6KI1

The transmembrane domain of a cyanobacterium bicarbonate transporter BicA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural mechanism of the active bicarbonate transporter from cyanobacteria.

Wang, C.Sun, B.Zhang, X.Huang, X.Zhang, M.Guo, H.Chen, X.Huang, F.Chen, T.Mi, H.Yu, F.Liu, L.N.Zhang, P.

(2019) Nat Plants 5: 1184-1193

  • DOI: https://doi.org/10.1038/s41477-019-0538-1
  • Primary Citation of Related Structures:  
    6KI1, 6KI2

  • PubMed Abstract: 

    Bicarbonate transporters play essential roles in pH homeostasis in mammals and photosynthesis in aquatic photoautotrophs. A number of bicarbonate transporters have been characterized, among which is BicA-a low-affinity, high-flux SLC26-family bicarbonate transporter involved in cyanobacterial CO 2 -concentrating mechanisms (CCMs) that accumulate CO 2 and improve photosynthetic carbon fixation. Here, we report the three-dimensional structure of BicA from Synechocystis sp. PCC6803. Crystal structures of the transmembrane domain (BicA TM ) and the cytoplasmic STAS domain (BicA STAS ) of BicA were solved. BicA TM was captured in an inward-facing HCO 3 - -bound conformation and adopts a '7+7' fold monomer. HCO 3 - binds to a cytoplasm-facing hydrophilic pocket within the membrane. BicA STAS is assembled as a compact homodimer structure and is required for the dimerization of BicA. The dimeric structure of BicA was further analysed using cryo-electron microscopy and physiological analysis of the full-length BicA, and may represent the physiological unit of SLC26-family transporters. Comparing the BicA TM structure with the outward-facing transmembrane domain structures of other bicarbonate transporters suggests an elevator transport mechanism that is applicable to the SLC26/4 family of sodium-dependent bicarbonate transporters. This study advances our knowledge of the structures and functions of cyanobacterial bicarbonate transporters, and will inform strategies for bioengineering functional BicA in heterologous organisms to increase assimilation of CO 2 .


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Low affinity sulfate transporter
A, B
392Synechocystis sp. PCC 6803Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q55415 (Synechocystis sp. (strain ATCC 27184 / PCC 6803 / Kazusa))
Explore Q55415 
Go to UniProtKB:  Q55415
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ55415
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B]
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
BCT (Subject of Investigation/LOI)
Query on BCT

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
BICARBONATE ION
C H O3
BVKZGUZCCUSVTD-UHFFFAOYSA-M
NA (Subject of Investigation/LOI)
Query on NA

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.81 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 51.813α = 90
b = 103.346β = 95.4
c = 81.521γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
PDB_EXTRACTdata extraction
HKL-3000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of ChinaChina31861130356
Chinese Academy of SciencesChinaXDB27020103
Chinese Academy of SciencesChinaQYZDB-SSW-SMC006

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2019-12-25
    Changes: Database references
  • Version 1.2: 2023-11-22
    Changes: Data collection, Database references, Derived calculations, Refinement description