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Yorodumi- EMDB-36803: Potassium transporter KtrAB from Bacillus subtilis in ATP-bound s... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36803 | |||||||||
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Title | Potassium transporter KtrAB from Bacillus subtilis in ATP-bound state with addition of MgCl2 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | KtrAB / RCK / potassium / transporter / TRANSPORT PROTEIN | |||||||||
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 | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.48 Å | |||||||||
Authors | Chang YK / Chiang WT / Hu NJ / Tsai MD | |||||||||
Funding support | Taiwan, 1 items
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Citation | Journal: Nat Commun / Year: 2024 Title: Structural basis and synergism of ATP and Na+ activation in bacterial K+ uptake system KtrAB Authors: Chiang WT / Chang YK / Hui WH / Chang SW / Liao CY / Chang YC / Chen CJ / Wang WC / Lai CC / Wang CH / Luo SY / Huang YP / Chou SH / Horng TL / Hou MH / Muench SP / Chen RS / Tsai MD / Hu NJ | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36803.map.gz | 203.8 MB | EMDB map data format | |
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Header (meta data) | emd-36803-v30.xml emd-36803.xml | 21.9 KB 21.9 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36803_fsc.xml | 13.3 KB | Display | FSC data file |
Images | emd_36803.png | 107.4 KB | ||
Masks | emd_36803_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-36803.cif.gz | 6.7 KB | ||
Others | emd_36803_additional_1.map.gz emd_36803_half_map_1.map.gz emd_36803_half_map_2.map.gz | 191 MB 200.1 MB 200.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36803 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36803 | HTTPS FTP |
-Related structure data
Related structure data | 8k1tMC 8k16C 8k1kC 8k1sC 8k1uC 8xmhC 8xmiC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_36803.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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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
File | emd_36803_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: DeepEMhancer sharpening map
File | emd_36803_additional_1.map | ||||||||||||
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Annotation | DeepEMhancer sharpening map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36803_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36803_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-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: #1-#2 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). |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
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) |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
Molecular weight | Theoretical: 97 KDa |
-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) |
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-Macromolecule #1: Ktr system potassium uptake protein A
Macromolecule | Name: Ktr system potassium uptake protein A / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
Molecular weight | Theoretical: 24.91676 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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: Ktr system potassium uptake protein B
Macromolecule | Name: Ktr system potassium uptake protein B / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
Molecular weight | Theoretical: 48.471539 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
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 |
-Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 8 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #4: SODIUM ION
Macromolecule | Name: SODIUM ION / type: ligand / ID: 4 / Number of copies: 4 |
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Molecular weight | Theoretical: 22.99 Da |
-Macromolecule #5: POTASSIUM ION
Macromolecule | Name: POTASSIUM ION / type: ligand / ID: 5 / Number of copies: 4 / Formula: K |
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Molecular weight | Theoretical: 39.098 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.15 mg/mL |
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Buffer | pH: 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 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / 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 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 105000 |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 6052 / Average exposure time: 2.5 sec. / Average electron dose: 36.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |