7Y09

Cryo-EM structure of human IgM-Fc in complex with the J chain and the DBL domain of DBLMSP

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth R]	PF05424	e7y09R2	A: alpha bundles	X: Duffy-binding-like domain, N-terminal subdomain (From Topology)	H: Duffy-binding-like domain, N-terminal subdomain (From Topology)	T: Duffy-binding-like domain, N-terminal subdomain	F: PF05424	ECOD (1.6)
A [auth R]	F_UNCLASSIFIED	e7y09R1	A: alpha bundles	X: Duffy-binding-like domain, C-terminal subdomain (From Topology)	H: Duffy-binding-like domain, C-terminal subdomain (From Topology)	T: Duffy-binding-like domain, C-terminal subdomain	F: F_UNCLASSIFIED	ECOD (1.6)
C [auth B]	PF07654	e7y09B2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
B [auth A]	PF07654	e7y09A2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
D [auth C]	PF07654	e7y09C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
E [auth D]	PF07654	e7y09D2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
F [auth E]	PF07654	e7y09E1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
G [auth F]	PF07654	e7y09F1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
H [auth G]	PF07654	e7y09G2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
I [auth H]	PF07654	e7y09H2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
J [auth K]	PF07654	e7y09K1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
K [auth L]	PF07654	e7y09L2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth R]	PF05424	Duffy binding domain (Duffy_binding)	Duffy binding domain	-	Family
B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H], J [auth K], K [auth L]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
L [auth J]	PF15097	Immunoglobulin J chain (Ig_J_chain)	Immunoglobulin J chain	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth R]	Putative erythrocyte membrane protein	host cell surface binding binding host cell surface receptor binding	-	membrane cellular anatomical entity
B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H], J [auth K], K [auth L]	Immunoglobulin heavy constant mu	binding antigen binding	cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process cellular response to stimulus immune response-regulating cell surface receptor signaling pathway regulation of cellular process response to stimulus signaling positive regulation of biological process cell communication positive regulation of response to stimulus immune response-activating signaling pathway immune response-regulating signaling pathway positive regulation of immune response regulation of immune system process signal transduction positive regulation of immune system process regulation of biological process cell surface receptor signaling pathway immune response-activating cell surface receptor signaling pathway immune response B cell receptor signaling pathway biological regulation regulation of response to stimulus immune system process regulation of immune response cellular process antigen receptor-mediated signaling pathway activation of immune response adaptive immune response 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 leukocyte mediated immunity complement activation, classical pathway immunoglobulin mediated immune response immune effector process B cell mediated immunity biological process involved in interspecies interaction between organisms response to other organism defense response response to external stimulus defense response to Gram-negative bacterium response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus antibacterial humoral response defense response to symbiont antimicrobial humoral response innate immune response multicellular organismal process cellular developmental process immature B cell differentiation cellular biosynthetic process cell development mononuclear cell differentiation pre-B cell allelic exclusion pre-B cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation organic substance metabolic process cell differentiation anatomical structure development organic substance biosynthetic process developmental process regulation of biosynthetic process hemopoiesis B cell activation cellular metabolic process cell activation regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process leukocyte differentiation	hexameric IgM immunoglobulin complex protein-containing complex IgM immunoglobulin complex IgM immunoglobulin complex, circulating extracellular region extracellular space cellular anatomical entity immunoglobulin complex, circulating immunoglobulin complex blood microparticle plasma membrane protein complex membrane plasma membrane IgM B cell receptor complex hexameric IgM immunoglobulin complex protein-containing complex IgM immunoglobulin complex IgM immunoglobulin complex, circulating extracellular region extracellular space cellular anatomical entity immunoglobulin complex, circulating immunoglobulin complex blood microparticle plasma membrane protein complex membrane plasma membrane IgM B cell receptor complex membrane protein complex receptor complex B cell receptor complex cell periphery plasma membrane signaling receptor complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle pentameric IgM immunoglobulin complex cell surface
L [auth J]	Immunoglobulin J chain	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity protein-containing complex binding immunoglobulin binding IgA binding signaling receptor binding immunoglobulin receptor binding protein-macromolecule adaptor activity molecular adaptor activity antigen binding	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis positive regulation of metabolic process regulation of biological process positive regulation of respiratory burst respiratory burst biological regulation positive regulation of biological process metabolic process cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis positive regulation of metabolic process regulation of biological process positive regulation of respiratory burst respiratory burst biological regulation positive regulation of biological process metabolic process regulation of respiratory burst regulation of metabolic process response to stimulus immune response immune system process adaptive immune response humoral immune response biological process involved in interspecies interaction between organisms response to other organism defense response antibacterial humoral response defense response to symbiont response to external stimulus antimicrobial humoral response response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus innate immune response multicellular organismal process renal system process system process glomerular filtration renal filtration	extracellular region extracellular space cellular anatomical entity blood microparticle IgA immunoglobulin complex, circulating dimeric IgA immunoglobulin complex protein-containing complex IgA immunoglobulin complex polymeric IgA immunoglobulin complex immunoglobulin complex, circulating immunoglobulin complex secretory IgA immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular region extracellular space cellular anatomical entity blood microparticle IgA immunoglobulin complex, circulating dimeric IgA immunoglobulin complex protein-containing complex IgA immunoglobulin complex polymeric IgA immunoglobulin complex immunoglobulin complex, circulating immunoglobulin complex secretory IgA immunoglobulin complex extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle organelle vesicle extracellular membrane-bounded organelle monomeric IgA immunoglobulin complex IgM immunoglobulin complex IgM immunoglobulin complex, circulating pentameric IgM immunoglobulin complex secretory dimeric IgA immunoglobulin complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth R]	IPR008602	Duffy-antigen binding domain	Domain
A [auth R]	IPR010784	Merozoite surface protein-type	Family
A [auth R]	IPR042202	Duffy-antigen binding superfamily	Homologous Superfamily
B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H], J [auth K], K [auth L]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H], J [auth K], K [auth L]	IPR003597	Immunoglobulin C1-set	Domain
B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H], J [auth K], K [auth L]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H], J [auth K], K [auth L]	IPR007110	Immunoglobulin-like domain	Domain
B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H], J [auth K], K [auth L]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
L [auth J]	IPR024110	Immunoglobulin J chain	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H], J [auth K], K [auth L]	Pharos: P01871	autosomal recessive agammaglobulinemia 1 agammaglobulinemia periodontitis Sjogren syndrome acute myeloid leukemia cutaneous lupus erythematosus interstitial cystitis lung carcinoma medulloblastoma ovarian cancer plasma cell myeloma tuberculosis breast cancer esophageal adenocarcinoma lung adenocarcinoma autosomal recessive agammaglobulinemia 1 agammaglobulinemia periodontitis Sjogren syndrome acute myeloid leukemia cutaneous lupus erythematosus interstitial cystitis lung carcinoma medulloblastoma ovarian cancer plasma cell myeloma tuberculosis breast cancer esophageal adenocarcinoma lung adenocarcinoma malignant ependymoma non-small cell lung carcinoma pancreatic intraductal papillary-mucinous neoplasm sinusitis ulcerative colitis autosomal agammaglobulinemia Bruton-type agammaglobulinemia Hypogammaglobulinemia lung cancer malignant pancreatic neoplasm osteosarcoma
L [auth J]	Pharos: P01591	pancreatic intraductal papillary-mucinous neoplasm psoriasis B-cell chronic lymphocytic leukemia Bruton-type agammaglobulinemia cutaneous lupus erythematosus lung carcinoma malignant ependymoma malignant pancreatic neoplasm pancreatic ductal adenocarcinoma periodontitis tuberculosis breast cancer chronic kidney disease lung adenocarcinoma lymphoplasmacytic lymphoma pancreatic intraductal papillary-mucinous neoplasm psoriasis B-cell chronic lymphocytic leukemia Bruton-type agammaglobulinemia cutaneous lupus erythematosus lung carcinoma malignant ependymoma malignant pancreatic neoplasm pancreatic ductal adenocarcinoma periodontitis tuberculosis breast cancer chronic kidney disease lung adenocarcinoma lymphoplasmacytic lymphoma malignant glioma MALT lymphoma pancreatic intraductal papillary-mucinous carcinoma pituitary cancer ulcerative colitis breast carcinoma common variable immunodeficiency lung cancer malignant colon neoplasm malignant mesothelioma osteosarcoma

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 R01GM133198.