+Open data
-Basic information
Entry | Database: PDB / ID: 5n9y | ||||||
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Title | The full-length structure of ZntB | ||||||
Components | Zinc transport protein ZntBZinc transporter protein | ||||||
Keywords | MEMBRANE PROTEIN / ZntB / zinc transport / CorA | ||||||
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) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||
Authors | Cornelius, G. / Stetsenko, A. / Scheres, S.H.W. / Slotboom, D.J. / Guskov, A. | ||||||
Funding support | Netherlands, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5n9y.cif.gz | 275.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5n9y.ent.gz | 234.1 KB | Display | PDB format |
PDBx/mmJSON format | 5n9y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/5n9y ftp://data.pdbj.org/pub/pdb/validation_reports/n9/5n9y | HTTPS FTP |
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-Related structure data
Related structure data | 3605MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | Mass: 36652.082 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (strain K12) (bacteria) Gene: zntB, ydaN, b1342, JW1336 / Production host: Escherichia coli (E. coli) / References: UniProt: P64423 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Pentameric zntb transporter / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Escherichia coli (E. coli) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 100 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy |
Image recording | Electron dose: 2 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 333490 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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