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- PDB-7egk: Bicarbonate transporter complex SbtA-SbtB bound to AMP -

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Basic information

Entry
Database: PDB / ID: 7egk
TitleBicarbonate transporter complex SbtA-SbtB bound to AMP
Components
  • Membrane-associated protein SbtB
  • Sodium-dependent bicarbonate transporter SbtA
KeywordsTRANSPORT PROTEIN / Bicarbonate transporter / CO2 concentrating mechanism / Allosteric inhibition / Photosynthesis
Function / homologyNa+-dependent bicarbonate transporter superfamily / Na+-dependent bicarbonate transporter superfamily / Nitrogen regulatory PII-like, alpha/beta / Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal / plasma membrane-derived thylakoid membrane / membrane / ADENOSINE MONOPHOSPHATE / Slr1512 protein / Membrane-associated protein slr1513
Function and homology information
Biological speciesSynechocystis sp. (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsFang, S. / Huang, X. / Zhang, X. / Zhang, P.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: Molecular mechanism underlying transport and allosteric inhibition of bicarbonate transporter SbtA.
Authors: Sunzhenhe Fang / Xiaowei Huang / Xue Zhang / Minhua Zhang / Yahui Hao / Hui Guo / Lu-Ning Liu / Fang Yu / Peng Zhang /
Abstract: SbtA is a high-affinity, sodium-dependent bicarbonate transporter found in the cyanobacterial CO-concentrating mechanism (CCM). SbtA forms a complex with SbtB, while SbtB allosterically regulates the ...SbtA is a high-affinity, sodium-dependent bicarbonate transporter found in the cyanobacterial CO-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 sp. PCC 6803 SbtA-SbtB complex in both the presence and absence of HCO 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/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.
History
DepositionMar 24, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 26, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

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Assembly

Deposited unit
A: Sodium-dependent bicarbonate transporter SbtA
D: Membrane-associated protein SbtB
C: Sodium-dependent bicarbonate transporter SbtA
F: Membrane-associated protein SbtB
E: Sodium-dependent bicarbonate transporter SbtA
B: Membrane-associated protein SbtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,19012
Polymers155,0796
Non-polymers1,1116
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Sodium-dependent bicarbonate transporter SbtA


Mass: 39671.246 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Gene: slr1512 / Production host: Escherichia coli (E. coli) / References: UniProt: P73953
#2: Protein Membrane-associated protein SbtB


Mass: 12021.810 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Synechocystis sp. (strain PCC 6803 / Kazusa) (bacteria)
Gene: slr1513 / Production host: Escherichia coli (E. coli) / References: UniProt: P73954
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AMP / ADENOSINE MONOPHOSPHATE


Mass: 347.221 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H14N5O7P / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP*YM
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Bicarbonate transporter SbtA in complex with regulator SbtB
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Synechocystis sp. PCC 6803 (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

CTF correctionType: NONE
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 125998 / Symmetry type: POINT

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