7EGL

Bicarbonate transporter complex SbtA-SbtB bound to HCO3-


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.219 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Molecular mechanism underlying transport and allosteric inhibition of bicarbonate transporter SbtA.

Fang, S.Huang, X.Zhang, X.Zhang, M.Hao, Y.Guo, H.Liu, L.N.Yu, F.Zhang, P.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2101632118
  • Primary Citation of Related Structures:  
    7EGK, 7EGL

  • PubMed Abstract: 

    SbtA is a high-affinity, sodium-dependent bicarbonate transporter found in the cyanobacterial CO 2 -concentrating mechanism (CCM). SbtA forms a complex with SbtB, while SbtB allosterically regulates the transport activity of SbtA by binding with adenyl nucleotides. The underlying mechanism of transport and regulation of SbtA is largely unknown. In this study, we report the three-dimensional structures of the cyanobacterial Synechocystis sp. PCC 6803 SbtA-SbtB complex in both the presence and absence of HCO 3 - and/or AMP at 2.7 Å and 3.2 Å resolution. An analysis of the inward-facing state of the SbtA structure reveals the HCO 3 - /Na + binding site, providing evidence for the functional unit as a trimer. A structural comparison found that SbtA adopts an elevator mechanism for bicarbonate transport. A structure-based analysis revealed that the allosteric inhibition of SbtA by SbtB occurs mainly through the T-loop of SbtB, which binds to both the core domain and the scaffold domain of SbtA and locks it in an inward-facing state. T-loop conformation is stabilized by the AMP molecules binding at the SbtB trimer interfaces and may be adjusted by other adenyl nucleotides. The unique regulatory mechanism of SbtA by SbtB makes it important to study inorganic carbon uptake systems in CCM, which can be used to modify photosynthesis in crops.


  • Organizational Affiliation

    National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sodium-dependent bicarbonate transporter SbtA374Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: slr1512
Membrane Entity: Yes 
UniProt
Find proteins for P73953 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore P73953 
Go to UniProtKB:  P73953
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP73953
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Membrane-associated protein SbtB110Synechocystis sp. PCC 6803 substr. KazusaMutation(s): 0 
Gene Names: slr1513
Membrane Entity: Yes 
UniProt
Find proteins for P73954 (Synechocystis sp. (strain PCC 6803 / Kazusa))
Explore P73954 
Go to UniProtKB:  P73954
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP73954
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.213 
  • R-Value Observed: 0.219 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 107.239α = 90
b = 107.239β = 90
c = 352.219γ = 120
Software Package:
Software NamePurpose
HKL-3000data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-26
    Type: Initial release
  • Version 1.1: 2021-06-16
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Database references, Refinement description