5VNN

Crystal structure of Sec23a/Sec24a/Sec22 complexed with 4-phenylbutyric acid (50mM soaking)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	SNARE-like	8033932	3001113	SCOP2B (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	Sec23_BS	e5vnnA5	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	e5vnnA3	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	e5vnnA1	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	e5vnnA4	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	e5vnnA2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: zf-Sec23_Sec24	ECOD (1.6)
B	Sec23_BS	e5vnnB2	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)
B	Sec23_helical	e5vnnB1	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	e5vnnB5	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_trunk	e5vnnB3	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: Sec23_trunk	ECOD (1.6)
B	zf-Sec23_Sec24	e5vnnB4	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: zf-Sec23_Sec24	ECOD (1.6)
C	Longin	e5vnnC1	A: a+b three layers	X: Profilin-like	H: profilin-like (From Topology)	T: profilin-like	F: Longin	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)
C	3.30.450.50	Alpha Beta	2-Layer Sandwich	Beta-Lactamase	Longin domain	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
C	PF00957	Synaptobrevin (Synaptobrevin)	Synaptobrevin	-	Family
C	PF13774	Regulated-SNARE-like domain (Longin)	Regulated-SNARE-like domain	Longin is one of the approximately 26 components required for transporting proteins from the ER to the plasma membrane, via the Golgi apparatus. It is necessary for the steps of the transfer from the ER to the Golgi complex [1]. Longins are the only ...	Longin is one of the approximately 26 components required for transporting proteins from the ER to the plasma membrane, via the Golgi apparatus. It is necessary for the steps of the transfer from the ER to the Golgi complex [1]. Longins are the only R-SNAREs that are common to all eukaryotes, and they are characterised by a conserved N-terminal domain with a profilin-like fold called a longin domain [2].	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 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 protein localization to cell periphery protein localization to plasma membrane localization within membrane protein localization to membrane	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 Golgi membrane Golgi apparatus membrane bounding membrane of organelle 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 Golgi membrane Golgi apparatus membrane bounding membrane of organelle organelle membrane cytosol perinuclear region of cytoplasm 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 vesicle 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
B	Protein transport protein Sec24A	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 regulation of localization regulation of cellular process regulation of protein localization positive regulation of biological process positive regulation of establishment of protein localization positive regulation of secretion by cell protein localization to extracellular region positive regulation of protein transport regulation of secretion by cell secretion by cell positive regulation of secretion positive regulation of cellular process regulation of biological process regulation of transport secretion biological regulation regulation of establishment of protein localization establishment of protein localization to extracellular region export from cell regulation of protein transport protein secretion positive regulation of protein secretion regulation of protein secretion regulation of secretion positive regulation of transport regulation of cellular localization positive regulation of protein localization regulation of sterol transport lipid localization lipid transport regulation of lipid transport organic hydroxy compound transport regulation of lipid localization cholesterol transport sterol transport regulation of cholesterol 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 sterol homeostasis chemical homeostasis homeostatic process cholesterol homeostasis lipid homeostasis	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	Vesicle-trafficking protein SEC22b	protein binding binding SNARE binding syntaxin binding 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 protein localization establishment of protein localization cellular localization nitrogen compound transport protein transport cellular macromolecule localization macromolecule localization localization transport retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport protein localization establishment of protein localization cellular localization nitrogen compound transport protein transport cellular macromolecule localization macromolecule localization catabolic process regulation of cellular component organization regulation of cellular process macroautophagy autophagy negative regulation of biological process negative regulation of organelle assembly autophagosome organization regulation of autophagy cellular component biogenesis cellular component organization cellular component assembly negative regulation of cellular process cellular component organization or biogenesis process utilizing autophagic mechanism negative regulation of autophagosome assembly negative regulation of catabolic process regulation of biological process autophagosome assembly organelle assembly vacuole organization negative regulation of cellular component organization negative regulation of metabolic process biological regulation regulation of autophagosome assembly regulation of vacuole organization regulation of catabolic process regulation of cellular component biogenesis regulation of organelle organization negative regulation of macroautophagy organelle organization regulation of macroautophagy negative regulation of organelle organization negative regulation of autophagy regulation of organelle assembly metabolic process regulation of metabolic 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 protein metabolic process primary metabolic process regulation of macromolecule metabolic process protein catabolic process positive regulation of protein catabolic process positive regulation of catabolic process macromolecule metabolic process regulation of protein catabolic process establishment of localization in cell intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport	membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle COPI-coated vesicle intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle coated vesicle cytoplasm Golgi-associated vesicle vesicle pigment granule membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle COPI-coated vesicle intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle coated vesicle cytoplasm Golgi-associated vesicle vesicle pigment granule melanosome Golgi membrane Golgi apparatus membrane endomembrane system bounding membrane of organelle organelle membrane endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment SNARE complex protein-containing complex membrane protein complex transport vesicle transport vesicle membrane cytoplasmic vesicle membrane coated vesicle membrane COPII-coated ER to Golgi transport vesicle vesicle membrane ER to Golgi transport vesicle membrane synapse presynapse synaptic vesicle cell junction secretory vesicle exocytic vesicle organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR007123	Gelsolin-like domain	Domain
A	IPR029006	ADF-H/Gelsolin-like domain superfamily	Homologous Superfamily
A	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
A	IPR037550	Sec23, C-terminal	Domain
A	IPR006896	Sec23/Sec24, trunk domain	Domain
A	IPR036180	Gelsolin-like domain superfamily	Homologous Superfamily
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
A	IPR006900	Sec23/Sec24, helical domain	Domain
A	IPR006895	Zinc finger, Sec23/Sec24-type	Domain
A	IPR012990	Sec23/Sec24 beta-sandwich	Domain
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	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
B	IPR012990	Sec23/Sec24 beta-sandwich	Domain
C	IPR044565	Vesicle-trafficking protein Sec22	Family
C	IPR011012	Longin-like domain superfamily	Homologous Superfamily
C	IPR010908	Longin domain	Domain
C	IPR001388	Synaptobrevin-like	Family
C	IPR042855	v-SNARE, coiled-coil homology domain	Domain

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: O95486	spina bifida attention deficit hyperactivity disorder, inattentive type exocrine pancreatic carcinoma invasive ductal breast carcinoma malignant glioma myopathy pancreatic intraductal papillary-mucinous neoplasm pituitary cancer tuberculosis atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma malignant pancreatic neoplasm non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia spina bifida attention deficit hyperactivity disorder, inattentive type exocrine pancreatic carcinoma invasive ductal breast carcinoma malignant glioma myopathy pancreatic intraductal papillary-mucinous neoplasm pituitary cancer tuberculosis atypical teratoid rhabdoid tumor glioblastoma large cell medulloblastoma malignant pancreatic neoplasm non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia primitive neuroectodermal tumor ulcerative colitis Crohn disease interstitial cystitis malignant ependymoma medulloblastoma osteosarcoma pilocytic astrocytoma