7AHD

OpuA (E190Q) occluded

• PDB DOI:  https://doi.org/10.2210/pdb7AHD/pdb
• EM Map EMD-11783: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Lactococcus lactis subsp. lactis
• Expression System: Lactococcus lactis subsp. lactis
• Mutation(s): Yes 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2020-09-24 Released: 2020-11-25 
• Deposition Author(s): Sikkema, H.R., Rheinberger, J., Paulino, C., Poolman, B.
• Funding Organization(s): European Research Council (ERC), Netherlands Organisation for Scientific Research (NWO)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Gating by ionic strength and safety check by cyclic-di-AMP in the ABC transporter OpuA.

Sikkema, H.R., van den Noort, M., Rheinberger, J., de Boer, M., Krepel, S.T., Schuurman-Wolters, G.K., Paulino, C., Poolman, B.

(2020) Sci Adv 6

• PubMed: 33208376 
• DOI: https://doi.org/10.1126/sciadv.abd7697
• Primary Citation of Related Structures:  
  7AHC, 7AHD, 7AHE, 7AHH


• PubMed Abstract: 
  

(Micro)organisms are exposed to fluctuating environmental conditions, and adaptation to stress is essential for survival. Increased osmolality (hypertonicity) causes outflow of water and loss of turgor and is dangerous if the cell is not capable of rapidly restoring its volume. The osmoregulatory adenosine triphosphate-binding cassette transporter OpuA restores the cell volume by accumulating large amounts of compatible solute. OpuA is gated by ionic strength and inhibited by the second messenger cyclic-di-AMP, a molecule recently shown to affect many cellular processes. Despite the master regulatory role of cyclic-di-AMP, structural and functional insights into how the second messenger regulates (transport) proteins on the molecular level are lacking. Here, we present high-resolution cryo-electron microscopy structures of OpuA and in vitro activity assays that show how the osmoregulator OpuA is activated by high ionic strength and how cyclic-di-AMP acts as a backstop to prevent unbridled uptake of compatible solutes.

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Organizational Affiliation: 

Department of Biochemistry, Membrane Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, Netherlands. [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B1C1 Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Hetero 4-mer - A2B2 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 219.57 kDa 
• Atom Count: 10,562 
• Modelled Residue Count: 1,361 
• Deposited Residue Count: 1,986 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC-type proline/glycine betaine transport system ATPase component	A [auth C], C [auth D]	408	Lactococcus lactis subsp. lactis	Mutation(s): 1  Gene Names: FEZ45_03200, GJI88_00480, GJI90_00980, KF282_2364, LL275_1487, M20_1239, N42_0726 EC: 7.6.2.9
UniProt
Find proteins for Q9KIF7 (Lactococcus lactis subsp. lactis (strain IL1403)) Explore Q9KIF7  Go to UniProtKB:  Q9KIF7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ABC transporter permease subunit	B [auth A], D [auth B]	585	Lactococcus lactis subsp. lactis	Mutation(s): 0  Gene Names: FEZ45_03205, FIB48_03540, GJI88_00475, GJI90_00975, LL275_1486, N42_0725, KF201_2038 Membrane Entity: Yes
UniProt
Find proteins for A0A0V8ETW8 (Lactococcus lactis subsp. lactis) Explore A0A0V8ETW8  Go to UniProtKB:  A0A0V8ETW8

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ATP	E [auth C], F [auth D]	ADENOSINE-5'-TRIPHOSPHATE C10 H16 N5 O13 P3 ZKHQWZAMYRWXGA-KQYNXXCUSA-N
BET (Subject of Investigation/LOI)	G [auth B]	TRIMETHYL GLYCINE C5 H12 N O2 KWIUHFFTVRNATP-UHFFFAOYSA-O

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.40 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-11-25 
Deposition Author(s): Sikkema, H.R., Rheinberger, J., Paulino, C., Poolman, B.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	Netherlands	670578
Netherlands Organisation for Scientific Research (NWO)	Netherlands	722.017.001
Netherlands Organisation for Scientific Research (NWO)	Netherlands	740.018.016

Revision History  

• Version 1.0: 2020-11-25
  Type: Initial release
  
• Version 1.1: 2020-12-02
  Changes: Database references