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- EMDB-36801: Potassium transporter KtrAB from Bacillus subtilis in ADP-bound s... -
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Open data
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Basic information
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Title | Potassium transporter KtrAB from Bacillus subtilis in ADP-bound state, focused refined on KtrA octamer | |||||||||
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![]() | KtrAB / RCK / potassium / transporter / TRANSPORT PROTEIN | |||||||||
Function / homology | ![]() potassium:chloride symporter activity / monoatomic cation transmembrane transporter activity / potassium ion transport / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.84 Å | |||||||||
![]() | Chang YK / Chiang WT / Hu NJ / Tsai MD | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural basis and synergism of ATP and Na activation in bacterial K uptake system KtrAB. Authors: Wesley Tien Chiang / Yao-Kai Chang / Wei-Han Hui / Shu-Wei Chang / Chen-Yi Liao / Yi-Chuan Chang / Chun-Jung Chen / Wei-Chen Wang / Chien-Chen Lai / Chun-Hsiung Wang / Siou-Ying Luo / Ya- ...Authors: Wesley Tien Chiang / Yao-Kai Chang / Wei-Han Hui / Shu-Wei Chang / Chen-Yi Liao / Yi-Chuan Chang / Chun-Jung Chen / Wei-Chen Wang / Chien-Chen Lai / Chun-Hsiung Wang / Siou-Ying Luo / Ya-Ping Huang / Shan-Ho Chou / Tzyy-Leng Horng / Ming-Hon Hou / Stephen P Muench / Ren-Shiang Chen / Ming-Daw Tsai / Nien-Jen Hu / ![]() ![]() Abstract: The K uptake system KtrAB is essential for bacterial survival in low K environments. The activity of KtrAB is regulated by nucleotides and Na. Previous studies proposed a putative gating mechanism of ...The K uptake system KtrAB is essential for bacterial survival in low K environments. The activity of KtrAB is regulated by nucleotides and Na. Previous studies proposed a putative gating mechanism of KtrB regulated by KtrA upon binding to ATP or ADP. However, how Na activates KtrAB and the Na binding site remain unknown. Here we present the cryo-EM structures of ATP- and ADP-bound KtrAB from Bacillus subtilis (BsKtrAB) both solved at 2.8 Å. A cryo-EM density at the intra-dimer interface of ATP-KtrA was identified as Na, as supported by X-ray crystallography and ICP-MS. Thermostability assays and functional studies demonstrated that Na binding stabilizes the ATP-bound BsKtrAB complex and enhances its K flux activity. Comparing ATP- and ADP-BsKtrAB structures suggests that BsKtrB Arg417 and Phe91 serve as a channel gate. The synergism of ATP and Na in activating BsKtrAB is likely applicable to Na-activated K channels in central nervous system. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 204 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 18.3 KB 18.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.4 KB | Display | ![]() |
Images | ![]() | 91.8 KB | ||
Masks | ![]() | 216 MB | ![]() | |
Filedesc metadata | ![]() | 5.6 KB | ||
Others | ![]() ![]() | 200.4 MB 200.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 21.8 KB | Display | |
Data in CIF | ![]() | 28.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8k16C ![]() 8k1kC ![]() 8k1sC ![]() 8k1tC ![]() 8k1uC ![]() 8xmhC ![]() 8xmiC C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Density Histograms |
-Half map: #1
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Density Histograms |
-Half map: #2
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Density Histograms |
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Sample components
-Entire : Bacillus subtilis KtrAB potassium transporter
Entire | Name: Bacillus subtilis KtrAB potassium transporter |
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Components |
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-Supramolecule #1: Bacillus subtilis KtrAB potassium transporter
Supramolecule | Name: Bacillus subtilis KtrAB potassium transporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: KtrAB 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). The molecule weight of KtrAB complex (chain A-L) is 0.393 MDa |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 199 KDa |
-Supramolecule #2: KtrA octamer
Supramolecule | Name: KtrA octamer / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 Details: KtrA ocatmer (chain A-H) The molecule weight of KtrA octamer (chain A-H) is 0.199 MDa. |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: KtrB dimer
Supramolecule | Name: KtrB dimer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 Details: Two KtrB dimers (chain I-J and chain K-L) The molecule weight of each KtrB dimer is 0.097 MDa |
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-Macromolecule #1: KtrA
Macromolecule | Name: KtrA / type: protein_or_peptide / ID: 1 / Details: KtrA octamer / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MGRIKNKQFA VIGLGRFGGS ICKELHRMGH EVLAVDINEE KVNAYASYAT HAVIANATEE NELLSLGIRN FEYVIVAIGA NIQASTLTT LLLKELDIPN IWVKAQNYYH HKVLEKIGAD RIIHPEKDMG VKIAQSLSDE NVLNYIDLSD EYSIVELLAT R KLDSKSII ...String: MGRIKNKQFA VIGLGRFGGS ICKELHRMGH EVLAVDINEE KVNAYASYAT HAVIANATEE NELLSLGIRN FEYVIVAIGA NIQASTLTT LLLKELDIPN IWVKAQNYYH HKVLEKIGAD RIIHPEKDMG VKIAQSLSDE NVLNYIDLSD EYSIVELLAT R KLDSKSII DLNVRAKYGC TILAIKHHGD ICLSPAPEDI IREQDCLVIM GHKKDIKRFE NEGM UniProtKB: Ktr system potassium uptake protein A |
-Macromolecule #2: KtrB
Macromolecule | Name: KtrB / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MTLQKDKVIK WVRFTPPQVL AIGFFLTIII GAVLLMLPIS TTKPLSWIDA LFTAASATTV TGLAVVDTGT QFTVFGQTVI MGLIQIGGL GFMTFAVLIV MILGKKIGLK ERMLVQEALN QPTIGGVIGL VKVLFLFSIS IELIAALILS IRLVPQYGWS S GLFASLFH ...String: MTLQKDKVIK WVRFTPPQVL AIGFFLTIII GAVLLMLPIS TTKPLSWIDA LFTAASATTV TGLAVVDTGT QFTVFGQTVI MGLIQIGGL GFMTFAVLIV MILGKKIGLK ERMLVQEALN QPTIGGVIGL VKVLFLFSIS IELIAALILS IRLVPQYGWS S GLFASLFH AISAFNNAGF SLWPDNLMSY VGDPTVNLVI TFLFITGGIG FTVLFDVMKN RRFKTFSLHT KLMLTGTLML NA IAMLTVF ILEYSNPGTL GHLHIVDKLW ASYFQAVTPR TAGFNSLDFG SMREGTIVFT LLLMFIGAGS ASTASGIKLT TFI VILTSV IAYLRGKKET VIFRRSIKYP IIIKALAVSV TSLFIVFLGI FALTITEQAP FLQIVFETFS AFGTVGLTMG LTPE LTTAG KCIIIVIMFI GRIGPLTFVF SFAKTEQSNI RYPDGEVFTG UniProtKB: Ktr system potassium uptake protein B |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.24 mg/mL |
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Buffer | pH: 8 Details: 20 mM Tris-HCl pH 8.0, 70 mM NaCl, 30 mM KCl, 0.75 mM 6-cyclohexyl-1-hexyl-beta-D-maltoside, 0.1 mM ADP |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 15 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 6919 / Average exposure time: 2.5 sec. / Average electron dose: 36.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |