6VJZ | pdb_00006vjz

CryoEM structure of Hrd1-Usa1/Der1/Hrd3 complex of the expected topology

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
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)
C [auth A]	Sel1	e6vjzA1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: Sel1	ECOD (1.6)
A [auth C]	UNK_F_TYPE	e6vjzC1	A: alpha bundles	X: Rhomboid-like (From Topology)	H: Rhomboid-like (From Topology)	T: Rhomboid-like	F: UNK_F_TYPE	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth A]	PF08238	Sel1 repeat (Sel1)	Sel1 repeat	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	U1 SNP1-associating protein 1	molecular adaptor activity identical protein binding protein binding binding	cellular response to stimulus catabolic process response to stimulus proteolysis involved in protein catabolic process response to nitrogen compound 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 proteolysis cellular response to stimulus catabolic process response to stimulus proteolysis involved in protein catabolic process response to nitrogen compound 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 proteolysis cellular process metabolic process protein metabolic process macromolecule metabolic process response to endoplasmic reticulum stress regulation of cellular process regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological process regulation of protein autoubiquitination 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 regulation of biological process positive regulation of protein ubiquitination regulation of post-translational protein modification regulation of protein metabolic process protein autoubiquitination biological regulation regulation of macromolecule metabolic process macromolecule modification positive regulation of protein autoubiquitination post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal RNA splicing RNA metabolic process gene expression nucleobase-containing compound biosynthetic process mRNA processing mRNA metabolic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process biosynthetic process RNA splicing, via transesterification reactions mRNA splicing, via spliceosome RNA splicing, via transesterification reactions with bulged adenosine as nucleophile RNA processing	membrane-bounded organelle protein-containing complex cytoplasmic ubiquitin ligase complex intracellular anatomical structure ubiquitin ligase complex membrane protein complex transferase complex endomembrane system ER ubiquitin ligase complex endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex membrane-bounded organelle protein-containing complex cytoplasmic ubiquitin ligase complex intracellular anatomical structure ubiquitin ligase complex membrane protein complex transferase complex endomembrane system ER ubiquitin ligase complex endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane catalytic complex organelle subcompartment membrane intracellular membrane-bounded organelle organelle endoplasmic reticulum cytoplasm Hrd1p ubiquitin ligase complex organelle membrane intracellular protein-containing complex
C [auth A]	ERAD-associated E3 ubiquitin-protein ligase component HRD3	-	detection of stimulus detection of unfolded protein response to stimulus response to chemical response to topologically incorrect protein response to stress detection of chemical stimulus response to unfolded protein cellular response to stimulus catabolic process proteolysis involved in protein catabolic process response to nitrogen compound proteasomal protein catabolic process primary metabolic process detection of stimulus detection of unfolded protein response to stimulus response to chemical response to topologically incorrect protein response to stress detection of chemical stimulus response to unfolded protein cellular response to stimulus catabolic process proteolysis involved in protein catabolic process response to nitrogen compound proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress proteolysis cellular process metabolic process protein metabolic process macromolecule metabolic process response to endoplasmic reticulum stress protein exit from endoplasmic reticulum cellular localization establishment of protein localization nitrogen compound transport transport localization establishment of localization in cell intracellular protein localization endoplasmic reticulum to cytosol transport intracellular transport establishment of localization protein transport retrograde protein transport, ER to cytosol macromolecule localization intracellular protein transport negative regulation of post-translational protein modification regulation of cellular process regulation of protein modification process negative regulation of biological process regulation of protein autoubiquitination regulation of protein ubiquitination regulation of primary metabolic process protein ubiquitination negative regulation of protein modification process negative regulation of cellular process regulation of protein modification by small protein conjugation or removal protein modification process negative regulation of protein ubiquitination negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biological process negative regulation of protein autoubiquitination negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification regulation of protein metabolic process protein autoubiquitination negative regulation of metabolic process biological regulation 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	membrane-bounded organelle protein-containing complex cytoplasmic ubiquitin ligase complex intracellular anatomical structure ubiquitin ligase complex membrane protein complex transferase complex endomembrane system ER ubiquitin ligase complex endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex membrane-bounded organelle protein-containing complex cytoplasmic ubiquitin ligase complex intracellular anatomical structure ubiquitin ligase complex membrane protein complex transferase complex endomembrane system ER ubiquitin ligase complex endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane catalytic complex organelle subcompartment membrane intracellular membrane-bounded organelle organelle endoplasmic reticulum cytoplasm Hrd1p ubiquitin ligase complex organelle membrane intracellular protein-containing complex Hrd1p ubiquitin ligase ERAD-M complex membrane-enclosed lumen intracellular organelle lumen endoplasmic reticulum lumen organelle lumen luminal surveillance complex Hrd1p ubiquitin ligase ERAD-L complex
B	ERAD-associated E3 ubiquitin-protein ligase HRD1	aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding ubiquitin-like protein ligase activity ubiquitin protein ligase activity identical protein binding protein binding	catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process cellular response to stimulus catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis ubiquitin-dependent protein catabolic process metabolic process cellular process macromolecule metabolic process protein metabolic process cellular response to stimulus response to stimulus response to nitrogen compound proteasomal protein catabolic process ERAD pathway cellular response to stress response to chemical response to stress response to endoplasmic reticulum stress protein polyubiquitination protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein K48-linked ubiquitination protein modification by small protein conjugation protein modification by small protein conjugation or removal fungal-type cell wall organization cellular component organization fungal-type cell wall organization or biogenesis cell wall organization or biogenesis cell wall organization cellular component organization or biogenesis external encapsulating structure organization protein autoubiquitination protein exit from endoplasmic reticulum cellular localization establishment of protein localization nitrogen compound transport transport localization establishment of localization in cell intracellular protein localization endoplasmic reticulum to cytosol transport intracellular transport establishment of localization protein transport retrograde protein transport, ER to cytosol macromolecule localization intracellular protein transport regulation of biological process cellular response to topologically incorrect protein regulation of cellular process signaling biological regulation endoplasmic reticulum unfolded protein response cellular response to unfolded protein response to unfolded protein intracellular signal transduction cell communication response to topologically incorrect protein signal transduction	membrane-bounded organelle protein-containing complex cytoplasmic ubiquitin ligase complex intracellular anatomical structure ubiquitin ligase complex membrane protein complex transferase complex endomembrane system ER ubiquitin ligase complex endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex membrane-bounded organelle protein-containing complex cytoplasmic ubiquitin ligase complex intracellular anatomical structure ubiquitin ligase complex membrane protein complex transferase complex endomembrane system ER ubiquitin ligase complex endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane catalytic complex organelle subcompartment membrane intracellular membrane-bounded organelle organelle endoplasmic reticulum cytoplasm Hrd1p ubiquitin ligase complex organelle membrane intracellular protein-containing complex Hrd1p ubiquitin ligase ERAD-M complex Hrd1p ubiquitin ligase ERAD-L complex
A [auth C]	Degradation in the endoplasmic reticulum protein 1	ribonucleoprotein complex binding protein-containing complex binding binding signal recognition particle binding protein binding misfolded protein binding	cellular localization establishment of protein localization nitrogen compound transport transport misfolded protein transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization intracellular protein transport cellular localization establishment of protein localization nitrogen compound transport transport misfolded protein transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization intracellular protein transport cellular response to stimulus catabolic process response to stimulus proteolysis involved in protein catabolic process response to nitrogen compound 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 proteolysis metabolic process protein metabolic process macromolecule metabolic process response to endoplasmic reticulum stress protein quality control for misfolded or incompletely synthesized proteins protein exit from endoplasmic reticulum endoplasmic reticulum to cytosol transport retrograde protein transport, ER to cytosol regulation of biological process cellular response to topologically incorrect protein regulation of cellular process signaling biological regulation endoplasmic reticulum unfolded protein response cellular response to unfolded protein response to unfolded protein intracellular signal transduction cell communication response to topologically incorrect protein signal transduction	membrane-bounded organelle protein-containing complex cytoplasmic ubiquitin ligase complex intracellular anatomical structure ubiquitin ligase complex membrane protein complex transferase complex endomembrane system ER ubiquitin ligase complex endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex membrane-bounded organelle protein-containing complex cytoplasmic ubiquitin ligase complex intracellular anatomical structure ubiquitin ligase complex membrane protein complex transferase complex endomembrane system ER ubiquitin ligase complex endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane catalytic complex organelle subcompartment membrane intracellular membrane-bounded organelle organelle endoplasmic reticulum cytoplasm Hrd1p ubiquitin ligase complex organelle membrane intracellular protein-containing complex Hrd1p ubiquitin ligase ERAD-L complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
D	IPR000626	Ubiquitin-like domain	Domain
C [auth A]	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
C [auth A]	IPR050767	Sel1/AlgK	Family
C [auth A]	IPR006597	Sel1-like repeat	Repeat
B	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
B	IPR050731	HRD1 family E3 ubiquitin-protein ligases	Family
B	IPR001841	Zinc finger, RING-type	Domain
A [auth C]	IPR007599	Derlin	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth C], B, C [auth A], 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 [auth C], B, C [auth A], D	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth C], B, C [auth A], D	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Sec, Translocase, and Insertase Proteins	ER-associated protein degradation (ERAD) protein Hrd1 ubiquitin ligase complex

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.