+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3605 | |||||||||
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Title | The full-length structure of ZntB | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information zinc efflux transmembrane transporter activity / zinc ion import across plasma membrane / solute:proton symporter activity / zinc ion transmembrane transporter activity / cobalt ion transmembrane transporter activity / zinc ion transmembrane transport / magnesium ion transmembrane transporter activity / cobalt ion binding / plasma membrane => GO:0005886 / magnesium ion binding Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) / Escherichia coli (strain K12) (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Cornelius G / Stetsenko A / Scheres SHW / Slotboom DJ / Guskov A | |||||||||
Funding support | Netherlands, 1 items
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Citation | Journal: Nat Commun / Year: 2017 Title: The structural basis of proton driven zinc transport by ZntB. Authors: Cornelius Gati / Artem Stetsenko / Dirk J Slotboom / Sjors H W Scheres / Albert Guskov / Abstract: Zinc is an essential microelement to sustain all forms of life. However, excess of zinc is toxic, therefore dedicated import, export and storage proteins for tight regulation of the zinc ...Zinc is an essential microelement to sustain all forms of life. However, excess of zinc is toxic, therefore dedicated import, export and storage proteins for tight regulation of the zinc concentration have evolved. In Enterobacteriaceae, several membrane transporters are involved in zinc homeostasis and linked to virulence. ZntB has been proposed to play a role in the export of zinc, but the transport mechanism of ZntB is poorly understood and based only on experimental characterization of its distant homologue CorA magnesium channel. Here, we report the cryo-electron microscopy structure of full-length ZntB from Escherichia coli together with the results of isothermal titration calorimetry, and radio-ligand uptake and fluorescent transport assays on ZntB reconstituted into liposomes. Our results show that ZntB mediates Zn uptake, stimulated by a pH gradient across the membrane, using a transport mechanism that does not resemble the one proposed for homologous CorA channels. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_3605.map.gz | 2.5 MB | EMDB map data format | |
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Header (meta data) | emd-3605-v30.xml emd-3605.xml | 9.6 KB 9.6 KB | Display Display | EMDB header |
Images | emd_3605.png | 128.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3605 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3605 | HTTPS FTP |
-Validation report
Summary document | emd_3605_validation.pdf.gz | 227.9 KB | Display | EMDB validaton report |
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Full document | emd_3605_full_validation.pdf.gz | 227 KB | Display | |
Data in XML | emd_3605_validation.xml.gz | 5.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3605 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3605 | HTTPS FTP |
-Related structure data
Related structure data | 5n9yMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_3605.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.43 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Pentameric zntb transporter
Entire | Name: Pentameric zntb transporter |
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Components |
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-Supramolecule #1: Pentameric zntb transporter
Supramolecule | Name: Pentameric zntb transporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
-Macromolecule #1: Zinc transport protein ZntB
Macromolecule | Name: Zinc transport protein ZntB / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Escherichia coli (strain K12) (bacteria) |
Molecular weight | Theoretical: 36.652082 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MEAIKGSDVN VPDAVFAWML DGRGGVKPLE NTDVIDEAHP CWLHLNYVHH DSAQWLATTP LLPNNVRDAL AGESTRPRVS RLGEGTLIT LRCINGSTDE RPDQLVAMRV YMDGRLIVST RQRKVLALDD VVSDLEEGTG PTDCGGWLVD VCDALTDHSS E FIEQLHDK ...String: MEAIKGSDVN VPDAVFAWML DGRGGVKPLE NTDVIDEAHP CWLHLNYVHH DSAQWLATTP LLPNNVRDAL AGESTRPRVS RLGEGTLIT LRCINGSTDE RPDQLVAMRV YMDGRLIVST RQRKVLALDD VVSDLEEGTG PTDCGGWLVD VCDALTDHSS E FIEQLHDK IIDLEDNLLD QQIPPRGFLA LLRKQLIVMR RYMAPQRDVY ARLASERLPW MSDDQRRRMQ DIADRLGRGL DE IDACIAR TGVMADEIAQ VMQENLARRT YTMSLMAMVF LPSTFLTGLF GVNLGGIPGG GWQFGFSIFC ILLVVLIGGV ALW LHRSKW L |
-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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Grid | Model: Quantifoil / Material: GOLD / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 100 K |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 2.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 333490 |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: NOT APPLICABLE |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-5n9y: |