3EH2 | pdb_00003eh2

Crystal structure of the human COPII-coat protein Sec24c

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	V-set	e3eh2A2	A: a/b three-layered sandwiches	X: Profilin-like	H: sensor domains	T: sensor domains	F: V-set	ECOD (v294.1)
A	RNA_pol_Rpb1_5	e3eh2A5	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: RNA_pol_Rpb1_5	ECOD (v294.1)
B	Piwi	e3eh2B14	A: a/b three-layered sandwiches	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: Piwi	ECOD (v294.1)
B	RNA_pol_Rpb1_5	e3eh2B4	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: RNA_pol_Rpb1_5	ECOD (v294.1)
C	Peptidase_M49	e3eh2C22	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Peptidase_M49	ECOD (v294.1)
C	RNA_pol_Rpb1_5	e3eh2C4	A: a/b three-layered sandwiches	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: RNA_pol_Rpb1_5	ECOD (v294.1)

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)
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	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	2.30.30.380	Mainly Beta	Roll	SH3 type barrels.	Zn-finger domain of Sec23/24	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	3.40.50.410	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	von Willebrand factor, type A domain	CATH (4.3.0)
C	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, B, 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, B, C	PF00626	Gelsolin repeat (Gelsolin)	Gelsolin repeat		Domain
A, B, C	PF08033	Sec23/Sec24 beta-sandwich domain (Sec23_BS)	Sec23/Sec24 beta-sandwich domain		Domain
A, B, 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, B, 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
A, B, C	Protein transport protein Sec24C	protein binding binding SNARE binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	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 membrane organization vesicle budding from membrane 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 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR007123	Gelsolin-like domain	Domain
A, B, C	IPR029006	ADF-H/Gelsolin-like domain superfamily	Homologous Superfamily
A, B, C	IPR036465	von Willebrand factor A-like domain superfamily	Homologous Superfamily
A, B, C	IPR012990	Sec23/Sec24, beta-sandwich	Domain
A, B, C	IPR006896	Sec23/Sec24, trunk domain	Domain
A, B, C	IPR050550	SEC23/SEC24 family, SEC24 subfamily	Family
A, B, C	IPR036180	Gelsolin-like domain superfamily	Homologous Superfamily
A, B, C	IPR036175	Sec23/Sec24 helical domain superfamily	Homologous Superfamily
A, B, C	IPR036174	Zinc finger, Sec23/Sec24-type superfamily	Homologous Superfamily
A, B, C	IPR006900	Sec23/Sec24, helical domain	Domain
A, B, C	IPR041742	Sec24-like, trunk domain	Domain
A, B, C	IPR006895	Zinc finger, Sec23/Sec24-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: P53992	22q11 Deletion Syndrome astrocytic tumor bipolar disorder major depressive disorder osteosarcoma psoriasis myocardial infarction ovarian cancer 22q11.2 deletion syndrome atrial fibrillation DiGeorge syndrome oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia

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.