1XU2

The crystal structure of APRIL bound to BCMA

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	d1xu2a_	All beta proteins	TNF-like	TNF-like	TNF-like	A proliferation-inducing ligand, APRIL	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d1xu2b_	All beta proteins	TNF-like	TNF-like	TNF-like	A proliferation-inducing ligand, APRIL	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth D]	d1xu2d_	All beta proteins	TNF-like	TNF-like	TNF-like	A proliferation-inducing ligand, APRIL	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D [auth R]	d1xu2r_	Small proteins	TNF receptor-like	TNF receptor-like	BAFF receptor-like	Tumor necrosis factor receptor superfamily member 17, BCMA	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E [auth S]	d1xu2s_	Small proteins	TNF receptor-like	TNF receptor-like	BAFF receptor-like	Tumor necrosis factor receptor superfamily member 17, BCMA	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
F [auth T]	d1xu2t_	Small proteins	TNF receptor-like	TNF receptor-like	BAFF receptor-like	Tumor necrosis factor receptor superfamily member 17, BCMA	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)
A	SCOP2B Superfamily	TNF-like	8044164	3000061	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	TNF-like	8044164	3000061	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	TNF-like	8044164	3000061	SCOP2B (2022-06-29)
D [auth R]	SCOP2 Family	BAFF receptor-like	8031788	4003853	SCOP2 (2022-06-29)
D [auth R]	SCOP2 Superfamily	TNF receptor-like	8044166	3000971	SCOP2 (2022-06-29)
E [auth S]	SCOP2B Superfamily	TNF receptor-like	8044166	3000971	SCOP2B (2022-06-29)
F [auth T]	SCOP2B Superfamily	TNF receptor-like	8044166	3000971	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	PF00229	e1xu2A1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: PF00229	ECOD (1.6)
B	PF00229	e1xu2B1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: PF00229	ECOD (1.6)
C [auth D]	PF00229	e1xu2D1	A: beta sandwiches	X: jelly-roll	H: TNF-like (From Topology)	T: TNF-like	F: PF00229	ECOD (1.6)
D [auth R]	PF09257	e1xu2R1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: PF09257	ECOD (1.6)
E [auth S]	PF09257	e1xu2S1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: PF09257	ECOD (1.6)
F [auth T]	PF09257	e1xu2T1	A: few secondary structure elements	X: EGF-like	H: EGF-related	T: TNF receptor-like	F: PF09257	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
B	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
C [auth D]	2.60.120.40	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C [auth D]	PF00229	TNF(Tumour Necrosis Factor) family (TNF)	TNF(Tumour Necrosis Factor) family	-	Domain
D [auth R], E [auth S], F [auth T]	PF09257	BCMA, TALL-1 binding (BCMA-Tall_bind)	BCMA, TALL-1 binding	Members of this family, which are predominantly found in the tumour necrosis factor receptor superfamily member 17, BCMA, are required for binding to tumour necrosis factor ligand TALL-1 [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C [auth D]	Tumor necrosis factor ligand superfamily member 13	protein binding binding molecular function activator activity signaling receptor binding molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity cytokine receptor binding tumor necrosis factor receptor superfamily binding tumor necrosis factor receptor binding	regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation regulation of cell population proliferation biological regulation positive regulation of biological process cellular process positive regulation of cellular process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus immune response immune system process regulation of biological process cell population proliferation regulation of cellular process positive regulation of cell population proliferation regulation of cell population proliferation biological regulation positive regulation of biological process cellular process positive regulation of cellular process adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains lymphocyte mediated immunity response to stimulus immune response immune system process B cell mediated immunity leukocyte mediated immunity immunoglobulin mediated immune response adaptive immune response immune effector process developmental process anatomical structure morphogenesis anatomical structure formation involved in morphogenesis anatomical structure development germinal center formation regulation of response to stimulus regulation of immune response regulation of immune system process regulation of leukocyte activation regulation of cell activation B cell activation involved in immune response positive regulation of macromolecule biosynthetic process regulation of primary metabolic process multicellular organism development positive regulation of immune response organic substance biosynthetic process positive regulation of macromolecule metabolic process positive regulation of isotype switching to IgA isotypes system development positive regulation of DNA recombination positive regulation of immunoglobulin mediated immune response DNA recombination cellular metabolic process primary metabolic process DNA metabolic process regulation of gene expression biosynthetic process positive regulation of DNA metabolic process positive regulation of production of molecular mediator of immune response metabolic process regulation of macromolecule biosynthetic process regulation of DNA metabolic process immunoglobulin production regulation of developmental process positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains somatic cell DNA recombination positive regulation of cellular metabolic process somatic diversification of immunoglobulins involved in immune response positive regulation of lymphocyte activation somatic recombination of immunoglobulin gene segments positive regulation of biosynthetic process regulation of immunoglobulin mediated immune response leukocyte activation involved in immune response regulation of B cell activation positive regulation of isotype switching positive regulation of immune effector process production of molecular mediator of immune response positive regulation of immunoglobulin production regulation of isotype switching cell activation isotype switching to IgA isotypes regulation of macromolecule metabolic process macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process positive regulation of gene expression somatic diversification of immune receptors via germline recombination within a single locus positive regulation of cellular biosynthetic process regulation of lymphocyte activation multicellular organismal process regulation of immune effector process regulation of DNA recombination positive regulation of leukocyte mediated immunity cell activation involved in immune response nucleobase-containing compound metabolic process positive regulation of developmental process positive regulation of cell activation positive regulation of metabolic process positive regulation of leukocyte activation somatic diversification of immune receptors regulation of nucleobase-containing compound metabolic process positive regulation of adaptive immune response positive regulation of immune system process somatic recombination of immunoglobulin genes involved in immune response positive regulation of nucleobase-containing compound metabolic process regulation of adaptive immune response regulation of cellular metabolic process regulation of B cell mediated immunity somatic diversification of immunoglobulins organic cyclic compound metabolic process regulation of leukocyte mediated immunity positive regulation of multicellular organismal process macromolecule metabolic process regulation of production of molecular mediator of immune response regulation of metabolic process isotype switching immune system development immunoglobulin production involved in immunoglobulin-mediated immune response positive regulation of lymphocyte mediated immunity cellular biosynthetic process regulation of isotype switching to IgA isotypes lymphocyte activation positive regulation of B cell mediated immunity leukocyte activation positive regulation of response to stimulus organic substance metabolic process regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains regulation of multicellular organismal process lymphocyte activation involved in immune response regulation of biosynthetic process B cell activation gene expression positive regulation of B cell activation regulation of lymphocyte mediated immunity regulation of immunoglobulin production positive regulation of germinal center formation regulation of germinal center formation regulation of anatomical structure morphogenesis	cell periphery cell surface membrane plasma membrane cellular anatomical entity external side of plasma membrane side of membrane intracellular anatomical structure cytoplasm extracellular region extracellular space
D [auth R], E [auth S], F [auth T]	Tumor necrosis factor receptor superfamily member 17	molecular transducer activity signaling receptor activity	multicellular organismal process multicellular organismal-level homeostasis leukocyte homeostasis homeostatic process immune system process homeostasis of number of cells lymphocyte homeostasis response to stimulus immune response adaptive immune response cellular response to stimulus regulation of biological process regulation of cellular process signaling multicellular organismal process multicellular organismal-level homeostasis leukocyte homeostasis homeostatic process immune system process homeostasis of number of cells lymphocyte homeostasis response to stimulus immune response adaptive immune response cellular response to stimulus regulation of biological process regulation of cellular process signaling biological regulation cellular process signal transduction cell communication response to organic substance cell surface receptor signaling pathway response to cytokine cytokine-mediated signaling pathway cellular response to chemical stimulus cellular response to tumor necrosis factor response to chemical tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus cellular response to organic substance response to tumor necrosis factor	cellular anatomical entity endomembrane system cell periphery plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C [auth D]	IPR008983	Tumour necrosis factor-like domain superfamily	Homologous Superfamily
A, B, C [auth D]	IPR006052	Tumour necrosis factor domain	Domain
A, B, C [auth D]	IPR021184	Tumour necrosis factor, conserved site	Conserved Site
D [auth R], E [auth S], F [auth T]	IPR022320	Tumour necrosis factor receptor 17	Family
D [auth R], E [auth S], F [auth T]	IPR015337	BCMA, TALL-1 binding	Domain
D [auth R], E [auth S], F [auth T]	IPR043521	Tumor necrosis factor receptor 13C/17	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth R], E [auth S], F [auth T]	Pharos: Q02223	gastric carcinoma cancer exocrine pancreatic carcinoma hepatocellular carcinoma malignant colon neoplasm osteosarcoma Relapse multiple myeloma tuberculosis cutaneous lupus erythematosus gastric cancer interstitial cystitis malignant pancreatic neoplasm periodontitis sinusitis ulcerative colitis gastric carcinoma cancer exocrine pancreatic carcinoma hepatocellular carcinoma malignant colon neoplasm osteosarcoma Relapse multiple myeloma tuberculosis cutaneous lupus erythematosus gastric cancer interstitial cystitis malignant pancreatic neoplasm periodontitis sinusitis ulcerative colitis cystic fibrosis lung cancer MALT lymphoma plasma cell myeloma Sjogren syndrome

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.