9LLK | pdb_00009llk

The cryo-EM structure of the heterododecameric human Derlin-1/p97 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Cryo-EM structure of the human Derlin-1/p97 complex reveals a hexameric channel in ERAD.

Wang, Q.Yao, D.Rao, B.Xia, Y.Li, W.Li, S.Cao, M.Shen, Y.Qin, A.Cao, Y.

(2025) Commun Biol 8: 1481-1481

  • DOI: https://doi.org/10.1038/s42003-025-08880-5
  • Primary Citation of Related Structures:  
    9LLK

  • PubMed 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 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.


  • Organizational Affiliation
    • Department of Orthopaedics, Shanghai Key Laboratory of Orthopaedic Implant, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transitional endoplasmic reticulum ATPase787Homo sapiensMutation(s): 0 
Gene Names: VCPHEL-220HEL-S-70
EC: 3.6.4.6
UniProt & NIH Common Fund Data Resources
Find proteins for P55072 (Homo sapiens)
Explore P55072 
Go to UniProtKB:  P55072
PHAROS:  P55072
GTEx:  ENSG00000165280 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55072
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Derlin-1226Homo sapiensMutation(s): 0 
Gene Names: DERL1DER1UNQ243/PRO276
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BUN8 (Homo sapiens)
Explore Q9BUN8 
Go to UniProtKB:  Q9BUN8
PHAROS:  Q9BUN8
GTEx:  ENSG00000136986 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BUN8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
M [auth B]
N [auth B]
O [auth C]
P [auth C]
Q [auth F]
M [auth B],
N [auth B],
O [auth C],
P [auth C],
Q [auth F],
R [auth F],
S [auth A],
T [auth A],
U [auth D],
V [auth D],
W [auth E],
X [auth E]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.55 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China82072468(YC)

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-29
    Type: Initial release