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), 0.247 (DCC) 
• R-Value Work: 
  0.208 (Depositor), 0.211 (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 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.
Diamond Light Source, Harwell Science and Innovation Campus, Didcot OX11 0DE, UK.
Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK. Electronic address: [e-mail].

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 
• Modeled 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), 0.247 (DCC) 
• R-Value Work:  0.208 (Depositor), 0.211 (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