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- PDB-7egl: Bicarbonate transporter complex SbtA-SbtB bound to HCO3- -

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Basic information

Entry
Database: PDB / ID: 7egl
TitleBicarbonate transporter complex SbtA-SbtB bound to HCO3-
Components
  • Membrane-associated protein SbtB
  • Sodium-dependent bicarbonate transporter SbtA
KeywordsTRANSPORT PROTEIN / Bicarbonate transporter / CCM / 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 / BICARBONATE ION / Slr1512 protein / Membrane-associated protein slr1513
Function and homology information
Biological speciesSynechocystis sp. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 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
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)51,7774
Polymers51,6932
Non-polymers842
Water1267
1
A: Sodium-dependent bicarbonate transporter SbtA
B: Membrane-associated protein SbtB
hetero molecules

A: Sodium-dependent bicarbonate transporter SbtA
B: Membrane-associated protein SbtB
hetero molecules

A: Sodium-dependent bicarbonate transporter SbtA
B: Membrane-associated protein SbtB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,33112
Polymers155,0796
Non-polymers2526
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Unit cell
Length a, b, c (Å)107.239, 107.239, 352.219
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32

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Components

#1: Protein Sodium-dependent bicarbonate transporter SbtA


Mass: 39671.246 Da / Num. of mol.: 1
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.: 1
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-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.77 Å3/Da / Density % sol: 67.37 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 9
Details: 0.05M magnesium chloride, 0.1M glycine, 22% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9798 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 26, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9798 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. obs: 15727 / % possible obs: 100 % / Redundancy: 9.6 % / Rmerge(I) obs: 0.162 / Rpim(I) all: 0.054 / Rrim(I) all: 0.171 / Χ2: 0.966 / Net I/σ(I): 3.9
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
3.2-3.269.31.5536760.50.5291.6420.975
3.26-3.319.41.5086390.5360.5131.5940.985
3.31-3.389.61.3966510.6620.4671.4730.983
3.38-3.459.81.1016530.7350.3671.1620.985
3.45-3.529.80.9266410.8260.3070.9770.967
3.52-3.69.80.7496770.8740.2490.790.985
3.6-3.699.90.6236600.9180.2060.6571.029
3.69-3.799.80.5316610.9370.1770.560.982
3.79-3.919.70.4666490.9290.1570.4921.03
3.91-4.0390.3546570.9620.1250.3761.002
4.03-4.188.70.2596570.9750.0930.2751.009
4.18-4.3410.10.2266750.9880.0740.2381.01
4.34-4.5410.30.1996590.990.0650.211.02
4.54-4.7810.10.1586710.9940.0510.1660.978
4.78-5.089.90.1526670.9940.050.160.979
5.08-5.479.70.1566650.9940.0520.1640.966
5.47-6.028.60.1216800.9940.0430.1290.933
6.02-6.899.40.16800.9970.0340.1060.877
6.89-8.679.80.0496940.9990.0160.0520.894

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.14_3260refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EGK

7egk


Resolution: 3.2→48.774 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2695 916 10.01 %
Rwork0.2132 14147 -
obs0.2189 15727 63.02 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.48 Å2 / Biso mean: 40.1048 Å2 / Biso min: 11.62 Å2
Refinement stepCycle: final / Resolution: 3.2→48.774 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3182 0 5 7 3194
Biso mean--31.92 22.88 -
Num. residues----428
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.2001-3.30340.318280.345725212
3.3034-3.42140.4348760.306967633
3.4214-3.55830.29991160.2537104251
3.5583-3.72020.29031190.2539107453
3.7202-3.91630.29741180.2338106753
3.9163-4.16150.27231260.2113110854
4.1615-4.48260.23691400.1725125661
4.4826-4.93340.21681700.1535157978
4.9334-5.64630.26572260.18072037100
5.6463-7.11020.30562260.2572032100
Refinement TLS params.Method: refined / Origin x: -11.4841 Å / Origin y: 44.1124 Å / Origin z: 25.149 Å
111213212223313233
T0.2885 Å2-0.0626 Å2-0.1274 Å2-0.2183 Å2-0.0035 Å2--0.2668 Å2
L1.0794 °20.2951 °2-0.0013 °2-1.1791 °2-0.051 °2--0.7219 °2
S0.1023 Å °0.2038 Å °-0.1558 Å °-0.0313 Å °0.0411 Å °0.1608 Å °0.4208 Å °-0.2942 Å °-0.0879 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA2 - 402
2X-RAY DIFFRACTION1allB2 - 110
3X-RAY DIFFRACTION1allH2 - 18

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