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- EMDB-30508: The cryo-EM structure of the ERAD retrotranslocation channel form... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-30508 | |||||||||||||||
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Title | The cryo-EM structure of the ERAD retrotranslocation channel formed by human Derlin-1 | |||||||||||||||
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![]() | Endoplasmic reticulum associated degradation / Retrotranslocation / cryo-EM / Transmembrane channels / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | ![]() Derlin-1-VIMP complex / Hrd1p ubiquitin ligase ERAD-L complex / endoplasmic reticulum quality control compartment / signal recognition particle binding / misfolded protein binding / Derlin-1 retrotranslocation complex / cellular response to misfolded protein / retrograde protein transport, ER to cytosol / ubiquitin-specific protease binding / MHC class I protein binding ...Derlin-1-VIMP complex / Hrd1p ubiquitin ligase ERAD-L complex / endoplasmic reticulum quality control compartment / signal recognition particle binding / misfolded protein binding / Derlin-1 retrotranslocation complex / cellular response to misfolded protein / retrograde protein transport, ER to cytosol / ubiquitin-specific protease binding / MHC class I protein binding / response to unfolded protein / ERAD pathway / endoplasmic reticulum unfolded protein response / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / positive regulation of protein ubiquitination / Defective CFTR causes cystic fibrosis / protein destabilization / establishment of protein localization / ABC-family proteins mediated transport / late endosome / E3 ubiquitin ligases ubiquitinate target proteins / signaling receptor activity / ATPase binding / proteasome-mediated ubiquitin-dependent protein catabolic process / protease binding / early endosome / ubiquitin protein ligase binding / protein-containing complex binding / endoplasmic reticulum membrane / endoplasmic reticulum / identical protein binding / membrane Similarity search - Function | |||||||||||||||
Biological species | ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||||||||
![]() | Rao B / Li S | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The cryo-EM structure of an ERAD protein channel formed by tetrameric human Derlin-1. Authors: Bing Rao / Shaobai Li / Deqiang Yao / Qian Wang / Ying Xia / Yi Jia / Yafeng Shen / Yu Cao / ![]() Abstract: Endoplasmic reticulum-associated degradation (ERAD) is a process directing misfolded proteins from the ER lumen and membrane to the degradation machinery in the cytosol. A key step in ERAD is the ...Endoplasmic reticulum-associated degradation (ERAD) is a process directing misfolded proteins from the ER lumen and membrane to the degradation machinery in the cytosol. A key step in ERAD is the translocation of ER proteins to the cytosol. Derlins are essential for protein translocation in ERAD, but the mechanism remains unclear. Here, we solved the structure of human Derlin-1 by cryo-electron microscopy. The structure shows that Derlin-1 forms a homotetramer that encircles a large tunnel traversing the ER membrane. The tunnel has a diameter of about 12 to 15 angstroms, large enough to allow an α helix to pass through. The structure also shows a lateral gate within the membrane, providing access of transmembrane proteins to the tunnel, and thus, human Derlin-1 forms a protein channel for translocation of misfolded proteins. Our structure is different from the monomeric yeast Derlin structure previously reported, which forms a semichannel with another protein. | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 5.9 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 10.7 KB 10.7 KB | Display Display | ![]() |
Images | ![]() | 85.1 KB | ||
Filedesc metadata | ![]() | 5.1 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 374.7 KB | Display | ![]() |
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Full document | ![]() | 374.2 KB | Display | |
Data in XML | ![]() | 6.3 KB | Display | |
Data in CIF | ![]() | 7.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7czbMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.86 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Derlin-1
Entire | Name: Derlin-1 |
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Components |
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-Supramolecule #1: Derlin-1
Supramolecule | Name: Derlin-1 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Derlin-1
Macromolecule | Name: Derlin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 28.821664 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MSDIGDWFRS IPAITRYWFA ATVAVPLVGK LGLISPAYLF LWPEAFLYRF QIWRPITATF YFPVGPGTGF LYLVNLYFLY QYSTRLETG AFDGRPADYL FMLLFNWICI VITGLAMDMQ LLMIPLIMSV LYVWAQLNRD MIVSFWFGTR FKACYLPWVI L GFNYIIGG ...String: MSDIGDWFRS IPAITRYWFA ATVAVPLVGK LGLISPAYLF LWPEAFLYRF QIWRPITATF YFPVGPGTGF LYLVNLYFLY QYSTRLETG AFDGRPADYL FMLLFNWICI VITGLAMDMQ LLMIPLIMSV LYVWAQLNRD MIVSFWFGTR FKACYLPWVI L GFNYIIGG SVINELIGNL VGHLYFFLMF RYPMDLGGRN FLSTPQFLYR WLPSRRGGVS GFGVPPASMR RAADQNGGGG RH NWGQGFR LGDQ UniProtKB: Derlin-1 |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 2.7 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: OTHER |
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Final reconstruction | Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71761 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |