+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-14862 | |||||||||
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Title | KtrAB complex with N-terminal deletion of KtrB 1-19 | |||||||||
Map data | KtrAB complex with N-terminal deletion of KtrB 1-19 | |||||||||
Sample |
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Keywords | potassium transport / membrane protein / transporter | |||||||||
Function / homology | Function and homology information potassium:chloride symporter activity / monoatomic cation transmembrane transporter activity / potassium ion transport / ATP binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Vibrio alginolyticus (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.56 Å | |||||||||
Authors | Vonck J / Stautz J | |||||||||
Funding support | Germany, 2 items
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Citation | Journal: To Be Published Title: KtrAB complex with N-terminal deletion of KtrB 1-19 Authors: Stautz J | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_14862.map.gz | 26.6 MB | EMDB map data format | |
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Header (meta data) | emd-14862-v30.xml emd-14862.xml | 17.8 KB 17.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_14862_fsc.xml | 7.2 KB | Display | FSC data file |
Images | emd_14862.png | 168.4 KB | ||
Filedesc metadata | emd-14862.cif.gz | 6.1 KB | ||
Others | emd_14862_half_map_1.map.gz emd_14862_half_map_2.map.gz | 22.3 MB 22.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-14862 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-14862 | HTTPS FTP |
-Related structure data
Related structure data | 7zprMC 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_14862.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | KtrAB complex with N-terminal deletion of KtrB 1-19 | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2463 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_14862_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_14862_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : KtrAB complex with a second KtrB dimer attached
Entire | Name: KtrAB complex with a second KtrB dimer attached |
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Components |
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-Supramolecule #1: KtrAB complex with a second KtrB dimer attached
Supramolecule | Name: KtrAB complex with a second KtrB dimer attached / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: Vibrio alginolyticus (bacteria) |
Molecular weight | Theoretical: 390 KDa |
-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: Vibrio alginolyticus (bacteria) |
Molecular weight | Theoretical: 23.83692 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKTGDKQFAV IGLGRFGLAV CKELQDSGSQ VLAVDINEDR VKEAAGFVSQ AIVANCTHEE TVAELKLDDY DMVMIAIGAD VNASILATL IAKEAGVKSV WVKANDRFQA RVLQKIGADH IIMPERDMGI RVARKMLDKR VLEFHPLGSG LAMTEFVVGS R LMGKTLSD ...String: MKTGDKQFAV IGLGRFGLAV CKELQDSGSQ VLAVDINEDR VKEAAGFVSQ AIVANCTHEE TVAELKLDDY DMVMIAIGAD VNASILATL IAKEAGVKSV WVKANDRFQA RVLQKIGADH IIMPERDMGI RVARKMLDKR VLEFHPLGSG LAMTEFVVGS R LMGKTLSD LALCKVEGVQ VLGYKRGPEI IKAPDMSTTL EIGDLIIVVG PQDKLANKLK SL 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 / Details: N-terminal deletion of residue 1-19 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio alginolyticus (bacteria) |
Molecular weight | Theoretical: 47.411094 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: AKGGEPRIIL LSFLGVLLPS AVLLTLPVFS VSGLSITDAL FTATSAISVT GLGVVDTGQH FTLAGKILLM CLMQIGGLGQ MTLSAVLLY MFGVRLSLRQ QALAKEALGQ ERQVNLRRLV KKIVTFALVA EAIGFVFLSY RWVPEMGWQT GMFYALFHSI S AFNNAGFA ...String: AKGGEPRIIL LSFLGVLLPS AVLLTLPVFS VSGLSITDAL FTATSAISVT GLGVVDTGQH FTLAGKILLM CLMQIGGLGQ MTLSAVLLY MFGVRLSLRQ QALAKEALGQ ERQVNLRRLV KKIVTFALVA EAIGFVFLSY RWVPEMGWQT GMFYALFHSI S AFNNAGFA LFSDSMMSFV NDPLVSFTLA GLFIFGGLGF TVIGDVWRHW RKGFHFLHIH TKIMLIATPL LLLVGTVLFW LL ERHNPNT MGSLTTGGQW LAAFFQSASA RTAGFNSVDL TQFTQPALLI MIVLMLIGAG STSTGGGIKV STFAVAFMAT WTF LRQKKH VVMFKRTVNW PTVTKSLAII VVSGAILTTA MFLLMLTEKA SFDKVMFETI SAFATVGLTA GLTAELSEPG KYIM IVVMI IGRIGPLTLA YMLARPEPTL IKYPEDTVLT G UniProtKB: Ktr system potassium uptake protein B |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 8 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: ADENOSINE-5'-DIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 8 / Formula: ADP |
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Molecular weight | Theoretical: 427.201 Da |
Chemical component information | ChemComp-ADP: |
-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
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE / 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 | Calibrated defocus max: 2.5 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 60168 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.3000000000000003 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 105000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 7109 / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Initial model | PDB ID: Chain - Source name: PDB / Chain - Initial model type: experimental model |
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Details | The model was fitted to the map in Chimera and the missing residues were deleted. |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-7zpr: |