2YZ1 | pdb_00002yz1

Crystal structure of the ligand-binding domain of murine SHPS-1/SIRP alpha

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
B	d2yz1b_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d2yz1a_	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	house 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)
B	Abhydrolase_1	e2yz1B1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Abhydrolase_1	ECOD (v294.1)
A	Abhydrolase_1	e2yz1A1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: Nudix	F: Abhydrolase_1	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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	Tyrosine-protein phosphatase non-receptor type substrate 1	enzyme regulator activity phosphatase inhibitor activity molecular function inhibitor activity phosphatase regulator activity molecular function regulator activity protein phosphatase regulator activity protein phosphatase inhibitor activity enzyme inhibitor activity protein antigen binding protein binding binding antigen binding protein phosphatase binding phosphatase binding enzyme regulator activity phosphatase inhibitor activity molecular function inhibitor activity phosphatase regulator activity molecular function regulator activity protein phosphatase regulator activity protein phosphatase inhibitor activity enzyme inhibitor activity protein antigen binding protein binding binding antigen binding protein phosphatase binding phosphatase binding enzyme binding SH3 domain binding protein domain specific binding phosphoprotein binding protein phosphorylated amino acid binding protein tyrosine kinase binding kinase binding protein kinase binding cell adhesion molecule binding cell adhesion mediator activity cell-cell adhesion mediator activity GTPase regulator activity nucleoside-triphosphatase regulator activity protein binding involved in heterotypic cell-cell adhesion	membrane organization import into cell transport establishment of localization vesicle-mediated transport cellular component organization localization phagocytosis, engulfment membrane invagination cellular process phagocytosis cellular component organization or biogenesis endocytosis plasma membrane invagination membrane organization import into cell transport establishment of localization vesicle-mediated transport cellular component organization localization phagocytosis, engulfment membrane invagination cellular process phagocytosis cellular component organization or biogenesis endocytosis plasma membrane invagination multicellular organismal process regulation of tumor necrosis factor production regulation of cellular process negative regulation of biological process negative regulation of tumor necrosis factor production cytokine production regulation of cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process negative regulation of metabolic process biological regulation tumor necrosis factor superfamily cytokine production negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process tumor necrosis factor production regulation of gene expression negative regulation of gene expression regulation of tumor necrosis factor superfamily cytokine production biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process negative regulation of tumor necrosis factor superfamily cytokine production metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process interleukin-6 production regulation of interleukin-6 production negative regulation of interleukin-6 production leukocyte migration immune system process mononuclear cell migration cellular extravasation myeloid leukocyte migration cell migration cell motility monocyte extravasation regulation of type II interferon production type II interferon production cellular response to stimulus response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette signal transduction regulation of signaling negative regulation of response to stimulus regulation of MAPK cascade negative regulation of signal transduction negative regulation of ERK1 and ERK2 cascade regulation of response to stimulus MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade negative regulation of MAPK cascade regulation of localization positive regulation of cellular component organization regulation of cellular component organization positive regulation of biological process positive regulation of endocytosis positive regulation of cellular process regulation of endocytosis regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport positive regulation of phagocytosis positive regulation of transport granulocyte migration organelle organization cytoskeleton organization chemokine (C-C motif) ligand 5 production negative regulation of chemokine production negative regulation of chemokine (C-C motif) ligand 5 production regulation of chemokine production chemokine production regulation of chemokine (C-C motif) ligand 5 production regulation of lipopolysaccharide-mediated signaling pathway negative regulation of lipopolysaccharide-mediated signaling pathway regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms negative regulation of response to biotic stimulus regulation of response to external stimulus response to lipid cellular response to lipopolysaccharide response to biotic stimulus lipopolysaccharide-mediated signaling pathway cellular response to biotic stimulus response to bacterium response to external biotic stimulus cell surface receptor signaling pathway response to other organism response to oxygen-containing compound response to external stimulus cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound cellular response to chemical stimulus negative regulation of response to external stimulus response to chemical cellular response to lipid response to molecule of bacterial origin regulation of interleukin-1 production interleukin-1 production regulation of interleukin-1 beta production interleukin-1 beta production actin cytoskeleton organization actin filament organization actin filament-based process supramolecular fiber organization response to peptide cellular response to interleukin-1 response to cytokine cellular response to cytokine stimulus response to interleukin-1 phagocytosis, recognition cell recognition cell adhesion cell-matrix adhesion cell-substrate adhesion negative regulation of canonical NF-kappaB signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction regulation of defense response negative regulation of inflammatory response defense response regulation of inflammatory response response to stress regulation of response to stress negative regulation of defense response inflammatory response regulation of nitric oxide biosynthetic process reactive nitrogen species metabolic process nitric oxide metabolic process nitric oxide biosynthetic process negative regulation of nitric oxide biosynthetic process regulation of nitric oxide metabolic process negative regulation of type I interferon production regulation of interferon-beta production interferon-beta production type I interferon production negative regulation of interferon-beta production regulation of type I interferon production negative regulation of JNK cascade JNK cascade regulation of JNK cascade reactive oxygen species metabolic process positive regulation of reactive oxygen species metabolic process positive regulation of metabolic process regulation of reactive oxygen species metabolic process cellular response to oxidative stress cellular response to chemical stress cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species cellular response to stress immune response response to type II interferon defense response to symbiont cellular response to type II interferon defense response to other organism innate immune response negative regulation of transport negative regulation of endocytosis negative regulation of phagocytosis negative regulation of cellular component organization developmental process cellular developmental process hemopoiesis cell differentiation anatomical structure development cell development hematopoietic progenitor cell differentiation response to interleukin-12 cellular response to interleukin-12 regulation of leukocyte activation regulation of cell activation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation cell-cell adhesion T cell activation positive regulation of leukocyte activation regulation of immune system process regulation of cell-cell adhesion positive regulation of immune system process positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process regulation of lymphocyte activation negative regulation of macrophage inflammatory protein 1 alpha production macrophage inflammatory protein-1 alpha production regulation of macrophage inflammatory protein 1 alpha production regulation of cytokine production involved in inflammatory response negative regulation of cytokine production involved in inflammatory response production of molecular mediator involved in inflammatory response cytokine production involved in inflammatory response	cell surface cellular anatomical structure cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B	IPR013106	Immunoglobulin V-set domain	Domain
A, B	IPR003599	Immunoglobulin domain subtype	Domain
A, B	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
A, B	IPR051755	Immunoglobulin-like Cell Surface Receptor	Family
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR007110	Immunoglobulin-like domain	Domain
A, B	IPR003597	Immunoglobulin C1-set	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.