3EFO | pdb_00003efo

Crystal Structure of the mammalian COPII-coat protein Sec23/24 bound to the transport signal sequence of syntaxin 5

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Sec23_BS	e3efoA4	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: Sec23_BS	ECOD (1.6)
A	Sec23_helical	e3efoA2	A: alpha arrays	X: ERP29 C domain-like	H: Helical domain of Sec23/24 (From Topology)	T: Helical domain of Sec23/24	F: Sec23_helical	ECOD (1.6)
A	Gelsolin	e3efoA5	A: a+b three layers	X: Gelsolin-like (From Topology)	H: Gelsolin-like (From Topology)	T: Gelsolin-like	F: Gelsolin	ECOD (1.6)
A	Sec23_trunk	e3efoA1	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: Sec23_trunk	ECOD (1.6)
A	zf-Sec23_Sec24	e3efoA3	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: zf-Sec23_Sec24	ECOD (1.6)
B	Sec23_helical	e3efoB2	A: alpha arrays	X: ERP29 C domain-like	H: Helical domain of Sec23/24 (From Topology)	T: Helical domain of Sec23/24	F: Sec23_helical	ECOD (1.6)
B	Gelsolin	e3efoB3	A: a+b three layers	X: Gelsolin-like (From Topology)	H: Gelsolin-like (From Topology)	T: Gelsolin-like	F: Gelsolin	ECOD (1.6)
B	Sec23_BS,Sec23_trunk	e3efoB4	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: Sec23_BS,Sec23_trunk	ECOD (1.6)
B	Sec23_BS,zf-Sec23_Sec24	e3efoB1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Sec23_BS,zf-Sec23_Sec24	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.1670	Mainly Beta	Sandwich	Immunoglobulin-like	beta-sandwich domain of Sec23/24	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	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)
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	3.40.20.10	Alpha Beta	3-Layer(aba) Sandwich	Severin	Severin	CATH (4.3.0)
B	1.20.120.730	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Sec23/Sec24 helical domain	CATH (4.3.0)
B	2.30.30.380	Mainly Beta	Roll	SH3 type barrels.	Zn-finger domain of Sec23/24	CATH (4.3.0)
B	2.60.40.1670	Mainly Beta	Sandwich	Immunoglobulin-like	beta-sandwich domain of Sec23/24	CATH (4.3.0)
B	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)
B	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
B	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
B	PF00626	Gelsolin repeat (Gelsolin)	Gelsolin repeat		Domain
B	PF08033	Sec23/Sec24 beta-sandwich domain (Sec23_BS)	Sec23/Sec24 beta-sandwich domain		Domain
B	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
B	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
A	Protein transport protein Sec23A	GTPase regulator activity enzyme regulator activity enzyme activator activity GTPase activator activity molecular function activator activity nucleoside-triphosphatase regulator activity molecular function regulator activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	protein localization localization protein localization to cell periphery cellular localization protein localization to plasma membrane cellular macromolecule localization macromolecule localization cellular process localization within membrane protein localization to membrane establishment of protein localization nitrogen compound transport transport intracellular transport protein localization localization protein localization to cell periphery cellular localization protein localization to plasma membrane cellular macromolecule localization macromolecule localization cellular process localization within membrane protein localization to membrane establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization protein transport establishment of localization in cell intracellular protein transport membrane organization vesicle budding from membrane endoplasmic reticulum to Golgi vesicle-mediated transport vesicle cargo loading vesicle-mediated transport cellular component organization vesicle organization organelle organization COPII-coated vesicle cargo loading cellular component organization or biogenesis COPII-coated vesicle budding Golgi vesicle transport	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex vesicle coat intracellular vesicle transport vesicle membrane membrane protein complex endomembrane system intracellular organelle membrane coat bounding membrane of organelle cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex vesicle coat intracellular vesicle transport vesicle membrane membrane protein complex endomembrane system intracellular organelle membrane coat 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 organelle membrane organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane endoplasmic reticulum exit site Golgi membrane Golgi apparatus perinuclear region of cytoplasm
B	SEC24 related gene family, member D	protein binding binding SNARE binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	protein localization cellular localization establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process intracellular protein transport protein localization cellular localization establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process intracellular protein transport membrane organization vesicle budding from membrane endoplasmic reticulum to Golgi vesicle-mediated transport vesicle cargo loading vesicle-mediated transport cellular component organization vesicle organization organelle organization COPII-coated vesicle cargo loading cellular component organization or biogenesis COPII-coated vesicle budding Golgi vesicle transport developmental process multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching chordate embryonic development anatomical structure development embryo development in utero embryonic development	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle endoplasmic reticulum exit site endoplasmic reticulum cytoplasm intracellular membrane-bounded organelle endomembrane system cytosol transport vesicle membrane intracellular vesicle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle endoplasmic reticulum exit site endoplasmic reticulum cytoplasm intracellular membrane-bounded organelle endomembrane system cytosol transport vesicle membrane intracellular vesicle transport vesicle membrane cytoplasmic vesicle membrane bounding membrane of organelle coated vesicle membrane COPII-coated ER to Golgi transport vesicle vesicle membrane cytoplasmic vesicle ER to Golgi transport vesicle membrane coated vesicle vesicle organelle membrane protein-containing complex vesicle coat membrane protein complex membrane coat coated membrane COPII vesicle coat organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum membrane
C	Peptide	SNAP receptor activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding SNARE binding cell adhesion molecule binding cadherin binding	early endosome to Golgi transport cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport localization cytosolic transport retrograde transport, endosome to Golgi establishment of localization in cell cellular process Golgi vesicle transport cellular component disassembly early endosome to Golgi transport cellular localization transport intracellular transport establishment of localization vesicle-mediated transport endosomal transport localization cytosolic transport retrograde transport, endosome to Golgi establishment of localization in cell cellular process Golgi vesicle transport cellular component disassembly Golgi inheritance organelle inheritance Golgi disassembly cellular component organization organelle organization organelle disassembly cellular component organization or biogenesis Golgi organization endomembrane system organization membrane organization membrane fusion organelle membrane fusion vesicle organization organelle fusion vesicle fusion regulation of cellular process catabolic process positive regulation of protein metabolic process positive regulation of biological process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of cellular process regulation of biological process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process metabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process endoplasmic reticulum to Golgi vesicle-mediated transport protein localization establishment of protein localization nitrogen compound transport protein transport cellular macromolecule localization macromolecule localization intracellular protein transport retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum regulation of cellular component organization regulation of organelle organization regulation of Golgi organization organelle localization by membrane tethering organelle localization vesicle docking membrane docking	cellular anatomical structure endomembrane system membrane-bounded organelle organelle vesicle intracellular anatomical structure cytoplasm cytosol SNARE complex protein-containing complex membrane membrane protein complex organelle subcompartment intracellular membrane-bounded organelle cellular anatomical structure endomembrane system membrane-bounded organelle organelle vesicle intracellular anatomical structure cytoplasm cytosol SNARE complex protein-containing complex membrane membrane protein complex organelle subcompartment intracellular membrane-bounded organelle endoplasmic reticulum subcompartment intracellular organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane Golgi apparatus Golgi membrane bounding membrane of organelle endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment transport vesicle intracellular vesicle transport vesicle membrane cytoplasmic vesicle membrane coated vesicle membrane COPII-coated ER to Golgi transport vesicle vesicle membrane cytoplasmic vesicle ER to Golgi transport vesicle membrane coated vesicle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
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	IPR036180	Gelsolin-like domain superfamily	Homologous Superfamily
A	IPR006900	Sec23/Sec24, helical 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	IPR037550	Sec23, C-terminal	Domain
A	IPR037364	Protein transport protein Sec23	Family
A	IPR036175	Sec23/Sec24 helical domain superfamily	Homologous Superfamily
A	IPR036174	Zinc finger, Sec23/Sec24-type superfamily	Homologous Superfamily
B	IPR007123	Gelsolin-like domain	Domain
B	IPR029006	ADF-H/Gelsolin-like domain superfamily	Homologous Superfamily
B	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
B	IPR012990	Sec23/Sec24, beta-sandwich	Domain
B	IPR006896	Sec23/Sec24, trunk domain	Domain
B	IPR050550	SEC23/SEC24 family, SEC24 subfamily	Family
B	IPR036180	Gelsolin-like domain superfamily	Homologous Superfamily
B	IPR036175	Sec23/Sec24 helical domain superfamily	Homologous Superfamily
B	IPR006900	Sec23/Sec24, helical domain	Domain
B	IPR041742	Sec24-like, trunk domain	Domain
B	IPR006895	Zinc finger, Sec23/Sec24-type	Domain
C	IPR021538	Syntaxin-5, N-terminal, Sly1p-binding domain	Domain
C	IPR000727	Target SNARE coiled-coil homology domain	Domain
C	IPR006012	Syntaxin/epimorphin, conserved site	Conserved Site
C	IPR010989	SNARE	Homologous Superfamily
C	IPR045242	Syntaxin	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q15436	craniolenticulosutural dysplasia amyotrophic lateral sclerosis cataract hereditary spastic paraplegia malignant mesothelioma osteoarthritis osteosarcoma rheumatoid arthritis atypical teratoid rhabdoid tumor IgA glomerulonephritis malignant pancreatic neoplasm osteoarthritis susceptibility 1 ovarian cancer breast cancer gastric carcinoma craniolenticulosutural dysplasia amyotrophic lateral sclerosis cataract hereditary spastic paraplegia malignant mesothelioma osteoarthritis osteosarcoma rheumatoid arthritis atypical teratoid rhabdoid tumor IgA glomerulonephritis malignant pancreatic neoplasm osteoarthritis susceptibility 1 ovarian cancer breast cancer gastric carcinoma lung adenocarcinoma medulloblastoma Osteoarthrosis Deformans pancreatic ductal adenocarcinoma
B	Pharos: O94855	Cole-Carpenter syndrome Cole-Carpenter syndrome 2 osteogenesis imperfecta ulcerative colitis Crohn disease interstitial cystitis malignant ependymoma osteochondrodysplasia ovarian cancer psoriasis glioblastoma invasive ductal breast carcinoma malignant glioma pilocytic astrocytoma Sjogren syndrome Cole-Carpenter syndrome Cole-Carpenter syndrome 2 osteogenesis imperfecta ulcerative colitis Crohn disease interstitial cystitis malignant ependymoma osteochondrodysplasia ovarian cancer psoriasis glioblastoma invasive ductal breast carcinoma malignant glioma pilocytic astrocytoma Sjogren syndrome craniosynostosis hydrocephalus lung adenocarcinoma mucopolysaccharidosis type 4 osteosarcoma pituitary cancer
C	Pharos: Q13190	Malignant neoplasm of breast