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- PDB-7czb: The cryo-EM structure of the ERAD retrotranslocation channel form... -

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Entry
Database: PDB / ID: 7czb
TitleThe cryo-EM structure of the ERAD retrotranslocation channel formed by human Derlin-1
ComponentsDerlin-1
KeywordsMEMBRANE PROTEIN / Endoplasmic reticulum associated degradation / Retrotranslocation / cryo-EM / Transmembrane channels
Function / homology
Function and homology information


Derlin-1-VIMP complex / signal recognition particle binding / endoplasmic reticulum quality control compartment / 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 / endoplasmic reticulum unfolded protein response ...Derlin-1-VIMP complex / signal recognition particle binding / endoplasmic reticulum quality control compartment / 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 / endoplasmic reticulum unfolded protein response / ERAD pathway / positive regulation of protein ubiquitination / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / establishment of protein localization / Defective CFTR causes cystic fibrosis / protein destabilization / ABC-family proteins mediated transport / late endosome / signaling receptor activity / E3 ubiquitin ligases ubiquitinate target proteins / ATPase binding / protease binding / proteasome-mediated ubiquitin-dependent protein catabolic process / early endosome / ubiquitin protein ligase binding / endoplasmic reticulum membrane / protein-containing complex binding / endoplasmic reticulum / identical protein binding / membrane
Similarity search - Function
Derlin / Der1-like family / Rhomboid-like superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsRao, B. / Li, S. / Yao, D. / Wang, Q. / Xia, Y. / Jia, Y. / Shen, Y. / Cao, Y.
Funding support China, 4items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U1632132 China
National Natural Science Foundation of China (NSFC)31670849 China
Ministry of Science and Technology (MoST, China)2017YFC1001303 China
Ministry of Science and Technology (MoST, China)2018YFC1004704 China
CitationJournal: Sci Adv / Year: 2021
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
DepositionSep 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Derlin-1
B: Derlin-1
C: Derlin-1
D: Derlin-1


Theoretical massNumber of molelcules
Total (without water)115,2874
Polymers115,2874
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area2930 Å2
ΔGint-25 kcal/mol
Surface area46350 Å2

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Components

#1: Protein
Derlin-1 / Degradation in endoplasmic reticulum protein 1 / DERtrin-1 / Der1-like protein 1


Mass: 28821.664 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DERL1, DER1, UNQ243/PRO276 / Plasmid: pcDNA3.4 / Cell line (production host): Expi293F / Production host: Homo sapiens (human) / References: UniProt: Q9BUN8

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Derlin-1 / Type: CELL / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: Expi293F / Plasmid: pcDNA3.4
Buffer solutionpH: 8
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 283.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 2.7 sec. / Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71761 / Algorithm: FOURIER SPACE / Symmetry type: POINT

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