+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-19816 | |||||||||
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Title | Structure of KefC Asp156Asn variant | |||||||||
Map data | ||||||||||
Sample |
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Keywords | KefC / Potassium / GSH / Mutant / TRANSPORT PROTEIN | |||||||||
Function / homology | Function and homology information glutathione-regulated potassium exporter activity / response to methylglyoxal / potassium:proton antiporter complex / intracellular pH elevation / regulation of pH / antiporter activity / toxic substance binding / proton transmembrane transport / regulation of intracellular pH / response to hydrogen peroxide ...glutathione-regulated potassium exporter activity / response to methylglyoxal / potassium:proton antiporter complex / intracellular pH elevation / regulation of pH / antiporter activity / toxic substance binding / proton transmembrane transport / regulation of intracellular pH / response to hydrogen peroxide / potassium ion transport / response to toxic substance / nucleotide binding / enzyme binding / protein homodimerization activity / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.98 Å | |||||||||
Authors | Gulati A / Kokane S / Drew D | |||||||||
Funding support | Sweden, European Union, 2 items
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Citation | Journal: To Be Published Title: Structure of KefC Asp156Asn variant Authors: Gulati A / Kokane S / Drew D | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_19816.map.gz | 26.6 MB | EMDB map data format | |
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Header (meta data) | emd-19816-v30.xml emd-19816.xml | 16.3 KB 16.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_19816_fsc.xml | 7.9 KB | Display | FSC data file |
Images | emd_19816.png | 162.3 KB | ||
Masks | emd_19816_msk_1.map | 52.7 MB | Mask map | |
Filedesc metadata | emd-19816.cif.gz | 5.6 KB | ||
Others | emd_19816_additional_1.map.gz emd_19816_half_map_1.map.gz emd_19816_half_map_2.map.gz | 47 MB 49 MB 49 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-19816 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-19816 | HTTPS FTP |
-Validation report
Summary document | emd_19816_validation.pdf.gz | 955.1 KB | Display | EMDB validaton report |
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Full document | emd_19816_full_validation.pdf.gz | 954.7 KB | Display | |
Data in XML | emd_19816_validation.xml.gz | 15.7 KB | Display | |
Data in CIF | emd_19816_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19816 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-19816 | HTTPS FTP |
-Related structure data
Related structure data | 9embMC 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_19816.map.gz / Format: CCP4 / Size: 52.7 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: 0.9967 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_19816_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Sharpened map
File | emd_19816_additional_1.map | ||||||||||||
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Annotation | Sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_19816_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_19816_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Homodimer of KefC Asp156Asn variant
Entire | Name: Homodimer of KefC Asp156Asn variant |
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Components |
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-Supramolecule #1: Homodimer of KefC Asp156Asn variant
Supramolecule | Name: Homodimer of KefC Asp156Asn variant / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Glutathione-regulated potassium-efflux system protein KefC
Macromolecule | Name: Glutathione-regulated potassium-efflux system protein KefC type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Theoretical: 61.182238 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDSHTLIQAL IYLGSAALIV PIAVRLGLGS VLGYLIAGCI IGPWGLRLVT DAESILHFAE IGVVLMLFII GLELDPQRLW KLRAAVFGG GALQMVICGG LLGLFCMLLG LRWQVAELIG MTLALSSTAI AMQAMNERNL MVTQMGRSAF AVLLFQNIAA I PLVAMIPL ...String: MDSHTLIQAL IYLGSAALIV PIAVRLGLGS VLGYLIAGCI IGPWGLRLVT DAESILHFAE IGVVLMLFII GLELDPQRLW KLRAAVFGG GALQMVICGG LLGLFCMLLG LRWQVAELIG MTLALSSTAI AMQAMNERNL MVTQMGRSAF AVLLFQNIAA I PLVAMIPL LATSSASTTM GAFALSALKV AGALVLVVLL GRYVTRPALR FVARSGLREV FSAVALFLVF GFGLLLEEVG LS MAMGAFL AGVLLASSEY RHALESDIEP FKGLLLGLFF IGVGMSIDFG TLLENPLRIV ILLLGFLIIK IAMLWLIARP LQV PNKQRR WFAVLLGQGS EFAFVVFGAA QMANVLEPEW AKSLTLAVAL SMAATPILLV ILNRLEQSST EEAREADEID EEQP RVIIA GFGRFGQITG RLLLSSGVKM VVLDHDPDHI ETLRKFGMKV FYGDATRMDL LESAGAAKAE VLINAIDDPQ TNLQL TEMV KEHFPHLQII ARARDVDHYI RLRQAGVEKP ERETFEGALK TGRLALESLG LGPYEARERA DVFRRFNIQM VEEMAM V UniProtKB: Glutathione-regulated potassium-efflux system protein KefC |
-Macromolecule #2: ADENOSINE MONOPHOSPHATE
Macromolecule | Name: ADENOSINE MONOPHOSPHATE / type: ligand / ID: 2 / Number of copies: 2 / Formula: AMP |
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Molecular weight | Theoretical: 347.221 Da |
Chemical component information | ChemComp-AMP: |
-Macromolecule #3: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]o...
Macromolecule | Name: (1R)-2-{[(S)-{[(2S)-2,3-dihydroxypropyl]oxy}(hydroxy)phosphoryl]oxy}-1-[(hexadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate type: ligand / ID: 3 / Number of copies: 2 / Formula: PGW |
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Molecular weight | Theoretical: 749.007 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 54.6 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |