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Yorodumi- EMDB-0087: Template-free detection and classification of microsomal membrane... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0087 | |||||||||
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Title | Template-free detection and classification of microsomal membrane bound complexes | |||||||||
Map data | Non-translocon associated OST complex | |||||||||
Sample |
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Biological species | Canis lupus familiaris (dog) | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 16.0 Å | |||||||||
Authors | Martinez-Sanchez A / Lucic V | |||||||||
Citation | Journal: Nat Commun / Year: 2015 Title: Structure of the native Sec61 protein-conducting channel. Authors: Stefan Pfeffer / Laura Burbaum / Pia Unverdorben / Markus Pech / Yuxiang Chen / Richard Zimmermann / Roland Beckmann / Friedrich Förster / Abstract: In mammalian cells, secretory and membrane proteins are translocated across or inserted into the endoplasmic reticulum (ER) membrane by the universally conserved protein-conducting channel Sec61, ...In mammalian cells, secretory and membrane proteins are translocated across or inserted into the endoplasmic reticulum (ER) membrane by the universally conserved protein-conducting channel Sec61, which has been structurally studied in isolated, detergent-solubilized states. Here we structurally and functionally characterize native, non-solubilized ribosome-Sec61 complexes on rough ER vesicles using cryo-electron tomography and ribosome profiling. Surprisingly, the 9-Å resolution subtomogram average reveals Sec61 in a laterally open conformation, even though the channel is not in the process of inserting membrane proteins into the lipid bilayer. In contrast to recent mechanistic models for polypeptide translocation and insertion, our results indicate that the laterally open conformation of Sec61 is the only conformation present in the ribosome-bound translocon complex, independent of its functional state. Consistent with earlier functional studies, our structure suggests that the ribosome alone, even without a nascent chain, is sufficient for lateral opening of Sec61 in a lipid environment. | |||||||||
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_0087.map.gz | 14.4 MB | EMDB map data format | |
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Header (meta data) | emd-0087-v30.xml emd-0087.xml | 17.6 KB 17.6 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_0087_fsc.xml | 5.8 KB | Display | FSC data file |
Images | emd_0087.png | 30.5 KB | ||
Others | emd_0087_half_map_1.map.gz emd_0087_half_map_2.map.gz | 11.9 MB 11.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0087 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0087 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0087.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Non-translocon associated OST complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.62 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Non-translocon associated OST complex - 1st half
File | emd_0087_half_map_1.map | ||||||||||||
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Annotation | Non-translocon associated OST complex - 1st half | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Non-translocon associated OST complex - 2nd half
File | emd_0087_half_map_2.map | ||||||||||||
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Annotation | Non-translocon associated OST complex - 2nd half | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Canine pancreatic ER vesicles
Entire | Name: Canine pancreatic ER vesicles |
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Components |
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-Supramolecule #1: Canine pancreatic ER vesicles
Supramolecule | Name: Canine pancreatic ER vesicles / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Details: The same sample as the one used for EMD-3068 - 72 |
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Source (natural) | Organism: Canis lupus familiaris (dog) / Organ: pancreas / Organelle: rough endoplasmic reticulum |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | subtomogram averaging |
Aggregation state | particle |
-Sample preparation
Concentration | 2.0 mg/mL | ||||||||||||
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Buffer | pH: 7.6 Component:
Details: The same as for EMD-3068 - 72 | ||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 70 % / Instrument: FEI VITROBOT MARK IV / Details: Blot 3 seconds before plunging.. | ||||||||||||
Details | The same sample was used for EMD-3068 - 72 |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.0 µm / Nominal defocus min: 3.0 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Details | The same as for EMD-3068 - 72 |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 0.75 e/Å2 / Details: The same as for EMD-3068 - 72 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Protocol: AB INITIO MODEL |
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