3UX9

Structural insights into a human anti-IFN antibody exerting therapeutic potential for systemic lupus erythematosus

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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	d3ux9a_	All alpha proteins	4-helical cytokines	4-helical cytokines	Interferons/interleukin-10 (IL-10)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3ux9c_	All alpha proteins	4-helical cytokines	4-helical cytokines	Interferons/interleukin-10 (IL-10)	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3ux9b1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3ux9d1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	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	SCOP2 Family	Interferons/interleukin-10 (IL-10)	8070376	4000854	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	4-helical cytokines	8070377	3001717	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	4-helical cytokines	8070377	3001717	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	PF00143	e3ux9A1	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: 4-helical cytokines (From Topology)	T: 4-helical cytokines	F: PF00143	ECOD (1.6)
C	PF00143	e3ux9C2	A: alpha bundles	X: Ferritin/Heme oxygenase/4-helical cytokines	H: 4-helical cytokines (From Topology)	T: 4-helical cytokines	F: PF00143	ECOD (1.6)
B	PF07686	e3ux9B4	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
D	PF07686	e3ux9D6	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.20.1250.10	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	CATH (4.3.0)
C	1.20.1250.10	Mainly Alpha	Up-down Bundle	Growth Hormone	Chain: A	CATH (4.3.0)
B	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D	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
B, D	scFv, anti-IFN	V-LAMBDA-VH	Homo sapiens (human)	IGLV1-4401, IGLJ302, IGHV3-2304, IGHJ401, IGHJ402, IGHJ403	V-DOMAIN V-LAMBDA, V-DOMAIN VH	IG	SCFV-LAMBDA-HEAVY	IMGT (202416-0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF00143	Interferon alpha/beta domain (Interferon)	Interferon alpha/beta domain	Type I interferons (alpha, beta) belong to the larger helical cytokine superfamily,which includes growth hormones, interleukins, several colony-stimulating factors and several other regulatory molecules.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	Interferon alpha-1/13	protein-containing complex binding binding protein binding type I interferon receptor binding signaling receptor binding cytokine receptor binding molecular function activator activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity	multicellular organismal process cell population proliferation B cell activation cell activation B cell proliferation lymphocyte activation leukocyte proliferation leukocyte activation immune system process mononuclear cell proliferation lymphocyte proliferation cellular process cellular response to stimulus response to organic substance multicellular organismal process cell population proliferation B cell activation cell activation B cell proliferation lymphocyte activation leukocyte proliferation leukocyte activation immune system process mononuclear cell proliferation lymphocyte proliferation cellular process cellular response to stimulus response to organic substance regulation of biological process regulation of cellular process response to stimulus cell surface receptor signaling pathway signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication cellular response to chemical stimulus response to chemical cellular response to cytokine stimulus cellular response to organic substance signal transduction developmental process cellular developmental process hemopoiesis cell development mononuclear cell differentiation lymphocyte differentiation B cell differentiation cell differentiation anatomical structure development leukocyte differentiation immune response adaptive immune response natural killer cell activation cell activation involved in immune response immune effector process natural killer cell activation involved in immune response leukocyte activation involved in immune response lymphocyte activation involved in immune response humoral immune response response to dsRNA response to nitrogen compound response to exogenous dsRNA response to organic cyclic compound T cell activation involved in immune response T cell activation biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to virus defense response to other organism response to stress response to external biotic stimulus response to virus cellular response to virus positive regulation of phosphorylation regulation of peptidyl-serine phosphorylation regulation of signal transduction positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process peptidyl-amino acid modification regulation of receptor signaling pathway via JAK-STAT positive regulation of macromolecule metabolic process protein modification process phosphorus metabolic process positive regulation of protein phosphorylation positive regulation of peptidyl-serine phosphorylation of STAT protein protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process cellular metabolic process primary metabolic process regulation of cellular metabolic process serine phosphorylation of STAT protein regulation of response to stimulus macromolecule modification metabolic process regulation of phosphorus metabolic process macromolecule metabolic process regulation of receptor signaling pathway via STAT regulation of metabolic process cell surface receptor signaling pathway via STAT regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of biological process regulation of peptidyl-serine phosphorylation of STAT protein positive regulation of cellular metabolic process peptidyl-serine modification positive regulation of protein modification process organic substance metabolic process peptidyl-serine phosphorylation protein metabolic process positive regulation of cellular process regulation of signaling organonitrogen compound metabolic process regulation of macromolecule metabolic process positive regulation of peptidyl-serine phosphorylation regulation of cell communication regulation of phosphorylation cell surface receptor signaling pathway via JAK-STAT interferon-mediated signaling pathway cellular response to type I interferon innate immune response type I interferon-mediated signaling pathway response to type I interferon	extracellular region cellular anatomical entity extracellular space
B, D	ScFv antibody	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR000471	Interferon alpha/beta/delta	Family
A, C	IPR009079	Four-helical cytokine-like, core	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C	Pharos: P01562	VIPoma hepatitis B virus infection adult T-cell leukemia/lymphoma melanoma Liver Cirrhosis, Experimental colorectal cancer skin disease liver cancer pancreatic cholera tubular adenocarcinoma granular cell carcinoma adenocarcinoma cirrhosis of liver epilepsy HIV infectious disease VIPoma hepatitis B virus infection adult T-cell leukemia/lymphoma melanoma Liver Cirrhosis, Experimental colorectal cancer skin disease liver cancer pancreatic cholera tubular adenocarcinoma granular cell carcinoma adenocarcinoma cirrhosis of liver epilepsy HIV infectious disease leukopenia lymphatic system disease malignant pancreatic neoplasm AIDS microphthalmia with limb anomalies bipolar disorder peripheral nervous system disease COVID-19 vaginal cancer cutaneous melanoma hepatitis C virus infection influenza liver disease acute T cell leukemia major depressive disorder arthritic joint disease cancer peripheral neuropathy colorectal carcinoma cribriform carcinoma hepatocellular carcinoma kidney disease liver neoplasm autoimmune disease pancreatic neoplasm pneumonia cribriform carcinoma of breast

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.