Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

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

Biological Assembly 2  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction | Predict Membrane 

Global Symmetry: Cyclic - C5  (3D View)
Global Stoichiometry: Homo 5-mer - A5 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 281.38 kDa 
• Atom Count: 19016 
• Modelled Residue Count: 2496 
• Deposited Residue Count: 2610 
• Unique protein chains: 1

4FC4

FNT family ion channel

• PDB DOI: 10.2210/pdb4FC4/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMD


• Deposited: 2012-05-24 Released: 2012-11-21 
• Deposition Author(s): Lue, W., Schwarzer, N., Du, J., Gerbig-Smentek, E., Andrade, S.L.A., Einsle, O.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.236 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 

Literature

Structural and functional characterization of the nitrite channel NirC from Salmonella typhimurium.

Lu, W., Schwarzer, N.J., Du, J., Gerbig-Smentek, E., Andrade, S.L., Einsle, O.

(2012) Proc Natl Acad Sci U S A 109: 18395-18400

• PubMed: 23090993 
• DOI: 10.1073/pnas.1210793109
• Primary Citation of Related Structures:  
  4FC4


• PubMed Abstract: 
  

Nitrite (NO(2)(-)) is a central intermediate in the nitrogen metabolism of microorganisms and plants, and is used as a cytotoxin by macrophages as part of the innate immune response. The bacterial membrane protein NirC acts as a specific channel to facilitate the transport of nitrite anions across lipid bilayers for cytoplasmic detoxification. Despite NirC's importance in nitrogen metabolism and in the pathogenicity of enteric bacteria, available biochemical data are scarce. Here we present a functional and structural characterization of NirC from Salmonella typhimurium by lipid bilayer electrophysiology and X-ray crystallography. NirC is a pentameric member of the formate/nitrite transporter family of membrane proteins that operates as a channel with high conductance. Single-channel measurements reveal fast and slow gating events but, in contrast to the related FocA formate channel, no pH-dependent gating. A 2.4Å crystal structure of NirC at pH 5 shows similarity to FocA and aquaporins, but lacks the structural asymmetry observed in the formate channel at similarly low pH. Resolved water molecules in the protomers suggest a transport mechanism that also permits a facultative NO(2)(-)/H(+) symport.

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Organizational Affiliation: 

Lehrstuhl für Biochemie, Institut für organische Chemie und Biochemie and BIOSS Centre for Biological Signalling Studies, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrite transporter NirC	A, B, C, D, E, F, G, H, I, J	261	Salmonella enterica subsp. enterica serovar Typhimurium str. ST4/74	Mutation(s): 0  Gene Names: nirC, STM474_3643 Membrane Entity: Yes
UniProt
Find proteins for E8XEH9 (Salmonella typhimurium (strain 4/74)) Explore E8XEH9  Go to UniProtKB:  E8XEH9

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BOG	K [auth F], L [auth F]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.236 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.3	α = 90
b = 101.84	β = 101.24
c = 205.3	γ = 90

Software Package:

Software Name	Purpose
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
XPREP	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-05-24 
• Released Date: 2012-11-21 
Deposition Author(s): Lue, W., Schwarzer, N., Du, J., Gerbig-Smentek, E., Andrade, S.L.A., Einsle, O.

Revision History  

• Version 1.0: 2012-11-21
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Structure summary
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary