1PD0 | pdb_00001pd0

Crystal structure of the COPII coat subunit, Sec24, complexed with a peptide from the SNARE protein Sed5 (yeast syntaxin-5)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1pd0a1	All alpha proteins	ERP29 C domain-like	Helical domain of Sec23/24	Helical domain of Sec23/24	Sec24	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1pd0a2	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	beta-sandwich domain of Sec23/24	beta-sandwich domain of Sec23/24	Sec24	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1pd0a3	Alpha and beta proteins (a/b)	vWA-like	vWA-like	Trunk domain of Sec23/24	Sec24	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1pd0a4	Alpha and beta proteins (a+b)	Gelsolin-like	C-terminal, gelsolin-like domain of Sec23/24	C-terminal, gelsolin-like domain of Sec23/24	Sec24	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1pd0a5	Small proteins	Rubredoxin-like	Zn-finger domain of Sec23/24	Zn-finger domain of Sec23/24	Sec24	(Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Helical domain of Sec23/24	8026146	4002392	SCOP2 (2022-06-29)
A	SCOP2 Family	beta-sandwich domain of sec23/24	8026152	4002652	SCOP2 (2022-06-29)
A	SCOP2 Family	Trunk domain of Sec23/24	8026154	4003060	SCOP2 (2022-06-29)
A	SCOP2 Family	C-terminal, gelsolin-like domain of Sec23/24	8026156	4003304	SCOP2 (2022-06-29)
A	SCOP2 Family	Zn-finger domain of Sec23/24	8026162	4003422	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Helical domain of Sec23/24	8038525	3001173	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	beta-sandwich domain of sec23/24	8038531	3001553	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	vWA-like	8038533	3000832	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	C-terminal, gelsolin-like domain of Sec23/24	8038535	3000569	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Zn-finger domain of Sec23/24	8038541	3000837	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A		e1pd0A1	A: Immunoglobulin-like beta-sandwich	X: Immunoglobulin-related	H: Common fold of diphtheria toxin/transcription factors/cytochrome f	T: Sec23_BS	F:	ECOD (20:10:01)
A		e1pd0A2	A: ERP29 C domain-like	X: Helical domain of Sec23/24	H: Helical domain of Sec23/24	T: Sec23_helical	F:	ECOD (20:10:01)
A		e1pd0A3	A: Gelsolin-like	X: Gelsolin-like	H: Gelsolin-like	T: Gelsolin	F:	ECOD (20:10:01)
A		e1pd0A4	A: Rubredoxin-like	X: Rubredoxin-related	H: Rubredoxin-related	T: zf-Sec23_Sec24	F:	ECOD (20:10:01)
A		e1pd0A5	A: Flavodoxin-like	X: HAD domain-related	H: vWA-like	T: Sec23_trunk	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.120.730	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Sec23/Sec24 helical domain	CATH (4.3.0)
A	2.30.30.380	Mainly Beta	Roll	SH3 type barrels.	Zn-finger domain of Sec23/24	CATH (4.3.0)
A	2.60.40.1670	Mainly Beta	Sandwich	Immunoglobulin-like	beta-sandwich domain of Sec23/24	CATH (4.3.0)
A	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)
A	3.40.20.10	Alpha Beta	3-Layer(aba) Sandwich	Severin	Severin	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF04815	Sec23/Sec24 helical domain (Sec23_helical)	Sec23/Sec24 helical domain	COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and ...	COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is composed of five alpha helices.	Domain
A	PF00626	Gelsolin repeat (Gelsolin)	Gelsolin repeat		Domain
A	PF08033	Sec23/Sec24 beta-sandwich domain (Sec23_BS)	Sec23/Sec24 beta-sandwich domain		Domain
A	PF04811	Sec23/Sec24 trunk domain (Sec23_trunk)	Sec23/Sec24 trunk domain	COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and ...	COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is known as the trunk domain and has an alpha/beta vWA fold and forms the dimer interface.	Domain
A	PF04810	Sec23/Sec24 zinc finger (zf-Sec23_Sec24)	Sec23/Sec24 zinc finger	COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and ...	COPII-coated vesicles carry proteins from the endoplasmic reticulum to the Golgi complex. This vesicular transport can be reconstituted by using three cytosolic components containing five proteins: the small GTPase Sar1p, the Sec23p/24p complex, and the Sec13p/Sec31p complex. This domain is found to be zinc binding domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B	COPII-binding peptide of the integral membrane protein SED5	protein binding binding SNARE binding SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity	localization transport cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport intra-Golgi vesicle-mediated transport regulation of biological process regulation of cellular process regulation of cellular component organization regulation of inclusion body assembly biological regulation inclusion body assembly regulation of cellular component biogenesis localization transport cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport intra-Golgi vesicle-mediated transport regulation of biological process regulation of cellular process regulation of cellular component organization regulation of inclusion body assembly biological regulation inclusion body assembly regulation of cellular component biogenesis cellular component biogenesis cellular component organization cellular component assembly cellular component organization or biogenesis cellular localization establishment of protein localization intracellular transport protein transport establishment of localization in cell macromolecule localization intracellular protein localization intracellular protein transport membrane organization membrane fusion organelle membrane fusion vesicle organization organelle fusion organelle organization vesicle fusion endoplasmic reticulum to Golgi vesicle-mediated transport vesicle fusion with Golgi apparatus Golgi organization endomembrane system organization organelle localization by membrane tethering organelle localization vesicle docking membrane docking	cellular anatomical structure endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus cis-Golgi network organelle intracellular membrane-bounded organelle cytoplasm membrane Golgi membrane bounding membrane of organelle organelle membrane cellular anatomical structure endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus cis-Golgi network organelle intracellular membrane-bounded organelle cytoplasm membrane Golgi membrane bounding membrane of organelle organelle membrane Golgi cis cisterna membrane Golgi cisterna membrane Golgi apparatus subcompartment organelle subcompartment Golgi cisterna Golgi cis cisterna Golgi stack SNARE complex protein-containing complex membrane protein complex endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane
A	Protein transport protein Sec24	signal sequence binding binding peptide binding protein binding SNARE binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	regulation of localization cellular localization regulation of cellular process transport positive regulation of biological process positive regulation of ER to Golgi vesicle-mediated transport vesicle-mediated transport localization establishment of localization in cell positive regulation of intracellular transport positive regulation of cellular process regulation of intracellular transport regulation of biological process regulation of ER to Golgi vesicle-mediated transport regulation of localization cellular localization regulation of cellular process transport positive regulation of biological process positive regulation of ER to Golgi vesicle-mediated transport vesicle-mediated transport localization establishment of localization in cell positive regulation of intracellular transport positive regulation of cellular process regulation of intracellular transport regulation of biological 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 establishment of localization positive regulation of transport regulation of cellular localization cellular process Golgi vesicle transport regulation of protein exit from endoplasmic reticulum protein exit from endoplasmic reticulum establishment of protein localization regulation of protein localization positive regulation of establishment of protein localization positive regulation of protein transport intracellular protein localization regulation of establishment of protein localization regulation of protein transport positive regulation of protein exit from endoplasmic reticulum protein transport macromolecule localization positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport intracellular protein transport catabolic process macroautophagy autophagy metabolic process process utilizing autophagic mechanism membrane organization vesicle budding from membrane vesicle cargo loading cellular component organization vesicle organization organelle organization COPII-coated vesicle cargo loading cellular component organization or biogenesis COPII-coated vesicle budding	membrane-bounded organelle protein-containing complex intracellular anatomical structure vesicle coat intracellular vesicle transport vesicle membrane membrane protein complex endomembrane system intracellular organelle membrane coat cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle membrane-bounded organelle protein-containing complex intracellular anatomical structure vesicle coat intracellular vesicle transport vesicle membrane membrane protein complex endomembrane system intracellular organelle membrane coat cellular anatomical structure bounding membrane of organelle vesicle membrane cytoplasmic vesicle ER to Golgi transport vesicle membrane coated vesicle vesicle transport vesicle membrane intracellular membrane-bounded organelle coated membrane COPII vesicle coat cytoplasmic vesicle membrane coated vesicle membrane COPII-coated ER to Golgi transport vesicle organelle cytoplasm organelle membrane organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane endoplasmic reticulum exit site vacuolar membrane storage vacuole lytic vacuole vacuole fungal-type vacuole lytic vacuole membrane fungal-type vacuole membrane Golgi membrane Golgi apparatus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B	IPR021538	Syntaxin-5, N-terminal, Sly1p-binding domain	Domain
B	IPR006012	Syntaxin/epimorphin, conserved site	Conserved Site
B	IPR000727	Target SNARE coiled-coil homology domain	Domain
B	IPR010989	SNARE	Homologous Superfamily
B	IPR045242	Syntaxin	Family
A	IPR029006	ADF-H/Gelsolin-like domain superfamily	Homologous Superfamily
A	IPR012990	Sec23/Sec24, beta-sandwich	Domain
A	IPR006896	Sec23/Sec24, trunk domain	Domain
A	IPR050550	SEC23/SEC24 family, SEC24 subfamily	Family
A	IPR036180	Gelsolin-like domain superfamily	Homologous Superfamily
A	IPR006900	Sec23/Sec24, helical domain	Domain
A	IPR041742	Sec24-like, trunk domain	Domain
A	IPR006895	Zinc finger, Sec23/Sec24-type	Domain
A	IPR007123	Gelsolin-like domain	Domain
A	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
A	IPR036175	Sec23/Sec24 helical domain superfamily	Homologous Superfamily
A	IPR036174	Zinc finger, Sec23/Sec24-type superfamily	Homologous Superfamily

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.