3D5O | pdb_00003d5o

Structural recognition and functional activation of FcrR by innate pentraxins

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3d5ob_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Pentraxin (pentaxin)	Serum amyloid P component (SAP)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3d5oc_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Pentraxin (pentaxin)	Serum amyloid P component (SAP)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d3d5oe_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Pentraxin (pentaxin)	Serum amyloid P component (SAP)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3d5od_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Pentraxin (pentaxin)	Serum amyloid P component (SAP)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3d5oa_	All beta proteins	Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	Pentraxin (pentaxin)	Serum amyloid P component (SAP)	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F	d3d5of1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	I set domains	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8041430	3000120	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8041430	3000120	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8041430	3000120	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8041430	3000120	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Concanavalin A-like lectins/glucanases	8041430	3000120	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8054817	3000071	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8055584	3000071	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)
B		e3d5oB1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: zf-CCCH_4	F:	ECOD (20:10:01)
C		e3d5oC1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: zf-CCCH_4	F:	ECOD (20:10:01)
E		e3d5oE1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: zf-CCCH_4	F:	ECOD (20:10:01)
D		e3d5oD1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: zf-CCCH_4	F:	ECOD (20:10:01)
A		e3d5oA1	A: HTH	X: HTH	H: tetra-helical, lambda repressor-like	T: zf-CCCH_4	F:	ECOD (20:10:01)
F		e3d5oF1	A: OB-fold	X: Nucleic acid-binding protein	H: Nucleic acid-binding protein	T: Flavodoxin_2	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
C	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
E	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
D	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
A	2.60.120.200	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
F	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
A, B, C, D, E	Pentraxin (APCS serum amyloid P component, SAP)	APCS (Pr20-223)	Homo sapiens (human)	APCS*01	R-LIKE-DOMAIN APCS (Pr20-223)	RPI	(APCS (Pr20-223))	IMGT (202609-0)
F	FCGR2A	2C-LIKE	Homo sapiens (human)	FCGR2A*01	C-LIKE-DOMAIN C-LIKE	RPI	2C-LIKE	IMGT (202609-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	PF00354	Pentaxin family (Pentaxin)	Pentaxin family	Pentaxins are also known as pentraxins.	Domain
F	PF13895	Immunoglobulin domain (Ig_2)	Immunoglobulin domain	This domain contains immunoglobulin-like domains.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E	Serum amyloid P-component	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding complement component C1q complex binding opsonin binding protein-containing complex binding protein binding complement binding carbohydrate binding unfolded protein binding virion binding cation binding ion binding binding calcium ion binding metal ion binding small molecule binding complement component C1q complex binding opsonin binding protein-containing complex binding protein binding complement binding carbohydrate binding unfolded protein binding virion binding identical protein binding	negative regulation of glycoprotein metabolic process regulation of biological process regulation of cellular process regulation of protein metabolic process negative regulation of metabolic process biological regulation negative regulation of biological process carbohydrate derivative metabolic process primary metabolic process regulation of macromolecule metabolic process glycoprotein metabolic process regulation of glycoprotein metabolic process regulation of primary metabolic process negative regulation of cellular process negative regulation of glycoprotein metabolic process regulation of biological process regulation of cellular process regulation of protein metabolic process negative regulation of metabolic process biological regulation negative regulation of biological process carbohydrate derivative metabolic process primary metabolic process regulation of macromolecule metabolic process glycoprotein metabolic process regulation of glycoprotein metabolic process regulation of primary metabolic process negative regulation of cellular process metabolic process cellular process protein metabolic process macromolecule metabolic process regulation of metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process cellular component organization cellular component biogenesis cellular component assembly chaperone-mediated protein complex assembly protein-containing complex organization protein-containing complex assembly cellular component organization or biogenesis protein folding biosynthetic process gene expression macromolecule biosynthetic process protein maturation negative regulation of viral process regulation of viral process viral process biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus host-mediated suppression of symbiont invasion host-mediated perturbation of symbiont process response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus modulation of process of another organism host-mediated suppression of viral proces host-mediated perturbation of viral process modulation by host of viral glycoprotein metabolic process negative regulation by host of viral glycoprotein metabolic process wound healing regulation of response to external stimulus negative regulation of response to stimulus negative regulation of wound healing negative regulation of response to wounding regulation of response to wounding regulation of response to stimulus regulation of response to stress negative regulation of response to external stimulus regulation of wound healing response to wounding acute-phase response inflammatory response acute inflammatory response regulation of defense response negative regulation of acute inflammatory response negative regulation of inflammatory response regulation of inflammatory response negative regulation of defense response regulation of acute inflammatory response myeloid leukocyte differentiation regulation of leukocyte differentiation multicellular organismal process cellular developmental process regulation of developmental process cell development mononuclear cell differentiation regulation of cell differentiation regulation of cell development multicellular organism development cell differentiation anatomical structure development regulation of immune system process regulation of multicellular organismal process negative regulation of cell differentiation monocyte differentiation negative regulation of hemopoiesis negative regulation of monocyte differentiation developmental process regulation of multicellular organismal development regulation of monocyte differentiation negative regulation of leukocyte differentiation hemopoiesis regulation of myeloid cell differentiation negative regulation of developmental process regulation of myeloid leukocyte differentiation negative regulation of myeloid cell differentiation negative regulation of myeloid leukocyte differentiation negative regulation of cell development myeloid cell differentiation negative regulation of immune system process regulation of hemopoiesis negative regulation of multicellular organismal process leukocyte differentiation	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle blood microparticle intracellular organelle intracellular anatomical structure nucleus extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle blood microparticle intracellular organelle intracellular anatomical structure nucleus intracellular membrane-bounded organelle
F	Low affinity immunoglobulin gamma Fc region receptor II-a	molecular transducer activity immunoglobulin receptor activity transmembrane signaling receptor activity signaling receptor activity IgG receptor activity immune receptor activity protein-containing complex binding binding immunoglobulin binding IgG binding	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus myeloid leukocyte mediated immunity inflammatory response to antigenic stimulus response to stress leukocyte mediated immunity antibody-dependent cellular cytotoxicity acute inflammatory response hypersensitivity defense response immune response leukocyte mediated cytotoxicity acute inflammatory response to antigenic stimulus adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus myeloid leukocyte mediated immunity inflammatory response to antigenic stimulus response to stress leukocyte mediated immunity antibody-dependent cellular cytotoxicity acute inflammatory response hypersensitivity defense response immune response leukocyte mediated cytotoxicity acute inflammatory response to antigenic stimulus immunoglobulin mediated immune response adaptive immune response immune effector process type II hypersensitivity immune system process type IIa hypersensitivity B cell mediated immunity cellular process inflammatory response cell killing cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway signaling biological regulation signal transduction cell communication regulation of localization import into cell positive regulation of cellular component organization regulation of cellular component organization transport positive regulation of biological process vesicle-mediated transport cellular component organization localization positive regulation of endocytosis phagocytosis cellular component organization or biogenesis positive regulation of cellular process regulation of endocytosis regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport establishment of localization positive regulation of phagocytosis positive regulation of transport endocytosis multicellular organismal process regulation of tumor necrosis factor production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of tumor necrosis factor superfamily cytokine production positive regulation of biosynthetic process cytokine production regulation of cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process regulation of biosynthetic process tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process tumor necrosis factor production regulation of gene expression regulation of tumor necrosis factor superfamily cytokine production biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle organelle membrane secretory granule membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR030476	Pentaxin, conserved site	Conserved Site
A, B, C, D, E	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
A, B, C, D, E	IPR001759	Pentraxin domain	Domain
A, B, C, D, E	IPR051005	Pentraxin domain-containing protein	Family
F	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
F	IPR003598	Immunoglobulin subtype 2	Domain
F	IPR050488	Immunoglobulin Fc region receptor	Family
F	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
F	IPR003599	Immunoglobulin domain subtype	Domain
F	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D, E	Pharos: P02743	coronary artery disease liver cancer congestive heart failure Heart Decompensation hepatocellular carcinoma AA amyloidosis ADan amyloidosis pancreatic ductal adenocarcinoma Alzheimer disease heart failure hypotrichosis 2 liver neoplasm ABri amyloidosis medullary thyroid gland carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia coronary artery disease liver cancer congestive heart failure Heart Decompensation hepatocellular carcinoma AA amyloidosis ADan amyloidosis pancreatic ductal adenocarcinoma Alzheimer disease heart failure hypotrichosis 2 liver neoplasm ABri amyloidosis medullary thyroid gland carcinoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia amyloidosis type 2 diabetes mellitus cerebral amyloid angiopathy, APP-related Finnish type amyloidosis ACys amyloidosis primary cutaneous amyloidosis Creutzfeldt Jacob disease
F	Pharos: P12318	ulcerative colitis rheumatoid arthritis mucocutaneous lymph node syndrome thrombocytopenia systemic lupus erythematosus malaria Sjogren syndrome cystic fibrosis Thrombus ankylosing spondylitis breast cancer inflammatory bowel disease autoimmune disease Crohn disease Takayasu arteritis ulcerative colitis rheumatoid arthritis mucocutaneous lymph node syndrome thrombocytopenia systemic lupus erythematosus malaria Sjogren syndrome cystic fibrosis Thrombus ankylosing spondylitis breast cancer inflammatory bowel disease autoimmune disease Crohn disease Takayasu arteritis thrombotic disease autoimmune thrombocytopenic purpura lung carcinoma MALT lymphoma schizophrenia

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.