6E48

Crystal Structure of the Murine Norovirus VP1 P domain in complex with the CD300lf Receptor and Lithocholic Acid

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
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	d6e48a_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	automated matches	automated matches	(Murine norovirus 1 ) [TaxId: 223997 ],	SCOPe (2.08)
B	d6e48b_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	automated matches	automated matches	(Murine norovirus 1 ) [TaxId: 223997 ],	SCOPe (2.08)
C [auth F]	d6e48f_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth G]	d6e48g_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Calici_coat_C_C	e6e48A1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Calici_coat_C_C	ECOD (1.6)
B	Calici_coat_C_C	e6e48B1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Calici_coat_C_C	ECOD (1.6)
C [auth F]	V-set_16	e6e48F1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_16	ECOD (1.6)
D [auth G]	V-set_16	e6e48G1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_16	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.510.10	Mainly Beta	Beta Barrel	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	CATH (4.3.0)
A	2.40.30.120	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
B	2.40.510.10	Mainly Beta	Beta Barrel	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	CATH (4.3.0)
B	2.40.30.120	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.3.0)
C [auth F]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth G]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
C [auth F], D [auth G]	CMRF35-like molecule 1	1V-LIKE	Mus musculus (house mouse)	CD300lf*01	V-LIKE-DOMAIN V-LIKE	RPI	1V-LIKE	IMGT (202444-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF08435	Calicivirus coat protein C-terminal (Calici_coat_C)	Calicivirus coat protein C-terminal	-	Family
C [auth F], D [auth G]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	VP1 P domain	-	-	virion component host cellular component host intracellular part host cell cytoplasm host cell part host intracellular region cellular anatomical entity
C [auth F], D [auth G]	CMRF35-like molecule 1	protein binding binding virus receptor activity exogenous protein binding signaling receptor binding cytokine receptor binding interleukin-4 receptor binding growth factor receptor binding amide binding ceramide binding sphingolipid binding lipid binding modified amino acid binding phospholipid binding protein binding binding virus receptor activity exogenous protein binding signaling receptor binding cytokine receptor binding interleukin-4 receptor binding growth factor receptor binding amide binding ceramide binding sphingolipid binding lipid binding modified amino acid binding phospholipid binding phosphatidylserine binding	import into cell regulation of localization regulation of cellular process regulation of cellular component organization transport negative regulation of biological process negative regulation of transport negative regulation of endocytosis vesicle-mediated transport cellular component organization localization negative regulation of phagocytosis negative regulation of cellular process phagocytosis import into cell regulation of localization regulation of cellular process regulation of cellular component organization transport negative regulation of biological process negative regulation of transport negative regulation of endocytosis vesicle-mediated transport cellular component organization localization negative regulation of phagocytosis negative regulation of cellular process phagocytosis apoptotic cell clearance cellular component organization or biogenesis regulation of endocytosis regulation of biological process negative regulation of cellular component organization regulation of transport biological regulation regulation of phagocytosis regulation of vesicle-mediated transport establishment of localization negative regulation of apoptotic cell clearance cellular process endocytosis regulation of apoptotic cell clearance developmental process myeloid leukocyte differentiation cellular developmental process hemopoiesis cell development myeloid cell differentiation cell differentiation osteoclast differentiation anatomical structure development leukocyte differentiation cellular response to stimulus interleukin-13-mediated signaling pathway response to stimulus cell surface receptor signaling pathway signaling cellular response to interleukin-13 response to cytokine cytokine-mediated signaling pathway cell communication response to peptide response to chemical response to interleukin-13 cellular response to cytokine stimulus signal transduction multicellular organismal process regulation of leukocyte activation cell activation regulation of cell activation myeloid leukocyte activation leukocyte activation negative regulation of cell activation negative regulation of mast cell activation negative regulation of immune system process immune system process mast cell activation regulation of mast cell activation regulation of multicellular organismal process regulation of immune system process negative regulation of multicellular organismal process negative regulation of leukocyte activation positive regulation of cell communication positive regulation of signal transduction positive regulation of biological process regulation of signal transduction positive regulation of response to cytokine stimulus response to interleukin-4 positive regulation of response to stimulus cellular response to interleukin-4 positive regulation of cellular process positive regulation of interleukin-4-mediated signaling pathway regulation of signaling interleukin-4-mediated signaling pathway regulation of cytokine-mediated signaling pathway regulation of interleukin-4-mediated signaling pathway regulation of response to cytokine stimulus regulation of response to stimulus regulation of cell communication positive regulation of cytokine-mediated signaling pathway positive regulation of signaling positive regulation of cellular component organization positive regulation of apoptotic cell clearance positive regulation of endocytosis positive regulation of phagocytosis positive regulation of transport positive regulation of response to biotic stimulus pattern recognition receptor signaling pathway toll-like receptor signaling pathway regulation of MyD88-dependent toll-like receptor signaling pathway response to biotic stimulus immune response-activating signaling pathway positive regulation of immune response positive regulation of immune system process innate immune response-activating signaling pathway immune response response to other organism regulation of innate immune response response to external stimulus defense response to other organism regulation of pattern recognition receptor signaling pathway positive regulation of defense response activation of innate immune response regulation of immune response regulation of toll-like receptor signaling pathway activation of immune response regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus negative regulation of signaling negative regulation of cell communication positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of response to stress response to stress innate immune response response to external biotic stimulus MyD88-dependent toll-like receptor signaling pathway positive regulation of innate immune response defense response negative regulation of response to stimulus defense response to symbiont negative regulation of signal transduction negative regulation of toll-like receptor signaling pathway negative regulation of MyD88-dependent toll-like receptor signaling pathway TRIF-dependent toll-like receptor signaling pathway MyD88-independent toll-like receptor signaling pathway	cell periphery plasma membrane membrane cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR029053	Viral coat protein subunit	Homologous Superfamily
A, B	IPR004005	Calicivirus coat protein	Domain
A, B	IPR013643	Calicivirus coat protein C-terminal	Domain
A, B	IPR033703	Picornavirus/Calicivirus coat protein	Domain
C [auth F], D [auth G]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth F], D [auth G]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth F], D [auth G]	IPR013106	Immunoglobulin V-set domain	Domain
C [auth F], D [auth G]	IPR003599	Immunoglobulin domain subtype	Domain
C [auth F], D [auth G]	IPR050671	CD300 family immune receptors	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.