3D4G | pdb_00003d4g

ZP-N domain of mammalian sperm receptor ZP3 (crystal form II)

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Type 2 solute binding protein-like	8058187	3000083	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	IL7	e3d4gH2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.1)
H	LysR_substrate	e3d4gH1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: LysR_substrate	ECOD (v294.1)
G	IL7	e3d4gG2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.1)
G	LysR_substrate	e3d4gG1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: LysR_substrate	ECOD (v294.1)
F	IL7	e3d4gF2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.1)
F	LysR_substrate	e3d4gF1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: LysR_substrate	ECOD (v294.1)
E	IL7	e3d4gE2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.1)
E	LysR_substrate	e3d4gE1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: LysR_substrate	ECOD (v294.1)
D	IL7	e3d4gD2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.1)
D	LysR_substrate	e3d4gD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: LysR_substrate	ECOD (v294.1)
C	IL7	e3d4gC2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.1)
C	LysR_substrate	e3d4gC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: LysR_substrate	ECOD (v294.1)
B	IL7	e3d4gB2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.1)
B	LysR_substrate	e3d4gB1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: LysR_substrate	ECOD (v294.1)
A	IL7	e3d4gA2	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: IL7	ECOD (v294.1)
A	LysR_substrate	e3d4gA1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: LysR_substrate	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
H	2.60.40.3210	Mainly Beta	Sandwich	Immunoglobulin-like	Zona pellucida, ZP-N domain	CATH (4.3.0)
G	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
G	2.60.40.3210	Mainly Beta	Sandwich	Immunoglobulin-like	Zona pellucida, ZP-N domain	CATH (4.3.0)
F	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
F	2.60.40.3210	Mainly Beta	Sandwich	Immunoglobulin-like	Zona pellucida, ZP-N domain	CATH (4.3.0)
E	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
E	2.60.40.3210	Mainly Beta	Sandwich	Immunoglobulin-like	Zona pellucida, ZP-N domain	CATH (4.3.0)
D	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
D	2.60.40.3210	Mainly Beta	Sandwich	Immunoglobulin-like	Zona pellucida, ZP-N domain	CATH (4.3.0)
C	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
C	2.60.40.3210	Mainly Beta	Sandwich	Immunoglobulin-like	Zona pellucida, ZP-N domain	CATH (4.3.0)
B	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
B	2.60.40.3210	Mainly Beta	Sandwich	Immunoglobulin-like	Zona pellucida, ZP-N domain	CATH (4.3.0)
A	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (4.3.0)
A	2.60.40.3210	Mainly Beta	Sandwich	Immunoglobulin-like	Zona pellucida, ZP-N domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF01547	Bacterial extracellular solute-binding protein (SBP_bac_1)	Bacterial extracellular solute-binding protein	-	Family
A, B, C, D, E A, B, C, D, E, F, G, H	PF23344	ZP-N domain (ZP-N)	ZP-N domain	This entry represents the N-terminal structural domain of the zona pellucida domain as defined by sequence.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	Maltose-binding periplasmic protein, LINKER, Zona pellucida protein 3	transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity oligosaccharide binding binding disaccharide binding carbohydrate binding maltose binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity structural constituent of egg coat transporter activity carbohydrate transmembrane transporter activity transmembrane transporter activity oligosaccharide binding binding disaccharide binding carbohydrate binding maltose binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity structural constituent of egg coat structural molecule activity extracellular matrix structural constituent protein binding acrosin binding enzyme binding identical protein binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process cell chemotaxis chemotaxis response to external stimulus cellular response to chemical stimulus taxis response to chemical cell migration cell motility locomotion localization transport carbohydrate transport oligosaccharide transport disaccharide transport establishment of localization maltose transport polysaccharide localization dextrin transport macromolecule localization maltodextrin transmembrane transport polysaccharide transport response to disaccharide response to oxygen-containing compound detection of maltose stimulus detection of stimulus response to carbohydrate detection of chemical stimulus detection of disaccharide stimulus response to maltose detection of carbohydrate stimulus regulation of cellular process negative regulation of biological process RNA metabolic process regulation of primary metabolic process negative regulation of RNA biosynthetic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process regulation of RNA metabolic process negative regulation of cellular process negative regulation of nucleobase-containing compound metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of DNA-templated transcription regulation of biological process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of DNA-templated transcription regulation of metabolic process negative regulation of RNA metabolic process developmental process multicellular organismal process chordate embryonic development embryo development in utero embryonic development multicellular organism development anatomical structure morphogenesis blastocyst formation embryo development ending in birth or egg hatching anatomical structure development anatomical structure formation involved in morphogenesis blastocyst development regulation of developmental process reproductive process sex differentiation positive regulation of biological process development of primary female sexual characteristics regulation of ovarian follicle development developmental process involved in reproduction positive regulation of developmental process development of primary sexual characteristics reproductive structure development ovarian follicle development system development gonad development reproductive system development positive regulation of ovarian follicle development female gonad development animal organ development female sex differentiation regulation of defense response regulation of response to external stimulus defense response regulation of inflammatory response positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of inflammatory response regulation of response to stimulus regulation of response to stress positive regulation of defense response inflammatory response sexual reproduction cellular developmental process multicellular organismal reproductive process oogenesis cell development cellular process involved in reproduction in multicellular organism female gamete generation gamete generation oocyte development cell differentiation germ cell development oocyte differentiation ovulation cycle process regulation of growth developmental growth regulation of reproductive process regulation of antral ovarian follicle growth ovulation cycle positive regulation of developmental growth positive regulation of reproductive process rhythmic process regulation of developmental growth growth positive regulation of growth positive regulation of antral ovarian follicle growth antral ovarian follicle growth cell-cell recognition fertilization binding of sperm to zona pellucida regulation of binding of sperm to zona pellucida sperm-egg recognition negative regulation of reproductive process negative regulation of binding of sperm to zona pellucida cell recognition single fertilization regulation of humoral immune response humoral immune response immune response positive regulation of humoral immune response positive regulation of immune response immune system process regulation of immune response regulation of immune system process positive regulation of immune system process egg coat formation adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of acute inflammatory response to antigenic stimulus lymphocyte mediated immunity regulation of immune effector process regulation of acute inflammatory response to antigenic stimulus T cell mediated immunity positive regulation of leukocyte mediated immunity inflammatory response to antigenic stimulus positive regulation of hypersensitivity leukocyte mediated immunity positive regulation of adaptive immune response regulation of T cell mediated immunity hypersensitivity regulation of adaptive immune response immune effector process positive regulation of type IV hypersensitivity regulation of leukocyte mediated immunity regulation of acute inflammatory response positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of lymphocyte mediated immunity positive regulation of acute inflammatory response regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of immune effector process regulation of type IV hypersensitivity acute inflammatory response regulation of hypersensitivity regulation of inflammatory response to antigenic stimulus type IV hypersensitivity acute inflammatory response to antigenic stimulus positive regulation of inflammatory response to antigenic stimulus adaptive immune response regulation of lymphocyte mediated immunity positive regulation of T cell mediated immunity positive regulation of locomotion regulation of cell motility regulation of leukocyte migration positive regulation of leukocyte migration positive regulation of cell migration leukocyte migration regulation of locomotion positive regulation of cell motility regulation of cell migration positive regulation of cellular process positive regulation of acrosome reaction acrosome reaction regulation of acrosome reaction positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process regulation of signaling signaling regulation of signaling receptor activity regulation of signal transduction cell communication regulation of molecular function regulation of cell communication signal transduction immunoglobulin mediated immune response humoral immune response mediated by circulating immunoglobulin B cell mediated immunity regulation of interleukin-4 production regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of interleukin-4 production interleukin-4 production positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of cytokine production positive regulation of cell population proliferation regulation of leukocyte activation regulation of cell activation positive regulation of cell activation T cell activation lymphocyte proliferation positive regulation of leukocyte activation regulation of leukocyte proliferation cell population proliferation positive regulation of T cell activation positive regulation of lymphocyte proliferation positive regulation of T cell proliferation regulation of cell population proliferation mononuclear cell proliferation regulation of leukocyte cell-cell adhesion positive regulation of leukocyte proliferation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte proliferation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation cell adhesion cell-cell adhesion positive regulation of mononuclear cell proliferation regulation of cell-cell adhesion T cell proliferation regulation of lymphocyte proliferation positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation regulation of T cell proliferation regulation of mononuclear cell proliferation regulation of lymphocyte activation regulation of localization regulated exocytosis regulation of calcium ion-dependent exocytosis positive regulation of secretion by cell vesicle-mediated transport positive regulation of exocytosis regulation of regulated secretory pathway secretion by cell regulation of secretion by cell positive regulation of secretion positive regulation of regulated secretory pathway positive regulation of acrosomal vesicle exocytosis calcium-ion regulated exocytosis positive regulation of calcium ion-dependent exocytosis secretion regulation of transport export from cell regulation of vesicle-mediated transport regulation of secretion exocytosis positive regulation of transport regulation of exocytosis acrosomal vesicle exocytosis regulation of acrosomal vesicle exocytosis regulation of type II interferon production type II interferon production positive regulation of type II interferon production	ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing maltose transport complex periplasmic space ATPase dependent transmembrane transport complex protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex transporter complex ATP-binding cassette (ABC) transporter complex cell periphery cellular anatomical structure transmembrane transporter complex ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing maltose transport complex periplasmic space outer membrane-bounded periplasmic space cell envelope extracellular matrix external encapsulating structure egg coat specialized extracellular matrix extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006061	Solute-binding family 1, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006060	Maltose/Cyclodextrin ABC transporter, substrate-binding protein	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR006059	Bacterial-type extracellular solute-binding protein	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR042235	Zona pellucida, ZP-C domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR055356	ZP-N domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR055355	ZP-C domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR017977	Zona pellucida domain, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR048290	Zona pellucida domain, chordate-type	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001507	Zona pellucida 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.