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Yorodumi- EMDB-36579: A cryo-EM structure of the bovine chromogranin B dimer at a nomin... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-36579 | |||||||||||||||||||||||||||||||||||||||
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Title | A cryo-EM structure of the bovine chromogranin B dimer at a nominal resolution of ~0.35 nm | |||||||||||||||||||||||||||||||||||||||
Map data | Chromogranin B dimers purified from bovine pancreatic granules studied by single particle cryo-EM. | |||||||||||||||||||||||||||||||||||||||
Sample |
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Keywords | CHGB dimer C2 symmetry anion shunt pathway secretory granule regulated secretory pathways / TRANSPORT PROTEIN | |||||||||||||||||||||||||||||||||||||||
Biological species | Bos taurus (cattle) | |||||||||||||||||||||||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||||||||||||||||||||||||||
Authors | Jiang Q-X / Zhu MX / Yadav GP | |||||||||||||||||||||||||||||||||||||||
Funding support | United States, 12 items
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Citation | Journal: Front Mol Neurosci / Year: 2023 Title: Chromogranin B (CHGB) is dimorphic and responsible for dominant anion channels delivered to cell surface via regulated secretion. Authors: Gaya P Yadav / Haiyuan Wang / Joke Ouwendijk / Stephen Cross / Qiaochu Wang / Feng Qin / Paul Verkade / Michael X Zhu / Qiu-Xing Jiang / Abstract: Regulated secretion is conserved in all eukaryotes. In vertebrates granin family proteins function in all key steps of regulated secretion. Phase separation and amyloid-based storage of proteins and ...Regulated secretion is conserved in all eukaryotes. In vertebrates granin family proteins function in all key steps of regulated secretion. Phase separation and amyloid-based storage of proteins and small molecules in secretory granules require ion homeostasis to maintain their steady states, and thus need ion conductances in granule membranes. But granular ion channels are still elusive. Here we show that granule exocytosis in neuroendocrine cells delivers to cell surface dominant anion channels, to which chromogranin B (CHGB) is critical. Biochemical fractionation shows that native CHGB distributes nearly equally in soluble and membrane-bound forms, and both reconstitute highly selective anion channels in membrane. Confocal imaging resolves granular membrane components including proton pumps and CHGB in puncta on the cell surface after stimulated exocytosis. High pressure freezing immuno-EM reveals a major fraction of CHGB at granule membranes in rat pancreatic β-cells. A cryo-EM structure of bCHGB dimer of a nominal 3.5 Å resolution delineates a central pore with end openings, physically sufficient for membrane-spanning and large single channel conductance. Together our data support that CHGB-containing (CHGB+) channels are characteristic of regulated secretion, and function in granule ion homeostasis near the plasma membrane or possibly in other intracellular processes. | |||||||||||||||||||||||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_36579.map.gz | 36.2 MB | EMDB map data format | |
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Header (meta data) | emd-36579-v30.xml emd-36579.xml | 15.6 KB 15.6 KB | Display Display | EMDB header |
Images | emd_36579.png | 163.2 KB | ||
Others | emd_36579_half_map_1.map.gz emd_36579_half_map_2.map.gz | 35.6 MB 35.6 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-36579 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-36579 | HTTPS FTP |
-Validation report
Summary document | emd_36579_validation.pdf.gz | 846.2 KB | Display | EMDB validaton report |
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Full document | emd_36579_full_validation.pdf.gz | 845.7 KB | Display | |
Data in XML | emd_36579_validation.xml.gz | 11.1 KB | Display | |
Data in CIF | emd_36579_validation.cif.gz | 12.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36579 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-36579 | HTTPS FTP |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_36579.map.gz / Format: CCP4 / Size: 38.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Chromogranin B dimers purified from bovine pancreatic granules studied by single particle cryo-EM. | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: first half map
File | emd_36579_half_map_1.map | ||||||||||||
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Annotation | first half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: 2nd half map
File | emd_36579_half_map_2.map | ||||||||||||
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Annotation | 2nd half map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : chromogranin B
Entire | Name: chromogranin B |
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Components |
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-Supramolecule #1: chromogranin B
Supramolecule | Name: chromogranin B / type: organelle_or_cellular_component / ID: 1 / Parent: 0 Details: bovine proteins purified from pancreatic secretory granules |
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Source (natural) | Organism: Bos taurus (cattle) / Organ: pancreas |
Molecular weight | Theoretical: 190 MDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 6.5 |
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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: 52.0 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: 3.5 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER Details: Ab initio model from cisTEM and cryoSPARC, and a reference model from angular reconstitution of a negative stain dataset. |
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Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) Details: CryoSPARC and relion were used for independent analyses to generate similar results. Number images used: 70000 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD Details: Initial assignment was based on the reference model. |
Final angle assignment | Type: MAXIMUM LIKELIHOOD Details: Refinement was done in cryoSPARC and relion separately. |