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- EMDB-30508: The cryo-EM structure of the ERAD retrotranslocation channel form... -

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Basic information

Entry
Database: EMDB / ID: EMD-30508
TitleThe cryo-EM structure of the ERAD retrotranslocation channel formed by human Derlin-1
Map data
Sample
  • Cell: Derlin-1
    • Protein or peptide: Derlin-1
KeywordsEndoplasmic reticulum associated degradation / Retrotranslocation / cryo-EM / Transmembrane channels / MEMBRANE PROTEIN
Function / homology
Function and homology information


Derlin-1-VIMP complex / endoplasmic reticulum quality control compartment / signal recognition particle 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 / endoplasmic reticulum unfolded protein response ...Derlin-1-VIMP complex / endoplasmic reticulum quality control compartment / signal recognition particle 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 / 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 / E3 ubiquitin ligases ubiquitinate target proteins / signaling receptor activity / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsRao B / Li S
Funding support China, 4 items
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, 2020-
Header (metadata) releaseMar 17, 2021-
Map releaseMar 17, 2021-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7czb
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7czb
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
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Supplemental images

emd_30508.png

Downloads & links

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Map

FileDownload / File: emd_30508.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 256 pix.
= 220.16 Å		0.86 Å/pix.
x 256 pix.
= 220.16 Å		0.86 Å/pix.
x 256 pix.
= 220.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-1.286818 - 1.786484
Average (Standard dev.)0.008280593 (±0.05530042)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 220.16 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.860.860.86
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z220.160220.160220.160
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-1.2871.7860.008

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Supplemental data

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Sample components

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Entire : Derlin-1

EntireName: Derlin-1
Components
  • Cell: Derlin-1
    • Protein or peptide: Derlin-1

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Supramolecule #1: Derlin-1

SupramoleculeName: Derlin-1 / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Derlin-1

MacromoleculeName: Derlin-1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 28.821664 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: 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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.5 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 283.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 2.7 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen 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 modelType of model: OTHER
Final reconstructionApplied 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 assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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