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- PDB-6ki2: The STAS domain of cyanobacteria bicarbonate transporter BicA -

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Basic information

Entry
Database: PDB / ID: 6ki2
TitleThe STAS domain of cyanobacteria 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


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
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 transporter BicA
Similarity search - Component
Biological speciesSynechocystis sp. PCC 6803 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.197 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 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification

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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)35,5113
Polymers35,4152
Non-polymers961
Water1,67593
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: cross-linking
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-57 kcal/mol
Surface area14880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.050, 62.109, 57.036
Angle α, β, γ (deg.)90.000, 119.860, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Low affinity sulfate transporter / BicA


Mass: 17707.529 Da / Num. of mol.: 2 / Fragment: STAS domain / Mutation: T485D
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.47 Å3/Da / Density % sol: 50.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 mM Magnesium chloride, 2 mM Cobalt chloride, 50 mM HEPES, pH7.5, 2.0 M Ammonium sulphate, 1 mM spermine.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS3 R CdTe 300K / Detector: PIXEL / Date: Jul 2, 2017
RadiationMonochromator: Se / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.197→30 Å / Num. obs: 34281 / % possible obs: 99.8 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.046 / Rrim(I) all: 0.113 / Χ2: 1.437 / Net I/σ(I): 6.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.285.80.35417570.9380.1590.3890.7599.9
2.28-2.376.20.28517300.9680.1240.3110.71599.8
2.37-2.486.20.25317930.9690.110.2770.70399.9
2.48-2.615.90.21117350.970.0940.2320.76599.9
2.61-2.776.50.17217340.9840.0730.1870.87899.8
2.77-2.996.30.14217770.9870.0610.1551.00299.9
2.99-3.2960.11417510.9910.0510.1251.31999.9
3.29-3.766.30.09417860.9920.0410.1021.97299.6
3.76-4.736.10.07417810.9950.0330.0812.30199.8
4.73-306.10.08318220.9780.0380.0913.85899.7

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Phasing

PhasingMethod: SAD

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Processing

Software
NameVersionClassification
HKL-3000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.25data extraction
HKL-3000data reduction
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.197→28.581 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.37 / Phase error: 24.1
Details: the entry contains Friedel pairs in F_Plus/Minus columns
RfactorNum. reflection% reflection
Rfree0.2301 3421 9.98 %
Rwork0.2131 --
obs-34281 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 110.84 Å2 / Biso mean: 39.9066 Å2 / Biso min: 19.26 Å2
Refinement stepCycle: final / Resolution: 2.197→28.581 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2214 0 5 93 2312
Biso mean--35.7 46.05 -
Num. residues----292
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082244
X-RAY DIFFRACTIONf_angle_d1.0133024
X-RAY DIFFRACTIONf_chiral_restr0.041348
X-RAY DIFFRACTIONf_plane_restr0.004396
X-RAY DIFFRACTIONf_dihedral_angle_d13.601832
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.1975-2.22880.28681240.2092115393
2.2288-2.26210.34041620.21771277100
2.2621-2.29740.28971380.21211337100
2.2974-2.33510.30461320.2051317100
2.3351-2.37530.27791410.2046129099
2.3753-2.41850.23881460.20491255100
2.4185-2.4650.28191480.20321303100
2.465-2.51530.26891210.2003126599
2.5153-2.56990.32911540.20641346100
2.5699-2.62970.26321520.18771256100
2.6297-2.69540.27231500.19331284100
2.6954-2.76820.2871220.18121298100
2.7682-2.84960.22231530.19661325100
2.8496-2.94150.19491250.21151254100
2.9415-3.04650.24281420.20021307100
3.0465-3.16830.24951540.1929132299
3.1683-3.31230.22361460.18171287100
3.3123-3.48670.22151360.19221282100
3.4867-3.70470.2121660.1623128599
3.7047-3.990.16641430.1519127899
3.99-4.39030.23531380.161299100
4.3903-5.02260.18431340.1609127999
5.0226-6.31660.22651370.2206131399
6.3166-28.5810.21051570.1887124898
Refinement TLS params.Method: refined / Origin x: -0.6098 Å / Origin y: 15.5038 Å / Origin z: 16.9194 Å
111213212223313233
T0.2062 Å2-0.0078 Å20.0163 Å2-0.2402 Å2-0.0159 Å2--0.2373 Å2
L0.3659 °2-0.4358 °20.3965 °2-1.3933 °2-0.8264 °2--0.8494 °2
S0.0288 Å °0.0287 Å °-0.017 Å °-0.0243 Å °-0.0315 Å °0.013 Å °0.0047 Å °0.0453 Å °0.0129 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA402 - 547
2X-RAY DIFFRACTION1allB402 - 547
3X-RAY DIFFRACTION1allC1
4X-RAY DIFFRACTION1allS1 - 93

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