auth C],
KC [auth D],
KD [auth F],
LB [auth C],
LD [auth F],
MD [auth F],
NC [auth D],
OA [auth B],
OC [auth D],
PA [auth B],
PB [auth C],
PC [auth D],
QA [auth B],
QB [auth C],
QD [auth F],
RA [auth B],
RB [auth C],
RD [auth F],
SC [auth D],
SD [auth F],
WC [auth E],
YC [auth E],
ZC [auth E]
3-HYDROXY-TETRADECANOIC ACID
C14 H28 O3
ATRNZOYKSNPPBF-CYBMUJFWSA-N
KDO
Query on KDO

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AA [auth A],
GC [auth D],
VC [auth E]
3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid
C8 H14 O8
NNLZBVFSCVTSLA-HXUQBWEZSA-N
MYR
Query on MYR

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BD [auth E]
EA [auth A]
MB [auth C]
MC [auth D]
ND [auth F]
BD [auth E],
EA [auth A],
MB [auth C],
MC [auth D],
ND [auth F],
QC [auth D],
SA [auth B],
SB [auth C],
TD [auth F]
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
DAO
Query on DAO

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CD [auth E]
FA [auth A]
FC [auth D]
HA [auth A]
HB [auth C]
CD [auth E],
FA [auth A],
FC [auth D],
HA [auth A],
HB [auth C],
LC [auth D],
NB [auth C],
OB [auth C],
OD [auth F],
PD [auth F],
RC [auth D],
TA [auth B],
TB [auth C],
UD [auth F],
XC [auth E]
LAURIC ACID
C12 H24 O2
POULHZVOKOAJMA-UHFFFAOYSA-N
SO4
Query on SO4

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P [auth A],
UB [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
PO4
Query on PO4

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EB [auth C]
EC [auth D]
GD [auth F]
NA [auth B]
UC [auth E]
EB [auth C],
EC [auth D],
GD [auth F],
NA [auth B],
UC [auth E],
Z [auth A]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
CA
Query on CA

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FB [auth C],
HD [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.156 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.749α = 90
b = 123.26β = 91.01
c = 116.01γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-10
    Type: Initial release
  • Version 1.1: 2016-08-17
    Changes: Database references
  • Version 1.2: 2016-09-28
    Changes: Database references
  • Version 1.3: 2018-02-21
    Changes: Advisory, Database references, Structure summary
  • Version 2.0: 2019-01-30
    Changes: Advisory, Atomic model, Data collection, Derived calculations
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Other, Structure summary
  • Version 4.0: 2022-04-20
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
  • Version 4.1: 2023-03-08
    Changes: Structure summary
  • Version 4.2: 2024-02-07
    Changes: Data collection, Refinement description