2A6Z

Crystal structure of Emp47p carbohydrate recognition domain (CRD), monoclinic crystal form 1

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)
A	d2a6za1	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Lectin leg-like	Emp47p N-terminal domain	baker's yeast (Saccharomyces cerevisiae ) [TaxId: 4932 ],	SCOPe (2.08)
A	d2a6za2	Artifacts	Tags	Tags	Tags	N-terminal Tags	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)
A	SCOP2 Family	Lectin leg-like	8024314	4002117	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Concanavalin A-like lectins/glucanases	8036693	3000120	SCOP2 (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	Lectin_leg-like	e2a6zA1	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)
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
A	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
A	Emp47p (form2)	binding D-mannose binding monosaccharide binding carbohydrate binding small molecule binding carbohydrate derivative binding	localization cellular localization transport establishment of localization in cell intracellular transport cellular process endoplasmic reticulum to Golgi vesicle-mediated transport establishment of localization Golgi vesicle transport vesicle-mediated transport	vacuolar membrane membrane-bounded organelle storage vacuole intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle fungal-type vacuole intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle vacuolar membrane membrane-bounded organelle storage vacuole intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle fungal-type vacuole intracellular organelle lytic vacuole membrane bounding membrane of organelle cellular anatomical structure organelle cytoplasm organelle membrane fungal-type vacuole membrane Golgi membrane Golgi apparatus endomembrane system intracellular vesicle COPII-coated ER to Golgi transport vesicle cytoplasmic vesicle coated vesicle vesicle endoplasmic reticulum-Golgi intermediate compartment organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR005052	Legume-like lectin	Domain
A	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A	IPR016710	Emp46/Emp47	Family
A	IPR051136	Intracellular Lectin and Glycoprotein Transporter	Family
A	IPR035661	EMP46/EMP47, N-terminal lectin domain	Domain

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.