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- EMDB-33611: The cryo-EM structure of human ERAD retro-translocation complex -

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Basic information

Entry
Database: EMDB / ID: EMD-33611
TitleThe cryo-EM structure of human ERAD retro-translocation complex
Map data
Sample
  • Complex: The cryo-EM structure of human ERAD retro-translocation complex
    • Protein or peptide: Derlin-1
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
KeywordsERAD / MEMBRANE PROTEIN
Function / homology
Function and homology information


Derlin-1-VIMP complex / signal recognition particle binding / endoplasmic reticulum quality control compartment / : / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / BAT3 complex binding / cellular response to arsenite ion ...Derlin-1-VIMP complex / signal recognition particle binding / endoplasmic reticulum quality control compartment / : / flavin adenine dinucleotide catabolic process / VCP-NSFL1C complex / endosome to lysosome transport via multivesicular body sorting pathway / endoplasmic reticulum stress-induced pre-emptive quality control / BAT3 complex binding / cellular response to arsenite ion / protein-DNA covalent cross-linking repair / cytoplasm protein quality control / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / positive regulation of oxidative phosphorylation / : / aggresome assembly / mitotic spindle disassembly / deubiquitinase activator activity / regulation of protein localization to chromatin / ubiquitin-modified protein reader activity / VCP-NPL4-UFD1 AAA ATPase complex / cellular response to misfolded protein / negative regulation of protein localization to chromatin / vesicle-fusing ATPase / positive regulation of mitochondrial membrane potential / K48-linked polyubiquitin modification-dependent protein binding / regulation of aerobic respiration / retrograde protein transport, ER to cytosol / stress granule disassembly / regulation of synapse organization / ATPase complex / ubiquitin-specific protease binding / MHC class I protein binding / positive regulation of ATP biosynthetic process / ubiquitin-like protein ligase binding / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / autophagosome maturation / endoplasmic reticulum to Golgi vesicle-mediated transport / response to unfolded protein / negative regulation of hippo signaling / HSF1 activation / translesion synthesis / interstrand cross-link repair / proteasomal protein catabolic process / Protein methylation / ATP metabolic process / endoplasmic reticulum unfolded protein response / Attachment and Entry / Josephin domain DUBs / ERAD pathway / positive regulation of protein ubiquitination / lipid droplet / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / proteasome complex / viral genome replication / Hh mutants are degraded by ERAD / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / Translesion Synthesis by POLH / negative regulation of smoothened signaling pathway / macroautophagy / positive regulation of protein-containing complex assembly / ABC-family proteins mediated transport / establishment of protein localization / positive regulation of non-canonical NF-kappaB signal transduction / protein destabilization / ADP binding / autophagy / Aggrephagy / Ovarian tumor domain proteases / KEAP1-NFE2L2 pathway / cytoplasmic stress granule / positive regulation of protein catabolic process / azurophil granule lumen / positive regulation of canonical Wnt signaling pathway / E3 ubiquitin ligases ubiquitinate target proteins / late endosome / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / site of double-strand break / double-strand break repair / Neddylation / signaling receptor activity / cellular response to heat / ATPase binding / protease binding / ubiquitin-dependent protein catabolic process / protein phosphatase binding / secretory granule lumen / regulation of apoptotic process / proteasome-mediated ubiquitin-dependent protein catabolic process / ficolin-1-rich granule lumen / Attachment and Entry / early endosome / protein ubiquitination / ciliary basal body / protein domain specific binding / DNA repair / intracellular membrane-bounded organelle
Similarity search - Function
Derlin / Der1-like family / Rhomboid-like superfamily / AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 ...Derlin / Der1-like family / Rhomboid-like superfamily / AAA ATPase, CDC48 family / Cell division protein 48 (CDC48), N-terminal domain / CDC48, N-terminal subdomain / Cell division protein 48 (CDC48) N-terminal domain / CDC48, domain 2 / Cell division protein 48 (CDC48), domain 2 / Cell division protein 48 (CDC48) domain 2 / : / CDC48 domain 2-like superfamily / Aspartate decarboxylase-like domain superfamily / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Transitional endoplasmic reticulum ATPase / Derlin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.61 Å
AuthorsCao Y / Rao B / Wang Q / Yao D / Xia Y / Li W / Li S / Shen Y
Funding support China, 2 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2018YFC1004704 China
National Natural Science Foundation of China (NSFC)82072468(YC) China
CitationJournal: Sci Adv / Year: 2023
Title: The cryo-EM structure of the human ERAD retrotranslocation complex.
Authors: Bing Rao / Qian Wang / Deqiang Yao / Ying Xia / Wenguo Li / Yuming Xie / Shaobai Li / Mi Cao / Yafeng Shen / An Qin / Jie Zhao / Yu Cao /
Abstract: Endoplasmic reticulum-associated degradation (ERAD) maintains protein homeostasis by retrieving misfolded proteins from the endoplasmic reticulum (ER) lumen into the cytosol for degradation. The ...Endoplasmic reticulum-associated degradation (ERAD) maintains protein homeostasis by retrieving misfolded proteins from the endoplasmic reticulum (ER) lumen into the cytosol for degradation. The retrotranslocation of misfolded proteins across the ER membrane is an energy-consuming process, with the detailed transportation mechanism still needing clarification. We determined the cryo-EM structures of the hetero-decameric complex formed by the Derlin-1 tetramer and the p97 hexamer. It showed an intriguing asymmetric complex and a putative coordinated squeezing movement in Derlin-1 and p97 parts. With the conformational changes of p97 induced by its ATP hydrolysis activities, the Derlin-1 channel could be torn into a "U" shape with a large opening to the lipidic environment, thereby forming an entry for the substrates in the ER membrane. The EM analysis showed that p97 formed a functional protein complex with Derlin-1, revealing the coupling mechanism between the ERAD retrotranslocation and the ATP hydrolysis activities.
History
DepositionJun 16, 2022-
Header (metadata) releaseOct 18, 2023-
Map releaseOct 18, 2023-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33611.png

Downloads & links

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Map

FileDownload / File: emd_33611.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.8079599 - 1.9723208
Average (Standard dev.)0.0041788984 (±0.057507504)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_33611_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_33611_half_map_2.map
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Sample components

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Entire : The cryo-EM structure of human ERAD retro-translocation complex

EntireName: The cryo-EM structure of human ERAD retro-translocation complex
Components
  • Complex: The cryo-EM structure of human ERAD retro-translocation complex
    • Protein or peptide: Derlin-1
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: The cryo-EM structure of human ERAD retro-translocation complex

SupramoleculeName: The cryo-EM structure of human ERAD retro-translocation complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 650 KDa

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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: 26.4781 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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 WLPSRRHNWG QGFRLGDQ

UniProtKB: Derlin-1

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Macromolecule #2: Transitional endoplasmic reticulum ATPase

MacromoleculeName: Transitional endoplasmic reticulum ATPase / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO / EC number: vesicle-fusing ATPase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 87.546711 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MNRPNRLIVD EAINEDNSVV SLSQPKMDEL QLFRGDTVLL KGKKRREAVC IVLSDDTCSD EKIRMNRVVR NNLRVRLGDV ISIQPCPDV KYGKRIHVLP IDDTVEGITG NLFEVYLKPY FLEAYRPIRK GDIFLVRGGM RAVEFKVVET DPSPYCIVAP D TVIHCEGE ...String:
MNRPNRLIVD EAINEDNSVV SLSQPKMDEL QLFRGDTVLL KGKKRREAVC IVLSDDTCSD EKIRMNRVVR NNLRVRLGDV ISIQPCPDV KYGKRIHVLP IDDTVEGITG NLFEVYLKPY FLEAYRPIRK GDIFLVRGGM RAVEFKVVET DPSPYCIVAP D TVIHCEGE PIKREDEEES LNEVGYDDIG GCRKQLAQIK EMVELPLRHP ALFKAIGVKP PRGILLYGPP GTGKTLIARA VA NETGAFF FLINGPEIMS KLAGESESNL RKAFEEAEKN APAIIFIDEL DAIAPKREKT HGEVERRIVS QLLTLMDGLK QRA HVIVMA ATNRPNSIDP ALRRFGRFDR EVDIGIPDAT GRLEILQIHT KNMKLADDVD LEQVANETHG HVGADLAALC SEAA LQAIR KKMDLIDLED ETIDAEVMNS LAVTMDDFRW ALSQSNPSAL RETVVEVPQV TWEDIGGLED VKRELQELVQ YPVEH PDKF LKFGMTPSKG VLFYGPPGCG KTLLAKAIAN ECQANFISIK GPELLTMWFG ESEANVREIF DKARQAAPCV LFFDEL DSI AKARGGNIGD GGGAADRVIN QILTEMDGMS TKKNVFIIGA TNRPDIIDPA ILRPGRLDQL IYIPLPDEKS RVAILKA NL RKSPVAKDVD LEFLAKMTNG FSGADLTEIC QRACKLAIRE SIESEIRRER ERQTNPSAME VEEDDPVPEI RRDHFEEA M RFARRSVSDN DIRKYEMFAQ TLQQSRGFGS FRFPSGNQGG AGPSQGSGGG TGGSVYTEDN DDDLYG

UniProtKB: Transitional endoplasmic reticulum ATPase

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 12 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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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

Concentration15 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 90 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 15 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average exposure time: 2.9 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 / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 81000
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: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 248684
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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