5VU0 | pdb_00005vu0

Crystal structure of the complex between afucosylated/galactosylated human IgG1 Fc and Fc gamma receptor IIIa (CD16A) with Man5 N-glycans

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
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d5vu0a1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5vu0b1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5vu0c1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	I set domains	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	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	VP4_haemagglut	e5vu0A1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: VP4_haemagglut	ECOD (develop294)
B	DEAD	e5vu0B1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
C	VP4_haemagglut	e5vu0C1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: VP4_haemagglut	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	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	IgG1 Fc fragment	CH2-CH3	Homo sapiens (human)	IGHG101, IGHG102, IGHG103, IGHG104, IGHG1*05	C-DOMAIN CH2, C-DOMAIN CH3	FPIA	CH2-CH3	IMGT (202610-0)
C	Fc gamma receptor IIIa (CD16A)	null	Homo sapiens (human)	-	-	RPI	Protein	IMGT (202610-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	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	Immunoglobulin gamma-1 heavy chain	-	response to stimulus immune response immune system process adaptive immune response	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex immunoglobulin complex extracellular region
C	Low affinity immunoglobulin gamma Fc region receptor III-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 low-affinity IgG receptor activity	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 immune response-regulating cell surface receptor signaling pathway regulation of biological process regulation of cellular process cell surface receptor signaling pathway signaling biological regulation cell communication Fc receptor signaling pathway immune response-regulating signaling pathway regulation of response to stimulus regulation of immune response regulation of immune system process signal transduction Fc-gamma receptor signaling pathway intracellular signal transduction intracellular signaling cassette phosphatidylinositol 3-kinase/protein kinase B signal transduction multicellular organismal process positive regulation of cell population proliferation regulation of leukocyte activation positive regulation of biological process regulation of cell activation lymphocyte activation positive regulation of natural killer cell proliferation leukocyte proliferation leukocyte activation positive regulation of lymphocyte activation positive regulation of cell activation lymphocyte proliferation positive regulation of leukocyte activation positive regulation of mononuclear cell proliferation regulation of multicellular organismal process positive regulation of immune system process regulation of natural killer cell activation positive regulation of cellular process regulation of lymphocyte proliferation regulation of leukocyte proliferation cell population proliferation cell activation positive regulation of lymphocyte proliferation positive regulation of natural killer cell activation natural killer cell activation natural killer cell proliferation mononuclear cell proliferation regulation of cell population proliferation positive regulation of leukocyte proliferation regulation of mononuclear cell proliferation positive regulation of multicellular organismal process regulation of lymphocyte activation regulation of natural killer cell proliferation calcium-mediated signaling regulated exocytosis cellular localization biological process involved in interspecies interaction between organisms transport cell activation involved in immune response leukocyte degranulation response to biotic stimulus vesicle-mediated transport localization secretion by cell natural killer cell activation involved in immune response leukocyte activation involved in immune response establishment of localization in cell innate immune response response to external biotic stimulus natural killer cell mediated immunity lymphocyte activation involved in immune response response to other organism secretion export from cell defense response to symbiont response to external stimulus establishment of localization exocytosis defense response to other organism natural killer cell degranulation natural killer cell mediated cytotoxicity macrophage activation myeloid leukocyte activation 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 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 metabolic process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production regulation of metabolic process	cell periphery protein-containing complex cellular anatomical structure plasma membrane protein complex membrane plasma membrane membrane protein complex Fc-gamma receptor III complex Fc receptor complex cell surface external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle cell periphery protein-containing complex cellular anatomical structure plasma membrane protein complex membrane plasma membrane membrane protein complex Fc-gamma receptor III complex Fc receptor complex cell surface external side of plasma membrane side of membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR003597	Immunoglobulin C1-set	Domain
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
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	IPR007110	Immunoglobulin-like domain	Domain
A, B	IPR050380	Immune Recognition and Response Modulators	Family
A, B	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
C	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C	IPR050488	Immunoglobulin Fc region receptor	Family
C	IPR003599	Immunoglobulin domain subtype	Domain
C	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C	Pharos: P08637	autosomal recessive primary immunodeficiency with defective spontaneous natural killer cell cytotoxicity Liver Cirrhosis, Experimental ulcerative colitis ankylosing spondylitis breast cancer central nervous system lupus HIV infectious disease plasma cell myeloma systemic lupus erythematosus autoimmune disease breast carcinoma Crohn disease inflammatory bowel disease lung adenocarcinoma mucocutaneous lymph node syndrome autosomal recessive primary immunodeficiency with defective spontaneous natural killer cell cytotoxicity Liver Cirrhosis, Experimental ulcerative colitis ankylosing spondylitis breast cancer central nervous system lupus HIV infectious disease plasma cell myeloma systemic lupus erythematosus autoimmune disease breast carcinoma Crohn disease inflammatory bowel disease lung adenocarcinoma mucocutaneous lymph node syndrome psoriasis Takayasu arteritis cancer Ebola hemorrhagic fever leukopenia lung carcinoma lymphatic system disease

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.