[English] 日本語
Yorodumi- PDB-6ki1: The transmembrane domain of a cyanobacterium bicarbonate transpor... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ki1 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | The transmembrane domain of a cyanobacterium bicarbonate transporter BicA | ||||||||||||
Components | Low affinity sulfate transporter | ||||||||||||
Keywords | TRANSPORT PROTEIN / Bicarbonate transporter / CO2-concentrating mechanisms (CCM) / cyanobacteria / solute carrier (SLC) / STAS domain | ||||||||||||
Function / homology | Function and homology information fumarate transmembrane transporter activity / fumarate transport / succinate transmembrane transport / succinate transmembrane transporter activity / L-aspartate transmembrane transporter activity / sodium ion transport / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Synechocystis sp. PCC 6803 (bacteria) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.809 Å | ||||||||||||
Authors | Zhang, P. / Wang, C.C. | ||||||||||||
Funding support | China, 3items
| ||||||||||||
Citation | Journal: Nat Plants / Year: 2019 Title: Structural mechanism of the active bicarbonate transporter from cyanobacteria. Authors: Chengcheng Wang / Bo Sun / Xue Zhang / Xiaowei Huang / Minhua Zhang / Hui Guo / Xin Chen / Fang Huang / Taiyu Chen / Hualing Mi / Fang Yu / Lu-Ning Liu / Peng Zhang / 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 ...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-concentrating mechanisms (CCMs) that accumulate CO 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) and the cytoplasmic STAS domain (BicA) of BicA were solved. BicA was captured in an inward-facing HCO-bound conformation and adopts a '7+7' fold monomer. HCO binds to a cytoplasm-facing hydrophilic pocket within the membrane. BicA 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 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. | ||||||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6ki1.cif.gz | 154.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6ki1.ent.gz | 119.8 KB | Display | PDB format |
PDBx/mmJSON format | 6ki1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/6ki1 ftp://data.pdbj.org/pub/pdb/validation_reports/ki/6ki1 | HTTPS FTP |
---|
-Related structure data
Related structure data | 9897C 6ki2C 5iofS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 40426.109 Da / Num. of mol.: 2 / Fragment: transmembrane domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Synechocystis sp. PCC 6803 (bacteria) / Strain: PCC 6803 / Production host: Escherichia coli (E. coli) / References: UniProt: Q55415 #2: Chemical | #3: Chemical | #4: Chemical | Has ligand of interest | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.79 % |
---|---|
Crystal grow | Temperature: 293 K / Method: lipidic cubic phase Details: 0.1M NaCl, 0.1 M Li2SO4, 0.1 M Na-citrate, pH5.0, 30% PEG600 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97923 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Apr 17, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97923 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.8→30 Å / Num. obs: 20636 / % possible obs: 98.6 % / Redundancy: 5.7 % / Biso Wilson estimate: 47.38 Å2 / Rmerge(I) obs: 0.138 / Rpim(I) all: 0.061 / Rrim(I) all: 0.147 / Χ2: 0.967 / Net I/σ(I): 4.7 / Num. measured all: 117334 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IOF Resolution: 2.809→29.277 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.48
| ||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 123.62 Å2 / Biso mean: 50.7666 Å2 / Biso min: 19.12 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.809→29.277 Å
| ||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
|