8JPG | pdb_00008jpg

Cryo-EM structure of full-length ERGIC-53 with MCFD2

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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 [auth E]	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8081158	3000120	SCOP2B (2022-06-29)
D [auth F]	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8081158	3000120	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8081158	3000120	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8081158	3000120	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)
H	DNA_topoisoIV	e8jpgH1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
G [auth D]	DNA_topoisoIV	e8jpgD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
F [auth G]	DNA_topoisoIV	e8jpgG1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
E [auth C]	DNA_topoisoIV	e8jpgC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
C [auth E]	DNA_topoisoIV	e8jpgE1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
D [auth F]	DNA_topoisoIV	e8jpgF1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
B	DNA_topoisoIV	e8jpgB1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
A	DNA_topoisoIV	e8jpgA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
E [auth C], F [auth G], G [auth D], H	PF13499	EF-hand domain pair (EF-hand_7)	EF-hand domain pair		Domain
A, B, C [auth E], D [auth F]	PF03388	Legume-like lectin family (Lectin_leg-like)	Legume-like lectin family	Lectins are structurally diverse proteins that bind to specific carbohydrates. This family includes the VIP36 Swiss:P49256 and ERGIC-53 Swiss:P49257 lectins. These two proteins were the first recognised members of a family of animal lectins similar ( ...	Lectins are structurally diverse proteins that bind to specific carbohydrates. This family includes the VIP36 Swiss:P49256 and ERGIC-53 Swiss:P49257 lectins. These two proteins were the first recognised members of a family of animal lectins similar (19-24%) to the leguminous plant lectins [1]. The alignment for this family aligns residues lying towards the N-terminus, where the similarity of VIP36 and ERGIC-53 is greatest. However, while Fiedler and Simons [1] identified these proteins as a new family of animal lectins, our alignment also includes yeast sequences. ERGIC-53 is a 53kD protein, localised to the intermediate region between the endoplasmic reticulum and the Golgi apparatus (ER-Golgi-Intermediate Compartment, ERGIC). It was identified as a calcium-dependent, mannose-specific lectin [2]. Its dysfunction has been associated with combined factors V and VIII deficiency OMIM:227300 OMIM:601567, suggesting an important and substrate-specific role for ERGIC-53 in the glycoprotein- secreting pathway [2,3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth C], F [auth G], G [auth D], H	Multiple coagulation factor deficiency protein 2	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding	localization transport cellular process establishment of localization vesicle-mediated transport biosynthetic process metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process establishment of protein localization protein transport macromolecule localization intracellular protein localization	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system transport vesicle membrane intracellular vesicle transport vesicle membrane cytoplasmic vesicle membrane membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure Golgi apparatus organelle cytoplasm intracellular membrane-bounded organelle endomembrane system 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 endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane
A, B, C [auth E], D [auth F]	Protein ERGIC-53	binding D-mannose binding monosaccharide binding carbohydrate binding small molecule binding cation binding ion binding metal ion binding	multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding protein folding biosynthetic process metabolic process multicellular organismal process regulation of body fluid levels wound healing response to stimulus hemostasis biological regulation blood coagulation response to stress coagulation regulation of biological quality response to wounding protein folding biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation localization establishment of protein localization protein transport transport macromolecule localization intracellular protein localization establishment of localization positive regulation of organelle organization regulation of biological process regulation of cellular component organization regulation of cellular process positive regulation of cellular component organization positive regulation of biological process regulation of organelle organization cellular component organization organelle organization cellular component organization or biogenesis positive regulation of cellular process cellular localization intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport vesicle-mediated transport intercellular transport establishment of localization in cell Golgi vesicle transport developmental process multicellular organism development embryo development ending in birth or egg hatching chordate embryonic development anatomical structure development embryo development in utero embryonic development endoplasmic reticulum organization endomembrane system organization Golgi organization	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle COPII-coated ER to Golgi transport vesicle cytoplasmic vesicle coated vesicle cytoplasm extracellular matrix external encapsulating structure organelle subcompartment endomembrane system endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane intracellular membraneless organelle sarcomere membraneless organelle contractile muscle fiber supramolecular fiber myofibril supramolecular polymer supramolecular complex Golgi membrane Golgi apparatus bounding membrane of organelle endoplasmic reticulum-Golgi intermediate compartment membrane endoplasmic reticulum-Golgi intermediate compartment transport vesicle transport vesicle membrane cytoplasmic vesicle membrane coated vesicle membrane vesicle membrane ER to Golgi transport vesicle membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
E [auth C], F [auth G], G [auth D], H	IPR052110	Multiple coagulation factor deficiency protein 2-like	Family
E [auth C], F [auth G], G [auth D], H	IPR018247	EF-Hand 1, calcium-binding site	Binding Site
E [auth C], F [auth G], G [auth D], H	IPR002048	EF-hand domain	Domain
E [auth C], F [auth G], G [auth D], H	IPR011992	EF-hand domain pair	Homologous Superfamily
A, B, C [auth E], D [auth F]	IPR005052	Legume-like lectin	Domain
A, B, C [auth E], D [auth F]	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, B, C [auth E], D [auth F]	IPR051136	Intracellular Lectin and Glycoprotein Transporter	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
E [auth C], F [auth G], G [auth D], H	: Q8NI22	factor 5 and Factor VIII, combined deficiency of, 2 combined deficiency of factor V and factor VIII factor V and factor VIII, combined deficiency of, type 1 malignant colon neoplasm medulloblastoma pancreatic intraductal papillary-mucinous carcinoma Sjogren syndrome Crohn disease glioblastoma malignant ependymoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis large cell medulloblastoma malignant pancreatic neoplasm factor 5 and Factor VIII, combined deficiency of, 2 combined deficiency of factor V and factor VIII factor V and factor VIII, combined deficiency of, type 1 malignant colon neoplasm medulloblastoma pancreatic intraductal papillary-mucinous carcinoma Sjogren syndrome Crohn disease glioblastoma malignant ependymoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis large cell medulloblastoma malignant pancreatic neoplasm pancreatic ductal adenocarcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia
A, B, C [auth E], D [auth F]	: P49257	factor V and factor VIII, combined deficiency of, type 1 atypical teratoid rhabdoid tumor invasive ductal breast carcinoma malignant ependymoma non-small cell lung carcinoma breast cancer Gaucher disease large cell medulloblastoma malignant glioma osteosarcoma combined deficiency of factor V and factor VIII glioblastoma lung cancer medulloblastoma pancreatic ductal adenocarcinoma

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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.