1M2O | pdb_00001m2o

Crystal Structure of the Sec23-Sar1 complex

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)
D	d1m2od_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	SAR1	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
B	d1m2ob_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	G proteins	SAR1	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1m2oc1	All alpha proteins	ERP29 C domain-like	Helical domain of Sec23/24	Helical domain of Sec23/24	Sec23	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1m2oc2	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	beta-sandwich domain of Sec23/24	beta-sandwich domain of Sec23/24	Sec23	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1m2oc3	Alpha and beta proteins (a/b)	vWA-like	vWA-like	Trunk domain of Sec23/24	Sec23	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1m2oc4	Alpha and beta proteins (a+b)	Gelsolin-like	C-terminal, gelsolin-like domain of Sec23/24	C-terminal, gelsolin-like domain of Sec23/24	Sec23	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
C	d1m2oc5	Small proteins	Rubredoxin-like	Zn-finger domain of Sec23/24	Zn-finger domain of Sec23/24	Sec23	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1m2oa1	All alpha proteins	ERP29 C domain-like	Helical domain of Sec23/24	Helical domain of Sec23/24	Sec23	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1m2oa2	All beta proteins	Common fold of diphtheria toxin/transcription factors/cytochrome f	beta-sandwich domain of Sec23/24	beta-sandwich domain of Sec23/24	Sec23	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1m2oa3	Alpha and beta proteins (a/b)	vWA-like	vWA-like	Trunk domain of Sec23/24	Sec23	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1m2oa4	Alpha and beta proteins (a+b)	Gelsolin-like	C-terminal, gelsolin-like domain of Sec23/24	C-terminal, gelsolin-like domain of Sec23/24	Sec23	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d1m2oa5	Small proteins	Rubredoxin-like	Zn-finger domain of Sec23/24	Zn-finger domain of Sec23/24	Sec23	baker's yeast (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)
D	SCOP2B Superfamily	Ras-like P-loop GTPases	8060249	3002022	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ras-like P-loop GTPases	8060249	3002022	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Helical domain of Sec23/24	8036407	3001173	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	beta-sandwich domain of sec23/24	8036409	3001553	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	C-terminal, gelsolin-like domain of Sec23/24	8036411	3000569	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Zn-finger domain of Sec23/24	8036412	3000837	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	beta-sandwich domain of sec23/24	8036409	3001553	SCOP2B (2022-06-29)
C	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	beta-sandwich domain of sec23/24	8036409	3001553	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	C-terminal, gelsolin-like domain of Sec23/24	8036411	3000569	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Helical domain of Sec23/24	8036407	3001173	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	vWA-like	8036410	3000832	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Zn-finger domain of Sec23/24	8036412	3000837	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)
D		e1m2oD1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GBP	F:	ECOD (20:10:01)
B		e1m2oB1	A: C-terminal subdomain in Lon-related proteases catalytic domains	X: C-terminal subdomain in Lon-related proteases catalytic domains	H: C-terminal subdomain in Lon-related proteases catalytic domains	T: GBP	F:	ECOD (20:10:01)
C		e1m2oC1	A: Four-helical up-and-down bundle	X: Glycosyl hydrolase domain	H: Glycosyl hydrolase domain	T: Phosphonate-bd	F:	ECOD (20:10:01)
A		e1m2oA1	A: Four-helical up-and-down bundle	X: Glycosyl hydrolase domain	H: Glycosyl hydrolase domain	T: Phosphonate-bd	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
C	2.60.40.1670	Mainly Beta	Sandwich	Immunoglobulin-like	beta-sandwich domain of Sec23/24	CATH (4.3.0)
C	2.30.30.380	Mainly Beta	Roll	SH3 type barrels.	Zn-finger domain of Sec23/24	CATH (4.3.0)
C	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)
C	1.20.120.730	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	Sec23/Sec24 helical domain	CATH (4.3.0)
C	3.40.20.10	Alpha Beta	3-Layer(aba) Sandwich	Severin	Severin	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	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	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, C	PF00626	Gelsolin repeat (Gelsolin)	Gelsolin repeat		Domain
A, C	PF08033	Sec23/Sec24 beta-sandwich domain (Sec23_BS)	Sec23/Sec24 beta-sandwich domain		Domain
A, C	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, C	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, D	GTP-binding protein SAR1	binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion 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	cellular localization establishment of protein localization transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization intracellular protein transport regulation of localization regulation of cellular process cellular localization establishment of protein localization transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization 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 cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle organelle membrane contact site mitochondria-associated endoplasmic reticulum membrane contact site endoplasmic reticulum exit site endoplasmic reticulum endomembrane system Golgi membrane membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle organelle membrane contact site mitochondria-associated endoplasmic reticulum membrane contact site endoplasmic reticulum exit site endoplasmic reticulum endomembrane system Golgi membrane Golgi apparatus membrane bounding membrane of organelle organelle membrane 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
A, C	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 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 vesicle cargo loading COPII-coated vesicle cargo loading 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 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 Golgi membrane Golgi apparatus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR005225	Small GTP-binding domain	Domain
B, D	IPR006687	Small GTPase superfamily, SAR1-type	Family
B, D	IPR006689	Small GTPase superfamily, ARF/SAR type	Family
B, D	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, C	IPR029006	ADF-H/Gelsolin-like domain superfamily	Homologous Superfamily
A, C	IPR012990	Sec23/Sec24, beta-sandwich	Domain
A, C	IPR006896	Sec23/Sec24, trunk domain	Domain
A, C	IPR036180	Gelsolin-like domain superfamily	Homologous Superfamily
A, C	IPR006900	Sec23/Sec24, helical domain	Domain
A, C	IPR006895	Zinc finger, Sec23/Sec24-type	Domain
A, C	IPR007123	Gelsolin-like domain	Domain
A, C	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
A, C	IPR037550	Sec23, C-terminal	Domain
A, C	IPR037364	Protein transport protein Sec23	Family
A, C	IPR036175	Sec23/Sec24 helical domain superfamily	Homologous Superfamily
A, C	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.