[English] 日本語
Yorodumi- EMDB-21931: Human ER membrane protein complex in a lipid nanodisc, multi-body... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-21931 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Human ER membrane protein complex in a lipid nanodisc, multi-body refinement, cytosolic map | |||||||||
Map data | 'cytosolic' human EMC post-processed, sharpened, and masked map. | |||||||||
Sample |
| |||||||||
Function / homology | Function and homology information extrinsic component of endoplasmic reticulum membrane / inorganic cation transmembrane transporter activity / EMC complex / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / magnesium ion transport / cobalt ion transmembrane transporter activity / Miscellaneous transport and binding events / tail-anchored membrane protein insertion into ER membrane / magnesium ion transmembrane transporter activity ...extrinsic component of endoplasmic reticulum membrane / inorganic cation transmembrane transporter activity / EMC complex / omegasome membrane / protein insertion into ER membrane by stop-transfer membrane-anchor sequence / magnesium ion transport / cobalt ion transmembrane transporter activity / Miscellaneous transport and binding events / tail-anchored membrane protein insertion into ER membrane / magnesium ion transmembrane transporter activity / ferrous iron transmembrane transporter activity / protein folding in endoplasmic reticulum / copper ion transport / autophagosome assembly / RHOA GTPase cycle / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / positive regulation of angiogenesis / early endosome membrane / carbohydrate binding / angiogenesis / early endosome / Golgi membrane / endoplasmic reticulum membrane / Golgi apparatus / endoplasmic reticulum / protein-containing complex / extracellular region / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Januszyk K / Tomaleri GP / Pleiner T / Voorhees RM | |||||||||
Funding support | United States, 1 items
| |||||||||
Citation | Journal: Science / Year: 2020 Title: Structural basis for membrane insertion by the human ER membrane protein complex. Authors: Tino Pleiner / Giovani Pinton Tomaleri / Kurt Januszyk / Alison J Inglis / Masami Hazu / Rebecca M Voorhees / Abstract: A defining step in the biogenesis of a membrane protein is the insertion of its hydrophobic transmembrane helices into the lipid bilayer. The nine-subunit endoplasmic reticulum (ER) membrane protein ...A defining step in the biogenesis of a membrane protein is the insertion of its hydrophobic transmembrane helices into the lipid bilayer. The nine-subunit endoplasmic reticulum (ER) membrane protein complex (EMC) is a conserved co- and posttranslational insertase at the ER. We determined the structure of the human EMC in a lipid nanodisc to an overall resolution of 3.4 angstroms by cryo-electron microscopy, permitting building of a nearly complete atomic model. We used structure-guided mutagenesis to demonstrate that substrate insertion requires a methionine-rich cytosolic loop and occurs via an enclosed hydrophilic vestibule within the membrane formed by the subunits EMC3 and EMC6. We propose that the EMC uses local membrane thinning and a positively charged patch to decrease the energetic barrier for insertion into the bilayer. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_21931.map.gz | 4.4 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-21931-v30.xml emd-21931.xml | 18.7 KB 18.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_21931_fsc.xml | 11.4 KB | Display | FSC data file |
Images | emd_21931.png | 45.5 KB | ||
Masks | emd_21931_msk_1.map | 125 MB | Mask map | |
Others | emd_21931_additional.map.gz emd_21931_half_map_1.map.gz emd_21931_half_map_2.map.gz | 90.5 MB 90.9 MB 90.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-21931 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-21931 | HTTPS FTP |
-Validation report
Summary document | emd_21931_validation.pdf.gz | 474.1 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_21931_full_validation.pdf.gz | 473.7 KB | Display | |
Data in XML | emd_21931_validation.xml.gz | 17.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21931 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-21931 | HTTPS FTP |
-Related structure data
Related structure data | 6ww7MC C: citing same article (ref.) M: atomic model generated by this map |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_21931.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | 'cytosolic' human EMC post-processed, sharpened, and masked map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.836 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Mask #1
File | emd_21931_msk_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Projections & Slices |
| ||||||||||||
Density Histograms |
-Additional map: Human EMC unprocessed, unsharpened, and unmasked 'cytosolic' map.
File | emd_21931_additional.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Human EMC unprocessed, unsharpened, and unmasked 'cytosolic' map. | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: 'cytosolic' human EMC half map
File | emd_21931_half_map_1.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | 'cytosolic' human EMC half map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Half map: 'cytosolic' human EMC half map
File | emd_21931_half_map_2.map | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | 'cytosolic' human EMC half map | ||||||||||||
Projections & Slices |
| ||||||||||||
Density Histograms |
-Sample components
-Entire : Human ER Membrane Protein Complex
Entire | Name: Human ER Membrane Protein Complex |
---|---|
Components |
|
-Supramolecule #1: Human ER Membrane Protein Complex
Supramolecule | Name: Human ER Membrane Protein Complex / type: complex / ID: 1 / Parent: 0 |
---|---|
Source (natural) | Organism: Homo sapiens (human) / Cell: HEK293 |
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.2 mg/mL | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Buffer | pH: 7.5 Component:
| ||||||||||||
Grid | Details: unspecified | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 279 K | ||||||||||||
Details | Sample solubilized and purified in DDM, then reconstituted into lipid nanodisc. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Specialist optics | Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 10 / Number real images: 6345 / Average exposure time: 2.0 sec. / Average electron dose: 59.2 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 59808 / Illumination mode: SPOT SCAN / Imaging mode: DARK FIELD / Cs: 2.7 mm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
---|---|
Output model | PDB-6ww7: |