+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33620 | |||||||||
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Title | Cryo-EM structure of a eukaryotic ZnT8 at a low pH | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Zinc transporter / SLC30 / ZnT / CDF / Proton-coupled antiporter / MEMBRANE PROTEIN | |||||||||
Function / homology | Function and homology information Insulin processing / Zinc efflux and compartmentalization by the SLC30 family / zinc ion import into organelle / zinc:proton antiporter activity / zinc ion transmembrane transporter activity / insulin secretion / transport vesicle membrane / response to zinc ion / response to glucose / secretory granule membrane ...Insulin processing / Zinc efflux and compartmentalization by the SLC30 family / zinc ion import into organelle / zinc:proton antiporter activity / zinc ion transmembrane transporter activity / insulin secretion / transport vesicle membrane / response to zinc ion / response to glucose / secretory granule membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Xenopus tropicalis (tropical clawed frog) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.72 Å | |||||||||
Authors | Zhang S / Fu C / Luo Y / Sun Z / Su Z / Zhou X | |||||||||
Funding support | China, 1 items
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Citation | Journal: J Struct Biol / Year: 2023 Title: Cryo-EM structure of a eukaryotic zinc transporter at a low pH suggests its Zn-releasing mechanism. Authors: Senfeng Zhang / Chunting Fu / Yongbo Luo / Qingrong Xie / Tong Xu / Ziyi Sun / Zhaoming Su / Xiaoming Zhou / Abstract: Zinc transporter 8 (ZnT8) is mainly expressed in pancreatic islet β cells and is responsible for H-coupled uptake (antiport) of Zn into the lumen of insulin secretory granules. Structures of human ...Zinc transporter 8 (ZnT8) is mainly expressed in pancreatic islet β cells and is responsible for H-coupled uptake (antiport) of Zn into the lumen of insulin secretory granules. Structures of human ZnT8 and its prokaryotic homolog YiiP have provided structural basis for constructing a plausible transport cycle for Zn. However, the mechanistic role that protons play in the transport process remains unclear. Here we present a lumen-facing cryo-EM structure of ZnT8 from Xenopus tropicalis (xtZnT8) in the presence of Zn at a luminal pH (5.5). Compared to a Zn-bound xtZnT8 structure at a cytosolic pH (7.5), the low-pH structure displays an empty transmembrane Zn-binding site with a disrupted coordination geometry. Combined with a Zn-binding assay our data suggest that protons may disrupt Zn coordination at the transmembrane Zn-binding site in the lumen-facing state, thus facilitating Zn release from ZnT8 into the lumen. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33620.map.gz | 59.5 MB | EMDB map data format | |
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Header (meta data) | emd-33620-v30.xml emd-33620.xml | 16.8 KB 16.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33620_fsc.xml | 8.9 KB | Display | FSC data file |
Images | emd_33620.png | 110.3 KB | ||
Filedesc metadata | emd-33620.cif.gz | 5.8 KB | ||
Others | emd_33620_half_map_1.map.gz emd_33620_half_map_2.map.gz | 59.2 MB 59.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33620 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33620 | HTTPS FTP |
-Validation report
Summary document | emd_33620_validation.pdf.gz | 808.1 KB | Display | EMDB validaton report |
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Full document | emd_33620_full_validation.pdf.gz | 807.7 KB | Display | |
Data in XML | emd_33620_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | emd_33620_validation.cif.gz | 21.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33620 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33620 | HTTPS FTP |
-Related structure data
Related structure data | 7y5hMC 7y5gC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_33620.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_33620_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_33620_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : xtZnT8 dimer complexed with zinc and proton
Entire | Name: xtZnT8 dimer complexed with zinc and proton |
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Components |
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-Supramolecule #1: xtZnT8 dimer complexed with zinc and proton
Supramolecule | Name: xtZnT8 dimer complexed with zinc and proton / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Xenopus tropicalis (tropical clawed frog) |
-Macromolecule #1: Zinc transporter 8
Macromolecule | Name: Zinc transporter 8 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Xenopus tropicalis (tropical clawed frog) |
Molecular weight | Theoretical: 41.539031 KDa |
Recombinant expression | Organism: Komagataella pastoris (fungus) |
Sequence | String: MKGSEEAYLV SDKATKMYSL TKDSEKNHPS KPPLQDEENP QSKYHCHNNN KKAYDARQRE QTFAKKKLCI ASLICFVFIS AEIVGGYIA GSLAVVTDAA HLLVDLSSFF ISLCSLWLSS KSSTTRLTFG WHRAEILGAL MSVITIWLVT GVLVYLACER L IRPDYTID ...String: MKGSEEAYLV SDKATKMYSL TKDSEKNHPS KPPLQDEENP QSKYHCHNNN KKAYDARQRE QTFAKKKLCI ASLICFVFIS AEIVGGYIA GSLAVVTDAA HLLVDLSSFF ISLCSLWLSS KSSTTRLTFG WHRAEILGAL MSVITIWLVT GVLVYLACER L IRPDYTID GTVMLITSAC ALGANLVLAL ILHQSGHGHS HAGGKHEHMA SEYKPQTNAS IRAAFIHVIG DLFQSISVLI SA LIIYFKP EYKMADPICT FIFSIFVLIT TVTVLRDLLT VLMEGTPRGI HYSDVKQSIL AVDGVKSVHS LHLWALTMNQ VIL SAHIAT DIVGESKRIL KDVTQNVFAR FPFHSVTIQV EPIEDQSPEC MFCYEPTQ UniProtKB: Proton-coupled zinc antiporter SLC30A8 |
-Macromolecule #2: ZINC ION
Macromolecule | Name: ZINC ION / type: ligand / ID: 2 / Number of copies: 4 / Formula: ZN |
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Molecular weight | Theoretical: 65.409 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 8.0 mg/mL |
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Buffer | pH: 5.5 Details: 20 mM MES-Na pH 5.5, 150 mM NaCl, 5 mM 2-mercaptoethanol and 0.5 mM DDM |
Grid | Model: Quantifoil R2/1 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV / Details: blot for 2-3 s before plunging. |
Details | This sample was monodisperse. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 63.9 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: -1.7 µm / Nominal defocus min: -1.1 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |