4TKO | pdb_00004tko

Structure of the periplasmic adaptor protein EmrA

• PDB DOI: https://doi.org/10.2210/pdb4TKO/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Aquifex aeolicus VF5
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-05-27 Released: 2014-07-09 
• Deposition Author(s): Hinchliffe, P., Greene, N.P., Paterson, N.G., Crow, A., Hughes, C., Koronakis, V.
• Funding Organization(s): Wellcome Trust

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free: 
  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.210 (Depositor) 

Literature

Structure of the periplasmic adaptor protein from a major facilitator superfamily (MFS) multidrug efflux pump.

Hinchliffe, P., Greene, N.P., Paterson, N.G., Crow, A., Hughes, C., Koronakis, V.

(2014) FEBS Lett 588: 3147-3153

• PubMed: 24996185 
• DOI: https://doi.org/10.1016/j.febslet.2014.06.055
• Primary Citation of Related Structures:  
  4TKO


• PubMed Abstract: 
  

  Periplasmic adaptor proteins are key components of bacterial tripartite efflux pumps. The 2.85 Å resolution structure of an MFS (major facilitator superfamily) pump adaptor, Aquifex aeolicus EmrA, shows linearly arranged α-helical coiled-coil, lipoyl, and β-barrel domains, but lacks the fourth membrane-proximal domain shown in other pumps to interact with the inner membrane transporter. The adaptor α-hairpin, which binds outer membrane TolC, is exceptionally long at 127 Å, and the β-barrel contains a conserved disordered loop. The structure extends the view of adaptors as flexible, modular components that mediate diverse pump assembly, and suggests that in MFS tripartite pumps a hexamer of adaptors could provide a periplasmic seal.

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Organizational Affiliation: 

Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content

• Total Structure Weight: 41.47 kDa 
• Atom Count: 2,669 
• Modelled Residue Count: 326 
• Deposited Residue Count: 358 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
EmrA	A [auth B]	358	Aquifex aeolicus VF5	Mutation(s): 0  Gene Names: aq_1060
UniProt
Find proteins for O67159 (Aquifex aeolicus (strain VF5)) Explore O67159  Go to UniProtKB:  O67159

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
IPA	C [auth B], D [auth B]	ISOPROPYL ALCOHOL C3 H8 O KFZMGEQAYNKOFK-UHFFFAOYSA-N
MG	B	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.85 Å
• R-Value Free:  0.248 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.366	α = 90
b = 81.366	β = 90
c = 541.695	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2014-07-09 
Deposition Author(s): Hinchliffe, P., Greene, N.P., Paterson, N.G., Crow, A., Hughes, C., Koronakis, V.

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Funding Organization	Location	Grant Number
Wellcome Trust	United Kingdom	093011/Z/10/Z

Revision History  

• Version 1.0: 2014-07-09
  Type: Initial release
  
• Version 1.1: 2014-07-23
  Changes: Database references
• Version 1.2: 2014-10-01
  Changes: Database references
• Version 1.3: 2015-02-04
  Changes: Derived calculations
• Version 1.4: 2023-12-27
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy, Structure summary