8EKI | pdb_00008eki

CryoEM structure of the Dsl1 complex bound to SNAREs Sec20 and Use1

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
E	SCOP2B Superfamily	Cullin repeat-like	8052696	3000059	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Sec39 repeat-like	8052705	3002137	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Sec39 repeat-like	8052704	3002137	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Sec39 repeat-like	8052703	3002137	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cullin repeat-like	8092383	3000059	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cullin repeat-like	8092384	3000059	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E	PF11989	Retrograde transport protein Dsl1 C terminal (Dsl1_C)	Retrograde transport protein Dsl1 C terminal	-	Repeat
E	PF11988	Retrograde transport protein Dsl1 N terminal (Dsl1_N)	Retrograde transport protein Dsl1 N terminal	-	Repeat
D	PF08314	Secretory pathway protein Sec39 (Sec39)	Secretory pathway protein Sec39	-	Repeat
C	PF04437	RINT-1/TIP-1 family (RINT1_TIP1)	RINT-1/TIP-1 family	-	Repeat
B	PF09753	Membrane fusion protein Use1 (Use1)	Membrane fusion protein Use1	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E	Protein transport protein DSL1	-	localization transport retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport establishment of protein localization nitrogen compound transport protein transport macromolecule localization intracellular protein localization cellular response to stimulus regulation of cellular process localization transport retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport establishment of protein localization nitrogen compound transport protein transport macromolecule localization intracellular protein localization cellular response to stimulus regulation of cellular process regulation of cell cycle phase transition response to stimulus negative regulation of biological process spindle checkpoint signaling negative regulation of cell cycle regulation of mitotic nuclear division intracellular signal transduction negative regulation of mitotic cell cycle cell communication negative regulation of mitotic sister chromatid segregation negative regulation of chromosome organization negative regulation of cell cycle phase transition mitotic spindle checkpoint signaling signal transduction cell cycle mitotic sister chromatid separation chromosome segregation negative regulation of sister chromatid segregation mitotic spindle assembly checkpoint signaling regulation of biological process negative regulation of cellular component organization regulation of cell cycle process sister chromatid segregation regulation of chromosome organization regulation of organelle organization regulation of mitotic cell cycle phase transition regulation of mitotic sister chromatid segregation mitotic cell cycle process regulation of chromosome separation negative regulation of mitotic nuclear division regulation of chromosome segregation regulation of cellular component organization regulation of mitotic sister chromatid separation regulation of metaphase/anaphase transition of cell cycle signaling spindle assembly checkpoint signaling cell cycle phase transition regulation of mitotic metaphase/anaphase transition mitotic cell cycle cellular component organization regulation of mitotic cell cycle negative regulation of cellular process mitotic sister chromatid segregation negative regulation of mitotic metaphase/anaphase transition cellular component organization or biogenesis regulation of cell cycle negative regulation of chromosome separation cell cycle process mitotic nuclear division negative regulation of mitotic cell cycle phase transition organelle fission biological regulation chromosome organization negative regulation of cell cycle process cell cycle checkpoint signaling mitotic cell cycle checkpoint signaling organelle organization nuclear division negative regulation of chromosome segregation negative regulation of nuclear division negative regulation of organelle organization chromosome separation regulation of sister chromatid segregation negative regulation of mitotic sister chromatid separation regulation of nuclear division negative regulation of metaphase/anaphase transition of cell cycle nuclear chromosome segregation metaphase/anaphase transition of mitotic cell cycle metaphase/anaphase transition of cell cycle mitotic cell cycle phase transition peroxisome organization ER-dependent peroxisome organization cellular localization establishment of localization in cell intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex RZZ complex intracellular membraneless organelle chromosome chromosomal region kinetochore intracellular organelle organelle membraneless organelle chromosome, centromeric region cellular anatomical structure intracellular anatomical structure cytoplasm cytosol protein-containing complex RZZ complex intracellular membraneless organelle chromosome chromosomal region kinetochore intracellular organelle organelle membraneless organelle chromosome, centromeric region condensed chromosome, centromeric region supramolecular complex condensed chromosome membrane-bounded organelle nucleus intracellular membrane-bounded organelle endomembrane system vesicle tethering complex Dsl1/NZR complex endoplasmic reticulum endoplasmic reticulum protein-containing complex organelle subcompartment membrane endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network organelle membrane endoplasmic reticulum membrane
D	Protein transport protein SEC39	-	localization transport cellular process establishment of localization vesicle-mediated transport retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum Golgi vesicle transport cellular component organization peroxisome organization organelle organization cellular component organization or biogenesis ER-dependent peroxisome organization establishment of protein localization nitrogen compound transport localization transport cellular process establishment of localization vesicle-mediated transport retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum Golgi vesicle transport cellular component organization peroxisome organization organelle organization cellular component organization or biogenesis ER-dependent peroxisome organization establishment of protein localization nitrogen compound transport protein transport macromolecule localization intracellular protein localization	membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system protein-containing complex vesicle tethering complex Dsl1/NZR complex endoplasmic reticulum membrane-bounded organelle intracellular organelle organelle envelope cellular anatomical structure intracellular anatomical structure organelle nuclear envelope nucleus intracellular membrane-bounded organelle endomembrane system protein-containing complex vesicle tethering complex Dsl1/NZR complex endoplasmic reticulum cytoplasm endoplasmic reticulum protein-containing complex organelle subcompartment membrane endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network organelle membrane endoplasmic reticulum membrane
C	Protein transport protein TIP20	-	localization transport retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport catabolic process autophagy metabolic process process utilizing autophagic mechanism establishment of protein localization nitrogen compound transport protein transport localization transport retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport catabolic process autophagy metabolic process process utilizing autophagic mechanism establishment of protein localization nitrogen compound transport protein transport macromolecule localization intracellular protein localization regulation of localization cellular localization regulation of biological process regulation of cellular process regulation of ER to Golgi vesicle-mediated transport regulation of transport biological regulation intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport regulation of vesicle-mediated transport regulation of cellular localization establishment of localization in cell regulation of intracellular transport	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex intracellular membrane-bounded organelle endomembrane system vesicle tethering complex intracellular organelle Dsl1/NZR complex organelle endoplasmic reticulum endoplasmic reticulum protein-containing complex cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex intracellular membrane-bounded organelle endomembrane system vesicle tethering complex intracellular organelle Dsl1/NZR complex organelle endoplasmic reticulum endoplasmic reticulum protein-containing complex organelle subcompartment membrane endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network organelle membrane endoplasmic reticulum membrane
B	Protein transport protein USE1	SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity	localization transport retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport membrane organization membrane fusion organelle membrane fusion endoplasmic reticulum organization vesicle organization cellular component organization organelle fusion localization transport retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport membrane organization membrane fusion organelle membrane fusion endoplasmic reticulum organization vesicle organization cellular component organization organelle fusion organelle organization cellular component organization or biogenesis vesicle fusion with endoplasmic reticulum vesicle fusion endomembrane system organization establishment of protein localization nitrogen compound transport protein transport macromolecule localization intracellular protein localization	SNARE complex protein-containing complex cellular anatomical structure intracellular anatomical structure membrane membrane protein complex cytoplasm membrane-bounded organelle organelle subcompartment cytoplasmic side of membrane intracellular membrane-bounded organelle endomembrane system side of membrane endoplasmic reticulum subcompartment SNARE complex protein-containing complex cellular anatomical structure intracellular anatomical structure membrane membrane protein complex cytoplasm membrane-bounded organelle organelle subcompartment cytoplasmic side of membrane intracellular membrane-bounded organelle endomembrane system side of membrane endoplasmic reticulum subcompartment intracellular organelle organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasmic side of endoplasmic reticulum membrane organelle membrane endoplasmic reticulum membrane intracellular vesicle transport vesicle membrane COPI-coated Golgi to ER transport vesicle COPI-coated vesicle bounding membrane of organelle vesicle membrane cytoplasmic vesicle coated vesicle Golgi-associated vesicle vesicle transport vesicle Golgi to ER transport vesicle membrane COPI-coated vesicle membrane cytoplasmic vesicle membrane coated vesicle membrane Golgi-associated vesicle membrane
A	Protein transport protein SEC20	SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity	localization transport retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport membrane organization membrane fusion organelle membrane fusion endoplasmic reticulum organization vesicle organization cellular component organization organelle fusion localization transport retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport membrane organization membrane fusion organelle membrane fusion endoplasmic reticulum organization vesicle organization cellular component organization organelle fusion organelle organization cellular component organization or biogenesis vesicle fusion with endoplasmic reticulum vesicle fusion endomembrane system organization establishment of protein localization nitrogen compound transport protein transport macromolecule localization intracellular protein localization	SNARE complex protein-containing complex cellular anatomical structure intracellular anatomical structure membrane membrane protein complex cytoplasm membrane-bounded organelle organelle subcompartment cytoplasmic side of membrane intracellular membrane-bounded organelle endomembrane system side of membrane endoplasmic reticulum subcompartment SNARE complex protein-containing complex cellular anatomical structure intracellular anatomical structure membrane membrane protein complex cytoplasm membrane-bounded organelle organelle subcompartment cytoplasmic side of membrane intracellular membrane-bounded organelle endomembrane system side of membrane endoplasmic reticulum subcompartment intracellular organelle organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasmic side of endoplasmic reticulum membrane organelle membrane endoplasmic reticulum membrane intracellular vesicle transport vesicle membrane COPI-coated Golgi to ER transport vesicle COPI-coated vesicle bounding membrane of organelle vesicle membrane cytoplasmic vesicle coated vesicle Golgi-associated vesicle vesicle transport vesicle Golgi to ER transport vesicle membrane COPI-coated vesicle membrane cytoplasmic vesicle membrane coated vesicle membrane Golgi-associated vesicle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E	IPR021875	Retrograde transport protein Dsl1 N-terminal domain	Domain
E	IPR038442	Dsl1, N-terminal domain superfamily	Homologous Superfamily
E	IPR046362	Zw10/DSL1, C-terminal	Homologous Superfamily
E	IPR021876	Retrograde transport protein Dsl1, C-terminal domain	Domain
D	IPR013244	Sec39 domain	Domain
C	IPR042042	Protein transport protein Tip20, domain B	Homologous Superfamily
C	IPR042040	Protein transport protein Tip20, domain E	Homologous Superfamily
C	IPR042044	EXOC6/PINT-1/Sec15/Tip20, C-terminal, domain 2	Homologous Superfamily
C	IPR042041	Protein transport protein Tip20, domain A	Homologous Superfamily
C	IPR042043	Protein transport protein Tip20, domain C	Homologous Superfamily
C	IPR007528	RINT-1/Tip20	Family
B	IPR019150	Vesicle transport protein, Use1	Family
A	IPR056173	Sec20, C-terminal	Domain
A	IPR005606	Sec20	Family

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.