5SV9

Structure of the SLC4 transporter Bor1p in an inward-facing conformation

Summary for 5SV9

• Entry DOI: 10.2210/pdb5sv9/pdb
• EMDB information: 8313
• Descriptor: Bor1p boron transporter (1 entity in total)
• Functional Keywords: boron transporter, anion exchanger family, alternating access mechanism, structural genomics, psi-biology, transcontinental em initiative for membrane protein structure, temimps, transport protein
• Biological source: Saccharomyces mikatae
• Total number of polymer chains: 2
• Total formula weight: 107659.53

Authors

Coudray, N.,Seyler, S.,Lasala, R.,Zhang, Z.,Clark, K.M.,Dumont, M.E.,Rohou, A.,Beckstein, O.,Stokes, D.L.,Transcontinental EM Initiative for Membrane Protein Structure (TEMIMPS) (deposition date: 2016-08-05, release date: 2016-08-17, Last modification date: 2024-03-06)

Primary citation

Coudray, N.,L Seyler, S.,Lasala, R.,Zhang, Z.,Clark, K.M.,Dumont, M.E.,Rohou, A.,Beckstein, O.,Stokes, D.L.
Structure of the SLC4 transporter Bor1p in an inward-facing conformation.
Protein Sci., 26:130-145, 2017

PubMed Abstract: Bor1p is a secondary transporter in yeast that is responsible for boron transport. Bor1p belongs to the SLC4 family which controls bicarbonate exchange and pH regulation in animals as well as borate uptake in plants. The SLC4 family is more distantly related to members of the Amino acid-Polyamine-organoCation (APC) superfamily, which includes well studied transporters such as LeuT, Mhp1, AdiC, vSGLT, UraA, SLC26Dg. Their mechanism generally involves relative movements of two domains: a core domain that binds substrate and a gate domain that in many cases mediates dimerization. To shed light on conformational changes governing transport by the SLC4 family, we grew helical membrane crystals of Bor1p from Saccharomyces mikatae and determined a structure at ∼6 Å resolution using cryo-electron microscopy. To evaluate the conformation of Bor1p in these crystals, a homology model was built based on the related anion exchanger from red blood cells (AE1). This homology model was fitted to the cryo-EM density map using the Molecular Dynamics (MD) Flexible Fitting method and then relaxed by all-atom MD simulation in explicit solvent and membrane. Mapping of water accessibility indicates that the resulting structure represents an inward-facing conformation. Comparisons of the resulting Bor1p model with the X-ray structure of AE1 in an outward-facing conformation, together with MD simulations of inward-facing and outward-facing Bor1p models, suggest rigid body movements of the core domain relative to the gate domain. These movements are consistent with the rocking-bundle transport mechanism described for other members of the APC superfamily.

PubMed: 27717063
DOI: 10.1002/pro.3061

Experimental method

ELECTRON MICROSCOPY (5.9 Å)