Annotations: 7CZB

The cryo-EM structure of the ERAD retrotranslocation channel formed by human Derlin-1

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	V-set	e7czbD1	A: beta barrels	X: DNA methylase specificity domain	H: Bromodomain	T: Bromodomain	F: V-set	ECOD (v294.2)
C	V-set	e7czbC1	A: beta barrels	X: DNA methylase specificity domain	H: Bromodomain	T: Bromodomain	F: V-set	ECOD (v294.2)
B	V-set	e7czbB1	A: beta barrels	X: DNA methylase specificity domain	H: Bromodomain	T: Bromodomain	F: V-set	ECOD (v294.2)
A	DctP	e7czbA1	A: beta barrels	X: DNA methylase specificity domain	H: Bromodomain	T: Bromodomain	F: DctP	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF04511	Der1-like family (DER1)	Der1-like family	This entry represents the Der1-like family, which includes yeast Der1 and its mammalian homologues, the Derlins. Der1 is a component of the Hrd1 ubiquitin ligase complex required for ER-associated degradation (ERAD) of misfolded luminal glycoproteins ...	This entry represents the Der1-like family, which includes yeast Der1 and its mammalian homologues, the Derlins. Der1 is a component of the Hrd1 ubiquitin ligase complex required for ER-associated degradation (ERAD) of misfolded luminal glycoproteins [1]. The cryo-EM structure reveals that Der1 contains six transmembrane segments and is structurally similar to rhomboid proteases, though it lacks catalytic activity [2]. Der1 has a lateral gate between transmembrane helices 2 and 5, and a hydrophilic luminal cavity. Unlike rhomboids, the luminal cavity of Der1 is perpetually open due to a shorter loop between TM5 and TM6 [2]. Within the Hrd1 complex, Der1 is linked to Hrd1 via the Usa1 protein on the cytosolic side. The lateral gates of Der1 and Hrd1 face one another and together form a retrotranslocon, with Der1 providing the luminal half-channel and Hrd1 providing the cytosolic half-channel [2]. The region between the lateral gates corresponds to a thinned membrane, facilitated in part by hydrophilic residues in TM2 of Der1. Der1 is required for stable loop insertion of substrates during retrotranslocation across the ER membrane [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Derlin-1	molecular transducer activity signaling receptor activity ribonucleoprotein complex binding protein-containing complex binding binding signal recognition particle binding protein binding enzyme binding protease binding ubiquitin-specific protease binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding MHC class I protein binding signaling receptor binding molecular transducer activity signaling receptor activity ribonucleoprotein complex binding protein-containing complex binding binding signal recognition particle binding protein binding enzyme binding protease binding ubiquitin-specific protease binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding MHC class I protein binding signaling receptor binding MHC protein binding ATPase binding identical protein binding	protein destabilization regulation of protein stability biological regulation regulation of biological quality localization establishment of protein localization establishment of localization cellular response to stimulus catabolic process response to stimulus proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process protein destabilization regulation of protein stability biological regulation regulation of biological quality localization establishment of protein localization establishment of localization cellular response to stimulus catabolic process response to stimulus proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical response to stress cellular process metabolic process protein metabolic process macromolecule metabolic process response to endoplasmic reticulum stress response to topologically incorrect protein response to unfolded protein regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process protein ubiquitination positive regulation of macromolecule metabolic process regulation of protein modification by small protein conjugation or removal protein modification process positive regulation of cellular process positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of biological process regulation of post-translational protein modification regulation of protein metabolic process regulation of macromolecule metabolic process macromolecule modification post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal proteasome-mediated ubiquitin-dependent protein catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process protein exit from endoplasmic reticulum cellular localization transport intercellular transport establishment of localization in cell intracellular protein localization endoplasmic reticulum to cytosol transport intracellular transport protein transport retrograde protein transport, ER to cytosol macromolecule localization intracellular protein transport cellular response to misfolded protein response to misfolded protein cellular response to topologically incorrect protein signaling endoplasmic reticulum unfolded protein response cellular response to unfolded protein intracellular signal transduction cell communication signal transduction	cellular anatomical structure membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure organelle subcompartment membrane protein complex intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle Derlin-1 retrotranslocation complex organelle nuclear outer membrane-endoplasmic reticulum membrane network cellular anatomical structure membrane membrane-bounded organelle protein-containing complex intracellular anatomical structure organelle subcompartment membrane protein complex intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle Derlin-1 retrotranslocation complex organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane Derlin-1-VIMP complex early endosome endosome intracellular vesicle cytoplasmic vesicle vesicle endoplasmic reticulum quality control compartment late endosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR007599	Derlin	Family
A, B, C, D	IPR035952	Rhomboid-like superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	: Q9BUN8	Stevens-Johnson syndrome breast cancer juvenile dermatomyositis pancreatic ductal adenocarcinoma plasma cell myeloma Stevens-Johnson Syndrome Toxic Epidermal Necrolysis Spectrum pancreatic intraductal papillary-mucinous carcinoma psoriasis toxic epidermal necrolysis glioblastoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D	OPM	Transmembrane	Alpha-helical polytopic	AAA-ATPase superfamily, transmembrane	ER retrotranslocon family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Sec, Translocase, and Insertase Proteins	Derlin-1 ERAD retrotranslocation channel

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.

7CZB | pdb_00007czb