8AE2 | pdb_00008ae2

Cryo-EM structure of full-length human immunoglobulin M - F(ab')2 conformation 5

External Resource: Annotation

Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
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)
P [auth S]	F5_F8_type_C	e8ae2S1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: F5_F8_type_C	ECOD (develop294)
K [auth L]	F5_F8_type_C	e8ae2L1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: F5_F8_type_C	ECOD (develop294)
N [auth Q]	F5_F8_type_C	e8ae2Q1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: F5_F8_type_C	ECOD (develop294)
G [auth H]	F5_F8_type_C	e8ae2H1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: F5_F8_type_C	ECOD (develop294)
L [auth N]	F5_F8_type_C	e8ae2N1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: F5_F8_type_C	ECOD (develop294)
Q [auth T]	F5_F8_type_C	e8ae2T1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: F5_F8_type_C	ECOD (develop294)
O [auth R]	F5_F8_type_C	e8ae2R1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: F5_F8_type_C	ECOD (develop294)
M [auth O]	F5_F8_type_C	e8ae2O1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: F5_F8_type_C	ECOD (develop294)
J [auth K]	F5_F8_type_C	e8ae2K1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: F5_F8_type_C	ECOD (develop294)
F [auth G]	F5_F8_type_C	e8ae2G1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: F5_F8_type_C	ECOD (develop294)
E [auth F]	F5_F8_type_C	e8ae2F1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: F5_F8_type_C	ECOD (develop294)
D [auth E]	F5_F8_type_C	e8ae2E1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: F5_F8_type_C	ECOD (develop294)
C [auth D]	F5_F8_type_C	e8ae2D1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: F5_F8_type_C	ECOD (develop294)
B [auth C]	F5_F8_type_C	e8ae2C1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: F5_F8_type_C	ECOD (develop294)
H [auth I]	F5_F8_type_C	e8ae2I1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: F5_F8_type_C	ECOD (develop294)
A [auth B]	F5_F8_type_C	e8ae2B1	A: alpha bundles	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: F5_F8_type_C	ECOD (develop294)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
K [auth L], P [auth S]	Light Chain	IGKV3	Kappa	-	SAbDab (2026-03-20)
G [auth H], N [auth Q]	Heavy Chain	IGHV2	-	-	SAbDab (2026-03-20)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], J [auth K], L [auth N], M [auth O], O [auth R], Q [auth T]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
K [auth L], P [auth S]	IgM Fab, light chain	-	-	-
I [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 regulation of biological process positive regulation of respiratory burst regulation of cellular process biological regulation positive regulation of biological process positive regulation of metabolic process respiratory burst cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis regulation of biological process positive regulation of respiratory burst regulation of cellular process biological regulation positive regulation of biological process positive regulation of metabolic process respiratory burst metabolic process regulation of respiratory burst regulation of metabolic process positive regulation of cellular 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	cellular anatomical structure extracellular region extracellular space 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 cellular anatomical structure extracellular region extracellular space 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
G [auth H], N [auth Q]	IgM Fab, heavy chain	-	-	-
B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], J [auth K], L [auth N], M [auth O], O [auth R], Q [auth T]	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 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 response to bacterium response to stress response to external biotic stimulus humoral immune response antibacterial humoral response defense response to symbiont antimicrobial humoral response defense response to other organism innate immune response multicellular organismal process cellular developmental process immature B cell differentiation cell development mononuclear cell differentiation pre-B cell allelic exclusion pre-B cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation anatomical structure development developmental process regulation of biosynthetic process hemopoiesis B cell activation cell activation regulation of macromolecule metabolic process gene expression macromolecule 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 cellular anatomical structure IgM immunoglobulin complex IgM immunoglobulin complex, circulating extracellular region extracellular space 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 cellular anatomical structure IgM immunoglobulin complex IgM immunoglobulin complex, circulating extracellular region extracellular space 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
A [auth B], H [auth I]	IgM C2-domain from mouse	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth J]	IPR024110	Immunoglobulin J chain	Family
B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], J [auth K], L [auth N], M [auth O], O [auth R], Q [auth T]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], J [auth K], L [auth N], M [auth O], O [auth R], Q [auth T]	IPR050380	Immune Recognition and Response Modulators	Family
B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], J [auth K], L [auth N], M [auth O], O [auth R], Q [auth T]	IPR003597	Immunoglobulin C1-set	Domain
B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], J [auth K], L [auth N], M [auth O], O [auth R], Q [auth T]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], J [auth K], L [auth N], M [auth O], O [auth R], Q [auth T]	IPR007110	Immunoglobulin-like domain	Domain
B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], J [auth K], L [auth N], M [auth O], O [auth R], Q [auth T]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
I [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
B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], B [auth C], C [auth D], D [auth E], E [auth F], F [auth G], J [auth K], L [auth N], M [auth O], O [auth R], Q [auth T]	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

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.