3D5S | pdb_00003d5s

Crystal Structure of Efb-C (R131A) / C3d Complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	d3d5sa2	All alpha proteins	alpha/alpha toroid	Terpenoid cyclases/Protein prenyltransferases	Complement components	Thio-ester containing domain (TED) from Complement C3, aka C3d or C3dg	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3d5sa3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth B]	d3d5sb2	All alpha proteins	alpha/alpha toroid	Terpenoid cyclases/Protein prenyltransferases	Complement components	Thio-ester containing domain (TED) from Complement C3, aka C3d or C3dg	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C [auth B]	d3d5sb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B [auth C]	d3d5sc1	All alpha proteins	Spectrin repeat-like	Efb C-domain-like	Efb C-domain-like	Fibrinogen-binding protein Efb (Fib)	(Staphylococcus aureus subsp. aureus str. Newman ) [TaxId: 426430 ],	SCOPe (2.08)
D	d3d5sd_	All alpha proteins	Spectrin repeat-like	Efb C-domain-like	Efb C-domain-like	Fibrinogen-binding protein Efb (Fib)	(Staphylococcus aureus subsp. aureus str. Newman ) [TaxId: 426430 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Terpenoid cyclases/Protein prenyltransferases	8038414	3001024	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Terpenoid cyclases/Protein prenyltransferases	8038414	3001024	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Efb C-domain-like	8058958	3001178	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Efb C-domain-like	8058958	3001178	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)
A	A2M_comp_2	e3d5sA1	A: alpha superhelices	X: Repetitive alpha hairpins	H: alpha/alpha toroid (From Topology)	T: alpha/alpha toroid	F: A2M_comp_2	ECOD (1.6)
C [auth B]	A2M_comp_2	e3d5sB1	A: alpha superhelices	X: Repetitive alpha hairpins	H: alpha/alpha toroid (From Topology)	T: alpha/alpha toroid	F: A2M_comp_2	ECOD (1.6)
B [auth C]	efb-c	e3d5sC1	A: alpha bundles	X: Spectrin repeat-like	H: Efb C-domain-like (From Topology)	T: Efb C-domain-like	F: efb-c	ECOD (1.6)
D	efb-c	e3d5sD1	A: alpha bundles	X: Spectrin repeat-like	H: Efb C-domain-like (From Topology)	T: Efb C-domain-like	F: efb-c	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.50.10.20	Mainly Alpha	Alpha/alpha barrel	Glycosyltransferase		CATH (4.3.0)
C [auth B]	1.50.10.20	Mainly Alpha	Alpha/alpha barrel	Glycosyltransferase		CATH (4.3.0)
B [auth C]	1.10.10.1270	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Sbi, C3 binding domain IV	CATH (4.3.0)
D	1.10.10.1270	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Sbi, C3 binding domain IV	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C [auth B]	PF07678	A-macroglobulin TED domain (TED_complement)	A-macroglobulin TED domain	-	Repeat
B [auth C], D	PF12199	Extracellular fibrinogen binding protein C terminal (efb-c)	Extracellular fibrinogen binding protein C terminal	This domain family is found in bacteria, and is approximately 70 amino acids in length. There is a conserved VLK sequence motif. It is the C terminal domain of bacterial extracellular fibrinogen binding protein. It contains a helical motif involved i ...	This domain family is found in bacteria, and is approximately 70 amino acids in length. There is a conserved VLK sequence motif. It is the C terminal domain of bacterial extracellular fibrinogen binding protein. It contains a helical motif involved in complement regulation. This motif binds to complement and changes its conformation to a form which cannot activate downstream components of the complement cascade.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C [auth B]	Complement C3	enzyme regulator activity peptidase activity peptidase regulator activity catalytic activity, acting on a protein hydrolase activity enzyme inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity molecular function inhibitor activity molecular function regulator activity catalytic activity endopeptidase activity C5L2 anaphylatoxin chemotactic receptor binding enzyme regulator activity peptidase activity peptidase regulator activity catalytic activity, acting on a protein hydrolase activity enzyme inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity molecular function inhibitor activity molecular function regulator activity catalytic activity endopeptidase activity C5L2 anaphylatoxin chemotactic receptor binding protein binding binding signaling receptor binding G protein-coupled receptor binding C5a anaphylatoxin chemotactic receptor binding molecular transducer activity molecular function activator activity signaling receptor activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity	cellular response to stimulus positive regulation of cell communication regulation of biological process regulation of signaling regulation of cellular process positive regulation of signal transduction response to stimulus signaling biological regulation positive regulation of biological process regulation of signal transduction positive regulation of G protein-coupled receptor signaling pathway cell communication positive regulation of response to stimulus regulation of response to stimulus cellular response to stimulus positive regulation of cell communication regulation of biological process regulation of signaling regulation of cellular process positive regulation of signal transduction response to stimulus signaling biological regulation positive regulation of biological process regulation of signal transduction positive regulation of G protein-coupled receptor signaling pathway cell communication positive regulation of response to stimulus regulation of response to stimulus regulation of cell communication G protein-coupled receptor signaling pathway cellular process signal transduction regulation of G protein-coupled receptor signaling pathway positive regulation of cellular process positive regulation of signaling neutral lipid metabolic process neutral lipid biosynthetic process regulation of triglyceride metabolic process regulation of lipid metabolic process lipid biosynthetic process regulation of primary metabolic process acylglycerol biosynthetic process triglyceride metabolic process triglyceride biosynthetic process regulation of biosynthetic process regulation of triglyceride biosynthetic process primary metabolic process biosynthetic process glycerolipid biosynthetic process metabolic process glycerolipid metabolic process regulation of lipid biosynthetic process acylglycerol metabolic process regulation of metabolic process lipid metabolic process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity humoral immune response complement activation humoral immune response mediated by circulating immunoglobulin positive regulation of immune response leukocyte mediated immunity regulation of immune system process positive regulation of immune system process complement activation, classical pathway immune response immunoglobulin mediated immune response adaptive immune response immune effector process immune system process B cell mediated immunity regulation of immune response activation of immune response developmental process multicellular organismal process cellular developmental process cell development developmental maturation nervous system development generation of neurons neurogenesis multicellular organism development neuron differentiation neuron remodeling anatomical structure maturation cell differentiation neuron development anatomical structure development neuron maturation cell maturation system development B cell activation cell activation lymphocyte activation leukocyte activation regulation of humoral immune response regulation of immune effector process positive regulation of humoral immune response positive regulation of complement activation positive regulation of immune effector process activation of membrane attack complex positive regulation of activation of membrane attack complex regulation of activation of membrane attack complex regulation of complement activation visual system development pattern specification process regionalization central nervous system development sensory system development vertebrate eye-specific patterning regulation of localization import into cell positive regulation of cellular component organization regulation of cellular component organization transport vesicle-mediated transport cellular component organization localization positive regulation of endocytosis cellular component organization or biogenesis positive regulation of receptor-mediated endocytosis regulation of endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport establishment of localization positive regulation of transport endocytosis receptor-mediated endocytosis biological process involved in interspecies interaction between organisms complement activation, alternative pathway response to biotic stimulus response to stress innate immune response response to external biotic stimulus response to other organism defense response defense response to symbiont response to external stimulus defense response to other organism epithelium development oviduct development reproductive system development oviduct epithelium development tube development reproductive process developmental process involved in reproduction tissue development reproductive structure development positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process regulation of cytokine production cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process regulation of vascular endothelial growth factor production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression vascular endothelial growth factor production positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of vascular endothelial growth factor production regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production positive regulation of membrane invagination regulation of phagocytosis, engulfment membrane invagination phagocytosis plasma membrane invagination membrane organization regulation of phagocytosis phagocytosis, engulfment positive regulation of phagocytosis positive regulation of phagocytosis, engulfment regulation of membrane invagination cellular component disassembly complement-mediated synapse pruning cell junction organization cell junction disassembly synapse pruning synapse organization immune response-regulating cell surface receptor signaling pathway complement receptor mediated signaling pathway immune response-activating signaling pathway immune response-regulating signaling pathway cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway amyloid-beta clearance lipid storage lipid localization positive regulation of lipid localization regulation of lipid storage regulation of lipid localization macromolecule localization nutrient storage positive regulation of lipid storage fatty acid metabolic process oxoacid metabolic process carboxylic acid metabolic process small molecule metabolic process monocarboxylic acid metabolic process organic acid metabolic process positive regulation of acute inflammatory response to antigenic stimulus regulation of myeloid leukocyte mediated immunity regulation of acute inflammatory response to antigenic stimulus positive regulation of leukocyte mediated immunity regulation of type IIa hypersensitivity myeloid leukocyte mediated immunity inflammatory response to antigenic stimulus positive regulation of hypersensitivity positive regulation of inflammatory response positive regulation of adaptive immune response regulation of type II hypersensitivity positive regulation of immunoglobulin mediated immune response hypersensitivity regulation of adaptive immune response regulation of inflammatory response regulation of B cell mediated immunity regulation of leukocyte mediated immunity type II hypersensitivity positive regulation of myeloid leukocyte mediated immunity type IIa hypersensitivity positive regulation of defense response regulation of acute inflammatory response inflammatory response regulation of defense response regulation of response to external stimulus 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 positive regulation of B cell mediated immunity regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains positive regulation of response to external stimulus regulation of immunoglobulin mediated immune response regulation of response to stress acute inflammatory response regulation of hypersensitivity regulation of inflammatory response to antigenic stimulus acute inflammatory response to antigenic stimulus positive regulation of inflammatory response to antigenic stimulus positive regulation of type IIa hypersensitivity regulation of lymphocyte mediated immunity positive regulation of type II hypersensitivity regulation of developmental process angiogenesis regulation of vasculature development positive regulation of developmental process tube morphogenesis regulation of anatomical structure morphogenesis blood vessel development regulation of multicellular organismal development blood vessel morphogenesis positive regulation of angiogenesis vasculature development circulatory system development anatomical structure morphogenesis positive regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis response to bacterium complement-dependent cytotoxicity cell killing positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of phosphate metabolic process positive regulation of protein modification process regulation of phosphate metabolic process phosphate-containing compound metabolic process protein metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein modification process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process macromolecule modification regulation of phosphorus metabolic process regulation of phosphorylation positive regulation of apoptotic cell clearance apoptotic cell clearance regulation of apoptotic cell clearance hexose transmembrane transport carbohydrate transport positive regulation of D-glucose transmembrane transport transmembrane transport regulation of transmembrane transport D-glucose transmembrane transport positive regulation of transmembrane transport regulation of D-glucose transmembrane transport monosaccharide transmembrane transport carbohydrate transmembrane transport	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen endoplasmic reticulum lumen intracellular organelle organelle lumen endoplasmic reticulum cytoplasm cell surface cell periphery plasma membrane membrane lytic vacuole intracellular vesicle cytoplasmic vesicle lumen vacuolar lumen cytoplasmic vesicle lysosome vesicle lumen azurophil granule vacuole secretory granule lumen azurophil granule lumen secretory granule primary lysosome secretory vesicle protein-containing complex blood microparticle
B [auth C], D	Fibrinogen-binding protein	protein binding binding complement binding	-	cellular anatomical structure extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C [auth B]	IPR019742	Alpha-2-macroglobulin, conserved site	Conserved Site
A, C [auth B]	IPR009048	Alpha-macroglobulin, receptor-binding	Domain
A, C [auth B]	IPR049466	Complement component 3, CUB domain, first segment	Domain
A, C [auth B]	IPR001599	Alpha-2-macroglobulin	Domain
A, C [auth B]	IPR001134	Netrin domain	Domain
A, C [auth B]	IPR011626	Alpha-macroglobulin-like, TED domain	Domain
A, C [auth B]	IPR002890	Macroglobulin domain	Domain
A, C [auth B]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, C [auth B]	IPR008930	Terpenoid cyclases/protein prenyltransferase alpha-alpha toroid	Homologous Superfamily
A, C [auth B]	IPR041555	Macroglobulin domain MG3	Domain
A, C [auth B]	IPR047565	Alpha-macroglobulin-like, thiol-ester bond-forming region	Conserved Site
A, C [auth B]	IPR048848	Complement component 3, CUB domain, second segment	Domain
A, C [auth B]	IPR018081	Anaphylatoxin, complement system	Homologous Superfamily
A, C [auth B]	IPR035815	Complement C3-like, NTR domain	Domain
A, C [auth B]	IPR018933	Netrin module, non-TIMP type	Domain
A, C [auth B]	IPR001840	Anaphylatoxin, complement system domain	Domain
A, C [auth B]	IPR041425	Complement C3/4/5, macroglobulin domain MG1	Domain
A, C [auth B]	IPR011625	Alpha-2-macroglobulin, bait region domain	Domain
A, C [auth B]	IPR008993	Tissue inhibitor of metalloproteinases-like, OB-fold	Homologous Superfamily
A, C [auth B]	IPR000020	Anaphylatoxin/fibulin	Domain
A, C [auth B]	IPR036595	Alpha-macroglobulin, receptor-binding domain superfamily	Homologous Superfamily
A, C [auth B]	IPR050473	Alpha-2-macroglobulin/Complement system	Family
A, C [auth B]	IPR040839	Macroglobulin domain MG4	Domain
B [auth C], D	IPR041909	Sbi, C3 binding domain IV	Homologous Superfamily
B [auth C], D	IPR021033	Extracellular fibrinogen binding protein, C-terminal	Domain
B [auth C], D	IPR036233	Efb, C-terminal domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C [auth B]	Pharos: P01024	complement component 3 deficiency age-related macular degeneration Henoch-Schoenlein purpura atypical hemolytic-uremic syndrome pemphigus age related macular degeneration 9 membranous glomerulonephritis pemphigus vulgaris Insulin Resistance transient ischemic attack atypical hemolytic-uremic syndrome with C3 anomaly primary immunodeficiency disease type 2 diabetes mellitus middle cerebral artery infarction hemolytic-uremic syndrome complement component 3 deficiency age-related macular degeneration Henoch-Schoenlein purpura atypical hemolytic-uremic syndrome pemphigus age related macular degeneration 9 membranous glomerulonephritis pemphigus vulgaris Insulin Resistance transient ischemic attack atypical hemolytic-uremic syndrome with C3 anomaly primary immunodeficiency disease type 2 diabetes mellitus middle cerebral artery infarction hemolytic-uremic syndrome paratuberculosis chronic kidney disease congestive heart failure juvenile dermatomyositis cystic fibrosis large cell medulloblastoma lung cancer acquired paroxysmal nocturnal hemoglobinuria subependymal giant cell astrocytoma malignant colon neoplasm maturity-onset diabetes of the young tuberculosis Emery-Dreifuss muscular dystrophy Gaucher disease non-small cell lung carcinoma hemolytic anemia pancreatic intraductal papillary-mucinous carcinoma Becker muscular dystrophy periodontitis chronic obstructive pulmonary disease kidney disease dermatomyositis Down syndrome lung carcinoma acute kidney failure malignant ependymoma adenoma Duchenne muscular dystrophy medulloblastoma Finnish type amyloidosis astrocytic tumor wet macular degeneration glioblastoma ovarian cancer atypical teratoid rhabdoid tumor pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia pemphigus foliaceus idiopathic membranous glomerulonephritis pilocytic astrocytoma invasive ductal breast carcinoma psoriasis Creutzfeldt Jacob disease retinal degeneration diabetes mellitus limb-girdle muscular dystrophy Sjogren syndrome macular degeneration drug-induced liver injury malignant mesothelioma adrenal cortex carcinoma ulcerative colitis gastric carcinoma myopathy head and neck cancer pancreatic ductal adenocarcinoma autoimmune disease