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- PDB-6ki1: The transmembrane domain of a cyanobacterium bicarbonate transpor... -

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Basic information

Entry
Database: PDB / ID: 6ki1
TitleThe transmembrane domain of a cyanobacterium bicarbonate transporter BicA
ComponentsLow affinity sulfate transporter
KeywordsTRANSPORT PROTEIN / Bicarbonate transporter / CO2-concentrating mechanisms (CCM) / cyanobacteria / solute carrier (SLC) / STAS domain
Function / homology
Function and homology information


sodium ion transport / transmembrane transport / metal ion binding / plasma membrane
Similarity search - Function
SLC26A/SulP transporter / SLC26A/SulP transporter domain / Sulfate permease family / STAS domain / STAS domain profile. / STAS domain / STAS domain superfamily
Similarity search - Domain/homology
BICARBONATE ION / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / Bicarbonate transporter BicA
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.809 Å
AuthorsZhang, P. / Wang, C.C.
Funding support China, 3items
OrganizationGrant numberCountry
National Natural Science Foundation of China31861130356 China
Chinese Academy of SciencesXDB27020103 China
Chinese Academy of SciencesQYZDB-SSW-SMC006 China
CitationJournal: 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
DepositionJul 17, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2019Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Low affinity sulfate transporter
B: Low affinity sulfate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,7338
Polymers80,8522
Non-polymers8816
Water00
1
A: Low affinity sulfate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8674
Polymers40,4261
Non-polymers4413
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-10 kcal/mol
Surface area17070 Å2
MethodPISA
2
B: Low affinity sulfate transporter
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8674
Polymers40,4261
Non-polymers4413
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-10 kcal/mol
Surface area17550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.813, 103.346, 81.521
Angle α, β, γ (deg.)90.000, 95.400, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Low affinity sulfate transporter / BicA


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 ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-OLC / (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate / 1-Oleoyl-R-glycerol


Mass: 356.540 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H40O4
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: 2.72 Å3/Da / Density % sol: 54.79 %
Crystal growTemperature: 293 K / Method: lipidic cubic phase
Details: 0.1M NaCl, 0.1 M Li2SO4, 0.1 M Na-citrate, pH5.0, 30% PEG600

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Apr 17, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 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

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allΧ2% possible allRrim(I) all
2.8-2.93.50.90718810.6270.4950.95190.4
2.9-3.024.10.86820220.6680.4530.97297.10.984
3.02-3.154.90.7720500.7270.3720.97899.60.858
3.15-3.3260.6620970.8450.2890.9991000.722
3.32-3.536.30.47620860.9320.2031.0041000.518
3.53-3.86.20.29220800.9720.1271.0491000.319
3.8-4.186.50.16321010.9880.0691.04199.90.178
4.18-4.786.40.09620970.9950.0411.00199.80.104
4.78-6.026.40.09720870.9950.0410.88199.70.106
6.02-306.20.04421350.9960.0190.79699.60.048

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-3000data reduction
PDB_EXTRACT3.25data extraction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IOF

5iof


Resolution: 2.809→29.277 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 29.48
RfactorNum. reflection% reflection
Rfree0.2726 889 5.01 %
Rwork0.2265 --
obs0.2289 17747 98.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 123.62 Å2 / Biso mean: 50.7666 Å2 / Biso min: 19.12 Å2
Refinement stepCycle: final / Resolution: 2.809→29.277 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5606 0 60 0 5666
Biso mean--57.49 --
Num. residues----777
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0145742
X-RAY DIFFRACTIONf_angle_d2.3397801
X-RAY DIFFRACTIONf_chiral_restr0.104989
X-RAY DIFFRACTIONf_plane_restr0.011962
X-RAY DIFFRACTIONf_dihedral_angle_d18.5182007
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.8092-2.98510.3179570.265108717
2.9851-3.21530.32431340.2615254739
3.2153-3.53840.2991720.2418326450
3.5384-4.04920.26671740.2265330651
4.0492-5.09720.26581740.2075330951
5.0972-29.2770.2471780.2216334552

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