1YU4 | pdb_00001yu4

Major Tropism Determinant U1 Variant

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)
C	d1yu4c1	All beta proteins	Pseudo beta-prism I	Bacteriophage trimeric proteins domain	Mtd domain-like	Major tropism determinant (Mtd), N-terminal domain	(Bordetella phage BMP-1 ) [TaxId: 263374 ],	SCOPe (2.08)
C	d1yu4c2	Alpha and beta proteins (a+b)	C-type lectin-like	C-type lectin-like	Mtd variable domain	Major tropism determinant (Mtd), C-terminal domain	(Bordetella phage BMP-1 ) [TaxId: 263374 ],	SCOPe (2.08)
B	d1yu4b1	All beta proteins	Pseudo beta-prism I	Bacteriophage trimeric proteins domain	Mtd domain-like	Major tropism determinant (Mtd), N-terminal domain	(Bordetella phage BMP-1 ) [TaxId: 263374 ],	SCOPe (2.08)
B	d1yu4b2	Alpha and beta proteins (a+b)	C-type lectin-like	C-type lectin-like	Mtd variable domain	Major tropism determinant (Mtd), C-terminal domain	(Bordetella phage BMP-1 ) [TaxId: 263374 ],	SCOPe (2.08)
A	d1yu4a1	All beta proteins	Pseudo beta-prism I	Bacteriophage trimeric proteins domain	Mtd domain-like	Major tropism determinant (Mtd), N-terminal domain	(Bordetella phage BMP-1 ) [TaxId: 263374 ],	SCOPe (2.08)
A	d1yu4a2	Alpha and beta proteins (a+b)	C-type lectin-like	C-type lectin-like	Mtd variable domain	Major tropism determinant (Mtd), C-terminal domain	(Bordetella phage BMP-1 ) [TaxId: 263374 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	C-type lectin-like	8034887	3001261	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Bacteriophage trimeric proteins domain	8034885	3000915	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	C-type lectin-like	8034887	3001261	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Bacteriophage trimeric proteins domain	8034885	3000915	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Bacteriophage trimeric proteins domain	8034885	3000915	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	C-type lectin-like	8034887	3001261	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)
C	mtd_2nd	e1yu4C2	A: beta sandwiches	X: Lactophage receptor-binding protein N-terminal domain-like (From Topology)	H: Lactophage receptor-binding protein N-terminal domain-like (From Topology)	T: Lactophage receptor-binding protein N-terminal domain-like	F: mtd_2nd	ECOD (1.6)
C	mtd_1st	e1yu4C4	A: beta duplicates or obligate multimers	X: Major tropism determinant (Mtd) trimerization domain-related (From Topology)	H: Major tropism determinant (Mtd) trimerization domain-related (From Topology)	T: Major tropism determinant (Mtd) trimerization domain-related	F: mtd_1st	ECOD (1.6)
C	FGE-sulfatase_1	e1yu4C3	A: a+b complex topology	X: C-type lectin-like (From Homology)	H: C-type lectin-like	T: Sulfatase-modifying factor-like	F: FGE-sulfatase_1	ECOD (1.6)
B	mtd_2nd	e1yu4B2	A: beta sandwiches	X: Lactophage receptor-binding protein N-terminal domain-like (From Topology)	H: Lactophage receptor-binding protein N-terminal domain-like (From Topology)	T: Lactophage receptor-binding protein N-terminal domain-like	F: mtd_2nd	ECOD (1.6)
B	mtd_1st	e1yu4B4	A: beta duplicates or obligate multimers	X: Major tropism determinant (Mtd) trimerization domain-related (From Topology)	H: Major tropism determinant (Mtd) trimerization domain-related (From Topology)	T: Major tropism determinant (Mtd) trimerization domain-related	F: mtd_1st	ECOD (1.6)
B	FGE-sulfatase_1	e1yu4B3	A: a+b complex topology	X: C-type lectin-like (From Homology)	H: C-type lectin-like	T: Sulfatase-modifying factor-like	F: FGE-sulfatase_1	ECOD (1.6)
A	mtd_2nd	e1yu4A2	A: beta sandwiches	X: Lactophage receptor-binding protein N-terminal domain-like (From Topology)	H: Lactophage receptor-binding protein N-terminal domain-like (From Topology)	T: Lactophage receptor-binding protein N-terminal domain-like	F: mtd_2nd	ECOD (1.6)
A	mtd_1st	e1yu4A4	A: beta duplicates or obligate multimers	X: Major tropism determinant (Mtd) trimerization domain-related (From Topology)	H: Major tropism determinant (Mtd) trimerization domain-related (From Topology)	T: Major tropism determinant (Mtd) trimerization domain-related	F: mtd_1st	ECOD (1.6)
A	FGE-sulfatase_1	e1yu4A3	A: a+b complex topology	X: C-type lectin-like (From Homology)	H: C-type lectin-like	T: Sulfatase-modifying factor-like	F: FGE-sulfatase_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C	2.10.10.30	Mainly Beta	Ribbon	Seminal Fluid Protein PDC-109 (Domain B)		CATH (4.3.0)
C	2.80.20.10	Mainly Beta	Trefoil	Tail fiber receptor-binding protein	Tail fiber receptor-binding protein	CATH (4.3.0)
C	3.90.1580.10	Alpha Beta	Alpha-Beta Complex	paralog of FGE (formylglycine-generating enzyme)	paralog of FGE (formylglycine-generating enzyme)	CATH (4.3.0)
B	2.10.10.30	Mainly Beta	Ribbon	Seminal Fluid Protein PDC-109 (Domain B)		CATH (4.3.0)
B	2.80.20.10	Mainly Beta	Trefoil	Tail fiber receptor-binding protein	Tail fiber receptor-binding protein	CATH (4.3.0)
B	3.90.1580.10	Alpha Beta	Alpha-Beta Complex	paralog of FGE (formylglycine-generating enzyme)	paralog of FGE (formylglycine-generating enzyme)	CATH (4.3.0)
A	2.10.10.30	Mainly Beta	Ribbon	Seminal Fluid Protein PDC-109 (Domain B)		CATH (4.3.0)
A	2.80.20.10	Mainly Beta	Trefoil	Tail fiber receptor-binding protein	Tail fiber receptor-binding protein	CATH (4.3.0)
A	3.90.1580.10	Alpha Beta	Alpha-Beta Complex	paralog of FGE (formylglycine-generating enzyme)	paralog of FGE (formylglycine-generating enzyme)	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF21916	Mtd second domain (mtd_2nd)	Mtd second domain	This entry represents the second domain of Mtd. The major tropism determinant (Mtd, 40 kDa), the receptor-binding protein of Bordetella bacteriophage, varies greatly in sequence. Variation in Mtd depends on a phage-encoded retroelement that belongs t ...	This entry represents the second domain of Mtd. The major tropism determinant (Mtd, 40 kDa), the receptor-binding protein of Bordetella bacteriophage, varies greatly in sequence. Variation in Mtd depends on a phage-encoded retroelement that belongs to a family of retroelements implicated in generating sequence diversity in various phage and bacterial genomes. The second domain forms a beta sandwich structure.	Domain
A, B, C	PF18454	Major tropism determinant N-terminal domain (Mtd_N)	Major tropism determinant N-terminal domain	This is the N-terminal domain of major tropism determinant (Mtd), a retroelement-encoded receptor-binding protein. Mtd-N forms a three-fold symmetric beta-prism. This resembles the pseudo three-fold-symmetric beta-prisms of monocot lectins, but lacks ...	This is the N-terminal domain of major tropism determinant (Mtd), a retroelement-encoded receptor-binding protein. Mtd-N forms a three-fold symmetric beta-prism. This resembles the pseudo three-fold-symmetric beta-prisms of monocot lectins, but lacks residues in these lectins identified as binding carbohydrates. The beta-prism and beta-sandwich domains reinforce overall trimeric assembly and therefore may have indirect roles in stabilizing the backbone of the variable region [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Major Tropism Determinant (Mtd-U1)	-	virion attachment to host cell biological process involved in interspecies interaction between organisms receptor-mediated virion attachment to host cell adhesion of symbiont to host cell viral process viral life cycle adhesion of symbiont to host adhesion receptor-mediated virion attachment to host cell biological process involved in interaction with host biological process involved in symbiotic interaction viral tropism switching symbiont entry into host cell symbiont entry into host	virus tail, fiber virus tail virion component

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR042095	Sulfatase-modifying factor enzyme superfamily	Homologous Superfamily
A, B, C	IPR041352	Major tropism determinant, N-terminal domain	Domain
A, B, C	IPR016187	C-type lectin fold	Homologous Superfamily
A, B, C	IPR054114	Major tropism determinant, second 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.