5MR3 | pdb_00005mr3

Crystal structure of red abalone egg VERL repeat 2 with linker in complex with sperm lysin at 1.8 A resolution

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)
G	d5mr3g_	All alpha proteins	Fertilization protein	Fertilization protein	Fertilization protein	automated matches	California red abalone (Haliotis rufescens ) [TaxId: 6454 ],	SCOPe (2.08)
E	d5mr3e_	All alpha proteins	Fertilization protein	Fertilization protein	Fertilization protein	automated matches	California red abalone (Haliotis rufescens ) [TaxId: 6454 ],	SCOPe (2.08)
C	d5mr3c_	All alpha proteins	Fertilization protein	Fertilization protein	Fertilization protein	automated matches	California red abalone (Haliotis rufescens ) [TaxId: 6454 ],	SCOPe (2.08)
A	d5mr3a_	All alpha proteins	Fertilization protein	Fertilization protein	Fertilization protein	automated matches	California red abalone (Haliotis rufescens ) [TaxId: 6454 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G	SCOP2B Superfamily	Fertilization protein	8036754	3001337	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Fertilization protein	8036754	3001337	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Fertilization protein	8036754	3001337	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Fertilization protein	8036754	3001337	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)
G	Egg_lysin	e5mr3G1	A: alpha arrays	X: Fertilization protein (From Topology)	H: Fertilization protein (From Topology)	T: Fertilization protein	F: Egg_lysin	ECOD (1.6)
E	Egg_lysin	e5mr3E1	A: alpha arrays	X: Fertilization protein (From Topology)	H: Fertilization protein (From Topology)	T: Fertilization protein	F: Egg_lysin	ECOD (1.6)
C	Egg_lysin	e5mr3C1	A: alpha arrays	X: Fertilization protein (From Topology)	H: Fertilization protein (From Topology)	T: Fertilization protein	F: Egg_lysin	ECOD (1.6)
A	Egg_lysin	e5mr3A1	A: alpha arrays	X: Fertilization protein (From Topology)	H: Fertilization protein (From Topology)	T: Fertilization protein	F: Egg_lysin	ECOD (1.6)
H	UNK_F_TYPE	e5mr3H1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: UNK_F_TYPE	ECOD (1.6)
F	UNK_F_TYPE	e5mr3F1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: UNK_F_TYPE	ECOD (1.6)
D	UNK_F_TYPE	e5mr3D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: UNK_F_TYPE	ECOD (1.6)
B	UNK_F_TYPE	e5mr3B1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: UNK_F_TYPE	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G	1.20.150.10	Mainly Alpha	Up-down Bundle	Lysin	Fertilization protein	CATH (4.3.0)
E	1.20.150.10	Mainly Alpha	Up-down Bundle	Lysin	Fertilization protein	CATH (4.3.0)
C	1.20.150.10	Mainly Alpha	Up-down Bundle	Lysin	Fertilization protein	CATH (4.3.0)
A	1.20.150.10	Mainly Alpha	Up-down Bundle	Lysin	Fertilization protein	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C, E, G	PF01303	Egg lysin (Sperm-lysin) (Egg_lysin)	Egg lysin (Sperm-lysin)	Egg lysin creates a hole in the envelope of the egg thereby allowing the sperm to pass through the envelope and fuse with the egg.	Domain
B, D, F, H	PF11386	Vitelline envelope receptor for lysin (VERL)	Vitelline envelope receptor for lysin	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C, E, G	Egg-lysin	-	sexual reproduction reproductive process fertilization single fertilization	membrane-bounded organelle intracellular anatomical structure intracellular vesicle membrane-enclosed lumen lytic vacuole cytoplasmic vesicle lumen vacuolar lumen endomembrane system intracellular organelle lumen intracellular organelle cellular anatomical structure cytoplasmic vesicle vesicle lysosome membrane-bounded organelle intracellular anatomical structure intracellular vesicle membrane-enclosed lumen lytic vacuole cytoplasmic vesicle lumen vacuolar lumen endomembrane system intracellular organelle lumen intracellular organelle cellular anatomical structure cytoplasmic vesicle vesicle lysosome acrosomal vesicle vesicle lumen vacuole intracellular membrane-bounded organelle secretory granule lumen acrosomal lumen lysosomal lumen organelle lumen organelle secretory granule secretory vesicle cytoplasm
B, D, F, H	Vitelline envelope sperm lysin receptor	-	sperm-egg recognition sexual reproduction cell-cell recognition reproductive process fertilization cell recognition cellular process single fertilization	cell periphery cellular anatomical structure plasma membrane membrane vitelline envelope extracellular matrix external encapsulating structure egg coat specialized extracellular matrix extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C, E, G	IPR035916	Egg-lysin superfamily	Homologous Superfamily
A, C, E, G	IPR001379	Egg lysin (Sperm-lysin)	Family
B, D, F, H	IPR001507	Zona pellucida domain	Domain
B, D, F, H	IPR021526	Vitelline envelope, lysin receptor	Family

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.