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- PDB-8k1t: Potassium transporter KtrAB from Bacillus subtilis in ATP-bound s... -

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Basic information

Entry
Database: PDB / ID: 8k1t
TitlePotassium transporter KtrAB from Bacillus subtilis in ATP-bound state with addition of MgCl2
Components
  • Ktr system potassium uptake protein A
  • Ktr system potassium uptake protein B
KeywordsTRANSPORT PROTEIN / KtrAB / RCK / potassium / transporter
Function / homology
Function and homology information


potassium:chloride symporter activity / monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / plasma membrane
Similarity search - Function
TrkH potassium transport family / Cation transporter / Cation transport protein / Regulator of K+ conductance, N-terminal / TrkA-N domain / RCK N-terminal domain profile. / Regulator of K+ conductance, C-terminal / Regulator of K+ conductance, C-terminal domain superfamily / TrkA-C domain / RCK C-terminal domain profile. / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / : / Ktr system potassium uptake protein A / Ktr system potassium uptake protein B
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsChang, Y.K. / Chiang, W.T. / Hu, N.J. / Tsai, M.D.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: Nat Commun / Year: 2024
Title: Structural basis and synergism of ATP and Na+ activation in bacterial K+ uptake system KtrAB
Authors: Chiang, W.T. / Chang, Y.K. / Hui, W.H. / Chang, S.W. / Liao, C.Y. / Chang, Y.C. / Chen, C.J. / Wang, W.C. / Lai, C.C. / Wang, C.H. / Luo, S.Y. / Huang, Y.P. / Chou, S.H. / Horng, T.L. / Hou, ...Authors: Chiang, W.T. / Chang, Y.K. / Hui, W.H. / Chang, S.W. / Liao, C.Y. / Chang, Y.C. / Chen, C.J. / Wang, W.C. / Lai, C.C. / Wang, C.H. / Luo, S.Y. / Huang, Y.P. / Chou, S.H. / Horng, T.L. / Hou, M.H. / Muench, S.P. / Chen, R.S. / Tsai, M.D. / Hu, N.J.
History
DepositionJul 11, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ktr system potassium uptake protein A
B: Ktr system potassium uptake protein A
C: Ktr system potassium uptake protein A
D: Ktr system potassium uptake protein A
E: Ktr system potassium uptake protein A
F: Ktr system potassium uptake protein A
G: Ktr system potassium uptake protein A
H: Ktr system potassium uptake protein A
I: Ktr system potassium uptake protein B
J: Ktr system potassium uptake protein B
K: Ktr system potassium uptake protein B
L: Ktr system potassium uptake protein B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)397,52628
Polymers393,22012
Non-polymers4,30616
Water0
1


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

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Components

#1: Protein
Ktr system potassium uptake protein A / K(+)-uptake protein KtrA


Mass: 24916.760 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ktrA, yuaA, BSU31090 / Production host: Escherichia coli (E. coli) / References: UniProt: O32080
#2: Protein
Ktr system potassium uptake protein B / K(+)-uptake protein KtrB


Mass: 48471.539 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: ktrB, yubG, BSU31100 / Production host: Escherichia coli (E. coli) / References: UniProt: O32081
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
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

Component
IDNameTypeDetailsEntity IDParent-IDSource
1Bacillus subtilis KtrAB potassium transporterCOMPLEXKtrAB complex(chain A-L). KtrAB complex in solution was composed of one KtrA octamer (chain A-H) and two KtrB dimer (chain I-J and chain K-L).#1-#20RECOMBINANT
2KtrA octamerCOMPLEXKtrA ocatmer (chain A-H)#11RECOMBINANT
3KtrB dimerCOMPLEXTwo KtrB dimers (chain I-J and chain K-L)#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.393 MDaNO
210.199 MDaNO
320.097 MDaNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Bacillus subtilis (bacteria)1423
32Bacillus subtilis (bacteria)1423
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
32Escherichia coli (E. coli)562
Buffer solutionpH: 8
Details: 20 mM Tris-HCl pH 8.0, 70 mM NaCl, 30 mM KCl, 2 mM MgCl2, 0.75 mM 6-cyclohexyl-1-hexyl-beta-D-maltoside, and 1 mM ATP
SpecimenConc.: 0.15 mg/ml / Embedding 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: 277 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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 1500 nm
Image recordingAverage exposure time: 2.5 sec. / Electron dose: 36 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 6052

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Processing

EM software
IDNameVersionCategory
7UCSF Chimera1.14model fitting
12cryoSPARC3.23D reconstruction
13PHENIX1.19.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 549841 / Symmetry type: POINT
Atomic model buildingPDB-ID: 4J7C

4j7c


Accession code: 4J7C / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00223152
ELECTRON MICROSCOPYf_angle_d0.40831464
ELECTRON MICROSCOPYf_dihedral_angle_d7.6888116
ELECTRON MICROSCOPYf_chiral_restr0.0393832
ELECTRON MICROSCOPYf_plane_restr0.0033816

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