4YGD | pdb_00004ygd

Crystal structure of ERGIC-53/MCFD2, monoclinic calcium-bound form 2

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
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
G	d4ygdg_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Lectin leg-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d4ygde_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Lectin leg-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d4ygdc_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Lectin leg-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d4ygda_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Lectin leg-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8081158	3000120	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8081158	3000120	SCOP2B (2022-06-29)
C	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	EF-hand_7_9	e4ygdH1	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: EF-hand_7_9	ECOD (1.6)
F	EF-hand_7_9	e4ygdF1	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: EF-hand_7_9	ECOD (1.6)
D	EF-hand_7_9	e4ygdD1	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: EF-hand_7_9	ECOD (1.6)
B	EF-hand_7_9	e4ygdB1	A: alpha arrays	X: EF-hand	H: EF-hand-related	T: EF-hand	F: EF-hand_7_9	ECOD (1.6)
G	Lectin_leg-like	e4ygdG1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Lectin_leg-like	ECOD (1.6)
E	Lectin_leg-like	e4ygdE1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Lectin_leg-like	ECOD (1.6)
C	Lectin_leg-like	e4ygdC1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Lectin_leg-like	ECOD (1.6)
A	Lectin_leg-like	e4ygdA1	A: beta sandwiches	X: jelly-roll	H: Concanavalin A-like	T: Concanavalin A-like lectins/glucanases	F: Lectin_leg-like	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
F	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
D	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
B	1.10.238.10	Mainly Alpha	Orthogonal Bundle	Recoverin	domain 1	CATH (4.3.0)
G	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
E	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
C	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
A	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D, F, H	PF13499	EF-hand domain pair (EF-hand_7)	EF-hand domain pair		Domain
A, C, E, G	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
B, D, F, 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 establishment of protein localization nitrogen compound transport 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, C, E, G	Protein ERGIC-53	binding D-mannose binding monosaccharide binding carbohydrate binding small molecule binding unfolded protein binding protein 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 nitrogen compound transport 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 establishment of localization in cell intracellular transport endoplasmic reticulum to Golgi vesicle-mediated transport Golgi vesicle transport vesicle-mediated transport negative regulation of protein targeting to mitochondrion regulation of localization negative regulation of establishment of protein localization to mitochondrion regulation of protein localization protein targeting regulation of protein targeting to mitochondrion regulation of establishment of protein localization negative regulation of biological process negative regulation of establishment of protein localization regulation of establishment of protein localization to mitochondrion establishment of protein localization to organelle regulation of protein targeting protein targeting to mitochondrion establishment of protein localization to mitochondrion endoplasmic reticulum organization endomembrane system organization Golgi organization	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space 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 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
B, D, F, H	IPR052110	Multiple coagulation factor deficiency protein 2-like	Family
B, D, F, H	IPR018247	EF-Hand 1, calcium-binding site	Binding Site
B, D, F, H	IPR002048	EF-hand domain	Domain
B, D, F, H	IPR011992	EF-hand domain pair	Homologous Superfamily
A, C, E, G	IPR005052	Legume-like lectin	Domain
A, C, E, G	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, C, E, G	IPR051136	Intracellular Lectin and Glycoprotein Transporter	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D, F, H	Pharos: 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, C, E, G	Pharos: 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

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.