6GNI

Cryo-tomography and subtomogram averaging of Sar1-Sec23-Sec24 - fitted model.

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD 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)
A	SCOP2B Superfamily	C-terminal gelsolin-like domain of Sec23/24	8036411	3000569	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Zn-finger domain of Sec23/24	8036412	3000837	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	beta-sandwich domain of sec23/24	8036409	3001553	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	vWA-like	8036410	3000832	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	beta-sandwich domain of sec23/24	8036409	3001553	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Helical domain of Sec23/24	8036407	3001173	SCOP2B (2022-06-29)
B [auth E]	SCOP2B Superfamily	beta-sandwich domain of sec23/24	8038531	3001553	SCOP2B (2022-06-29)
B [auth E]	SCOP2B Superfamily	vWA-like	8038533	3000832	SCOP2B (2022-06-29)
B [auth E]	SCOP2B Superfamily	Helical domain of Sec23/24	8038525	3001173	SCOP2B (2022-06-29)
B [auth E]	SCOP2B Superfamily	Zn-finger domain of Sec23/24	8038541	3000837	SCOP2B (2022-06-29)
B [auth E]	SCOP2B Superfamily	beta-sandwich domain of sec23/24	8038531	3001553	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Ras-like P-loop GTPases	8060249	3002022	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	PF08033	e6gniA5	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: PF08033	ECOD (1.6)
A	PF04815	e6gniA4	A: alpha arrays	X: ERP29 C domain-like	H: Helical domain of Sec23/24 (From Topology)	T: Helical domain of Sec23/24	F: PF04815	ECOD (1.6)
A	PF00626	e6gniA1	A: a+b three layers	X: Gelsolin-like (From Topology)	H: Gelsolin-like (From Topology)	T: Gelsolin-like	F: PF00626	ECOD (1.6)
A	PF04811	e6gniA3	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: PF04811	ECOD (1.6)
A	PF04810	e6gniA2	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PF04810	ECOD (1.6)
B [auth E]	PF08033	e6gniE3	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Common fold of diphtheria toxin/transcription factors/cytochrome f	F: PF08033	ECOD (1.6)
B [auth E]	PF04815	e6gniE5	A: alpha arrays	X: ERP29 C domain-like	H: Helical domain of Sec23/24 (From Topology)	T: Helical domain of Sec23/24	F: PF04815	ECOD (1.6)
B [auth E]	PF00626	e6gniE4	A: a+b three layers	X: Gelsolin-like (From Topology)	H: Gelsolin-like (From Topology)	T: Gelsolin-like	F: PF00626	ECOD (1.6)
B [auth E]	PF04811	e6gniE2	A: a/b three-layered sandwiches	X: HAD domain-like	H: HAD domain-related	T: vWA-like	F: PF04811	ECOD (1.6)
B [auth E]	PF04810	e6gniE1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: PF04810	ECOD (1.6)
C [auth B]	PF00025	e6gniB1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF00025	ECOD (1.6)

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 [auth E]	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 [auth E]	PF00626	Gelsolin repeat (Gelsolin)	Gelsolin repeat	-	Domain
B [auth E]	PF08033	Sec23/Sec24 beta-sandwich domain (Sec23_BS)	Sec23/Sec24 beta-sandwich domain	-	Domain
B [auth E]	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 [auth E]	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 [auth B]	PF00025	ADP-ribosylation factor family (Arf)	ADP-ribosylation factor family	Pfam combines a number of different Prosite families together	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Protein transport protein SEC23	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	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 establishment of organelle localization vesicle budding from membrane regulation of cellular component organization vesicle targeting, to, from or within Golgi vesicle targeting cellular component organization cellular component biogenesis vesicle organization regulation of protein-containing complex assembly cellular component assembly organelle localization protein-containing complex assembly vesicle coating regulation of COPII vesicle coating cellular component organization or biogenesis vesicle targeting, rough ER to cis-Golgi membrane organization vesicle localization protein-containing complex organization establishment of vesicle localization regulation of cellular component biogenesis regulation of organelle organization organelle organization COPII-coated vesicle budding COPII vesicle coating protein localization regulation of protein exit from endoplasmic reticulum protein exit from endoplasmic reticulum establishment of protein localization nitrogen compound transport regulation of protein localization positive regulation of establishment of protein localization positive regulation of protein transport cellular macromolecule localization organic substance transport 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 cellular catabolic process catabolic process macroautophagy cellular metabolic process autophagy metabolic process process utilizing autophagic mechanism vesicle cargo loading COPII-coated vesicle cargo loading cellular component disassembly organelle disassembly reticulophagy	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 bounding membrane of organelle vesicle membrane cytoplasmic vesicle ER to Golgi transport vesicle membrane 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 bounding membrane of organelle vesicle membrane cytoplasmic vesicle ER to Golgi transport vesicle membrane coated vesicle vesicle transport vesicle membrane cellular anatomical entity 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 Golgi membrane Golgi apparatus
B [auth E]	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 protein localization regulation of protein exit from endoplasmic reticulum protein exit from endoplasmic reticulum establishment of protein localization nitrogen compound transport regulation of protein localization positive regulation of establishment of protein localization positive regulation of protein transport cellular macromolecule localization organic substance transport 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 cellular catabolic process catabolic process macroautophagy cellular metabolic process 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 bounding membrane of organelle vesicle membrane cytoplasmic vesicle ER to Golgi transport vesicle membrane 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 bounding membrane of organelle vesicle membrane cytoplasmic vesicle ER to Golgi transport vesicle membrane coated vesicle vesicle transport vesicle membrane cellular anatomical entity 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
C [auth B]	Small COPII coat GTPase SAR1	binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding organic cyclic compound binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity GTPase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity	protein localization cellular localization establishment of protein localization nitrogen compound transport transport organic substance transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process protein localization cellular localization establishment of protein localization nitrogen compound transport transport organic substance 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 positive regulation of biological process positive regulation of ER to Golgi vesicle-mediated transport vesicle-mediated transport 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 endoplasmic reticulum to Golgi vesicle-mediated transport regulation of vesicle-mediated transport positive regulation of transport regulation of cellular localization Golgi vesicle transport membrane organization cellular component organization nucleus organization organelle organization nuclear envelope organization cellular component organization or biogenesis endomembrane system organization vesicle organization mitochondrial membrane organization mitochondrion organization establishment of organelle localization vesicle budding from membrane regulation of cellular component organization vesicle targeting, to, from or within Golgi vesicle targeting cellular component biogenesis regulation of protein-containing complex assembly cellular component assembly organelle localization protein-containing complex assembly vesicle coating regulation of COPII vesicle coating vesicle targeting, rough ER to cis-Golgi vesicle localization protein-containing complex organization establishment of vesicle localization regulation of cellular component biogenesis regulation of organelle organization COPII-coated vesicle budding COPII vesicle coating organelle fission mitochondrial fission regulation of protein exit from endoplasmic reticulum protein exit from endoplasmic reticulum regulation of protein localization positive regulation of establishment of protein localization positive regulation of protein transport regulation of establishment of protein localization regulation of protein transport positive regulation of protein exit from endoplasmic reticulum positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle endoplasmic reticulum exit site endoplasmic reticulum endomembrane system Golgi membrane Golgi apparatus membrane membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle endoplasmic reticulum exit site endoplasmic reticulum endomembrane system Golgi membrane Golgi apparatus membrane bounding membrane of organelle organelle membrane organelle membrane contact site mitochondria-associated endoplasmic reticulum membrane contact site protein-containing complex vesicle coat intracellular vesicle transport vesicle membrane membrane protein complex membrane coat vesicle membrane cytoplasmic vesicle ER to Golgi transport vesicle membrane coated vesicle vesicle transport vesicle coated membrane COPII vesicle coat cytoplasmic vesicle membrane coated vesicle membrane COPII-coated ER to Golgi transport vesicle organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR029006	ADF-H/Gelsolin-like domain superfamily	Homologous Superfamily
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
A	IPR012990	Sec23/Sec24 beta-sandwich	Domain
B [auth E]	IPR029006	ADF-H/Gelsolin-like domain superfamily	Homologous Superfamily
B [auth E]	IPR006896	Sec23/Sec24, trunk domain	Domain
B [auth E]	IPR036180	Gelsolin-like domain superfamily	Homologous Superfamily
B [auth E]	IPR006900	Sec23/Sec24, helical domain	Domain
B [auth E]	IPR041742	Sec24-like, trunk domain	Domain
B [auth E]	IPR006895	Zinc finger, Sec23/Sec24-type	Domain
B [auth E]	IPR007123	Gelsolin-like domain	Domain
B [auth E]	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
B [auth E]	IPR036175	Sec23/Sec24 helical domain superfamily	Homologous Superfamily
B [auth E]	IPR036174	Zinc finger, Sec23/Sec24-type superfamily	Homologous Superfamily
B [auth E]	IPR012990	Sec23/Sec24 beta-sandwich	Domain
C [auth B]	IPR006687	Small GTPase superfamily, SAR1-type	Family
C [auth B]	IPR005225	Small GTP-binding protein domain	Domain
C [auth B]	IPR006689	Small GTPase superfamily, ARF/SAR type	Family
C [auth B]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily