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- EMDB-63205: The cryo-EM structure of the heterododecameric human Derlin-1/p97... -

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Basic information

Entry
Database: EMDB / ID: EMD-63205
TitleThe cryo-EM structure of the heterododecameric human Derlin-1/p97 complex
Map data
Sample
  • Complex: The cryogenic electron-microscopic structure of the heterododecameric human Derlin-1/p97 complex
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
    • Protein or peptide: Derlin-1
  • 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 / Derlin-1 retrotranslocation complex / positive regulation of protein K63-linked deubiquitination / cytoplasm protein quality control / positive regulation of oxidative phosphorylation / : / aggresome assembly / deubiquitinase activator activity / mitotic spindle disassembly / ubiquitin-modified protein reader activity / regulation of protein localization to chromatin / VCP-NPL4-UFD1 AAA ATPase complex / cellular response to misfolded protein / negative regulation of protein localization to chromatin / positive regulation of mitochondrial membrane potential / vesicle-fusing ATPase / K48-linked polyubiquitin modification-dependent protein binding / regulation of aerobic respiration / retrograde protein transport, ER to cytosol / stress granule disassembly / ATPase complex / regulation of synapse organization / ubiquitin-specific protease binding / positive regulation of ATP biosynthetic process / MHC class I protein binding / ubiquitin-like protein ligase binding / RHOH GTPase cycle / polyubiquitin modification-dependent protein binding / autophagosome maturation / response to unfolded protein / negative regulation of hippo signaling / endoplasmic reticulum to Golgi vesicle-mediated transport / HSF1 activation / translesion synthesis / interstrand cross-link repair / ATP metabolic process / endoplasmic reticulum unfolded protein response / proteasomal protein catabolic process / Protein methylation / Attachment and Entry / ERAD pathway / lipid droplet / proteasome complex / viral genome replication / Josephin domain DUBs / positive regulation of protein ubiquitination / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / negative regulation of smoothened signaling pathway / macroautophagy / positive regulation of protein-containing complex assembly / Hh mutants are degraded by ERAD / establishment of protein localization / Hedgehog ligand biogenesis / Defective CFTR causes cystic fibrosis / positive regulation of non-canonical NF-kappaB signal transduction / Translesion Synthesis by POLH / protein destabilization / ADP binding / ABC-family proteins mediated transport / autophagy / cytoplasmic stress granule / Aggrephagy / positive regulation of protein catabolic process / azurophil granule lumen / KEAP1-NFE2L2 pathway / Ovarian tumor domain proteases / positive regulation of canonical Wnt signaling pathway / late endosome / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / double-strand break repair / signaling receptor activity / E3 ubiquitin ligases ubiquitinate target proteins / site of double-strand break / cellular response to heat / Neddylation / ATPase binding / protease binding / ubiquitin-dependent protein catabolic process / secretory granule lumen / protein phosphatase binding / regulation of apoptotic process / ficolin-1-rich granule lumen / proteasome-mediated ubiquitin-dependent protein catabolic process / 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 ...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: 3.55 Å
AuthorsCao Y / Wang Q / Yao D / Rao B / Xia Y / Li W / Li S / Shen Y
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82072468(YC) China
CitationJournal: Commun Biol / Year: 2025
Title: Cryo-EM structure of the human Derlin-1/p97 complex reveals a hexameric channel in ERAD.
Authors: Qian Wang / Deqiang Yao / Bing Rao / Ying Xia / Wenguo Li / Shaobai Li / Mi Cao / Yafeng Shen / An Qin / Yu Cao /
Abstract: The ER-associated degradation (ERAD) pathway retrotranslocates misfolded proteins from the ER lumen to the cytoplasm for proteasomal degradation. Derlin-1 and p97 are central to this process, forming ...The ER-associated degradation (ERAD) pathway retrotranslocates misfolded proteins from the ER lumen to the cytoplasm for proteasomal degradation. Derlin-1 and p97 are central to this process, forming a canonical 4:6 complex with tetrameric Derlin-1. Using cryo-electron microscopy, we identify a novel human Derlin-1/p97 complex with a 6:6 stoichiometry, where hexameric Derlin-1 assembles as three dimers. This hexameric channel forms a significantly larger trans-ER membrane tunnel, potentially accommodating bulkier substrates. Structural comparisons revealed conformational flexibility in Derlin-1, suggesting the "U"-shaped tetramer may act as an intermediate in hexamer formation. The formation of this hexameric channel is mediated by interactions with p97 and appears dependent on p97's ATPase activity, which provides the driving force for the transition between the tetrameric channel conformation to the intermediate "U"-shaped conformation. These findings highlight the dynamic nature of the Derlin-1/p97 complex and its implications for understanding ERAD retrotranslocation.
History
DepositionJan 17, 2025-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63205.png

Downloads & links

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Map

FileDownload / File: emd_63205.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
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
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-2.2596738 - 3.6697516
Average (Standard dev.)0.0040041343 (±0.07662028)
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: #1

Fileemd_63205_half_map_1.map
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63205_half_map_2.map
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Sample components

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Entire : The cryogenic electron-microscopic structure of the heterododecam...

EntireName: The cryogenic electron-microscopic structure of the heterododecameric human Derlin-1/p97 complex
Components
  • Complex: The cryogenic electron-microscopic structure of the heterododecameric human Derlin-1/p97 complex
    • Protein or peptide: Transitional endoplasmic reticulum ATPase
    • Protein or peptide: Derlin-1
  • Ligand: ADENOSINE-5'-DIPHOSPHATE

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Supramolecule #1: The cryogenic electron-microscopic structure of the heterododecam...

SupramoleculeName: The cryogenic electron-microscopic structure of the heterododecameric human Derlin-1/p97 complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 730 KDa

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Macromolecule #1: Transitional endoplasmic reticulum ATPase

MacromoleculeName: Transitional endoplasmic reticulum ATPase / type: protein_or_peptide / ID: 1 / 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 #2: Derlin-1

MacromoleculeName: Derlin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 6 / 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 #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: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 281.15 K

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
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: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 129127
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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