3LRB | pdb_00003lrb

Structure of E. coli AdiC

• PDB DOI: https://doi.org/10.2210/pdb3LRB/pdb
• Entry: 3LRB supersedes: 3H5M

• Classification: TRANSPORT PROTEIN
• Organism(s): Escherichia coli O157:H7
• Expression System: Escherichia coli
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2010-02-10 Released: 2010-02-23 
• Deposition Author(s): Gao, X., Lu, F., Zhou, L., Shi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.61 Å
• R-Value Free: 
  0.318 (Depositor), 0.299 (DCC) 
• R-Value Work: 
  0.295 (Depositor), 0.278 (DCC) 
• R-Value Observed: 
  0.296 (Depositor) 

Literature

Structure and mechanism of an amino acid antiporter

Gao, X., Lu, F., Zhou, L., Dang, S., Sun, L., Li, X., Wang, J., Shi, Y.

(2009) Science 324: 1565-1568

• PubMed: 19478139 
• DOI: https://doi.org/10.1126/science.1173654
• Primary Citation Related Structures: 
  3LRB, 3LRC


• PubMed Abstract: 
  

  Virulent enteric pathogens such as Escherichia coli strain O157:H7 rely on acid-resistance (AR) systems to survive the acidic environment in the stomach. A major component of AR is an arginine-dependent arginine:agmatine antiporter that expels intracellular protons. Here, we report the crystal structure of AdiC, the arginine:agmatine antiporter from E. coli O157:H7 and a member of the amino acid/polyamine/organocation (APC) superfamily of transporters at 3.6 A resolution. The overall fold is similar to that of several Na+-coupled symporters. AdiC contains 12 transmembrane segments, forms a homodimer, and exists in an outward-facing, open conformation in the crystals. A conserved, acidic pocket opens to the periplasm. Structural and biochemical analysis reveals the essential ligand-binding residues, defines the transport route, and suggests a conserved mechanism for the antiporter activity.

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Organizational Affiliation: 
• State Key Laboratory of Bio-membrane and Membrane Biotechnology, Tsinghua University, Beijing 100084, China.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 93.74 kDa 
• Atom Count: 6,072 
• Modeled Residue Count: 820 
• Deposited Residue Count: 890 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arginine/agmatine antiporter	A, B	445	Escherichia coli O157:H7	Mutation(s): 0  Gene Names: adiC, Z5717, ECs5097 Membrane Entity: Yes
UniProt
Find proteins for P60063 (Escherichia coli O157:H7) Explore P60063  Go to UniProtKB:  P60063

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.61 Å
• R-Value Free:  0.318 (Depositor), 0.299 (DCC) 
• R-Value Work:  0.295 (Depositor), 0.278 (DCC) 
• R-Value Observed: 0.296 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.81	α = 90
b = 108.3	β = 90
c = 138.11	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-23 
Deposition Author(s): Gao, X., Lu, F., Zhou, L., Shi, Y.
• This entry supersedes: 3H5M

Revision History  

• Version 1.0: 2010-02-23
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Refinement description