5SV9

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.90 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

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

Coudray, N.L Seyler, S.Lasala, R.Zhang, Z.Clark, K.M.Dumont, M.E.Rohou, A.Beckstein, O.Stokes, D.L.

(2017) Protein Sci 26: 130-145

  • DOI: 10.1002/pro.3061
  • Primary Citation of Related Structures:  
    5SV9

  • 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 ...

    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.


    Organizational Affiliation

    Skirball Institute for Biomolecular Medicine, Department of Cell Biology, New York University School of Medicine, New York, New York, 10016.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bor1p boron transporterA, B476Saccharomyces mikataeMutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for A0A1C7D1B8 (Saccharomyces mikatae)
Explore A0A1C7D1B8 
Go to UniProtKB:  A0A1C7D1B8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1C7D1B8
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.90 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU54 GM094598
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM095747
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesU54 GM094611
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM118772

Revision History  (Full details and data files)

  • Version 1.0: 2016-08-17
    Type: Initial release
  • Version 1.1: 2016-10-19
    Changes: Database references
  • Version 1.2: 2017-01-11
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence, Data collection
  • Version 1.4: 2019-01-23
    Changes: Data collection, Refinement description
  • Version 1.5: 2019-12-25
    Changes: Author supporting evidence