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Yorodumi- EMDB-36801: Potassium transporter KtrAB from Bacillus subtilis in ADP-bound s... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36801 | |||||||||
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Title | Potassium transporter KtrAB from Bacillus subtilis in ADP-bound state, focused refined on KtrA octamer | |||||||||
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: 2.84 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_36801.map.gz | 204 MB | EMDB map data format | |
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Header (meta data) | emd-36801-v30.xml emd-36801.xml | 17.8 KB 17.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_36801_fsc.xml | 13.4 KB | Display | FSC data file |
Images | emd_36801.png | 91.8 KB | ||
Masks | emd_36801_msk_1.map | 216 MB | Mask map | |
Filedesc metadata | emd-36801.cif.gz | 5.5 KB | ||
Others | emd_36801_half_map_1.map.gz emd_36801_half_map_2.map.gz | 200.4 MB 200.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36801 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36801 | HTTPS FTP |
-Related structure data
Related structure data | 8k16C 8k1kC 8k1sC 8k1tC 8k1uC 8xmhC 8xmiC 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_36801.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
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_36801_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36801_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36801_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: 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: 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) The molecule weight of KtrA octamer (chain A-H) is 0.199 MDa. |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
-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: Bacillus subtilis (bacteria) |
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: KtrB
Macromolecule | Name: KtrB / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Bacillus subtilis (bacteria) |
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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-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 |
-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: 6919 / Average exposure time: 2.5 sec. / Average electron dose: 36.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |