3R66 | pdb_00003r66

Crystal structure of human ISG15 in complex with NS1 N-terminal region from influenza virus B, Northeast Structural Genomics Consortium Target IDs HX6481, HR2873, and OR2

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
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B	d3r66b_	All alpha proteins	S15/NS1 RNA-binding domain	S15/NS1 RNA-binding domain	N-terminal, RNA-binding domain of nonstructural protein NS1	N-terminal, RNA-binding domain of nonstructural protein NS1	(Influenza B virus (B/Lee/1940) ) [TaxId: 518987 ],	SCOPe (2.08)
A	d3r66a_	All alpha proteins	S15/NS1 RNA-binding domain	S15/NS1 RNA-binding domain	N-terminal, RNA-binding domain of nonstructural protein NS1	N-terminal, RNA-binding domain of nonstructural protein NS1	(Influenza B virus (B/Lee/1940) ) [TaxId: 518987 ],	SCOPe (2.08)
D	d3r66d2	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3r66d1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3r66c2	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	Ubiquitin-related	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3r66c1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	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)
B	SCOP2B Superfamily	S15/NS1 RNA-binding domain	8033708	3001284	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	S15/NS1 RNA-binding domain	8033708	3001284	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ubiquitin-like	8035114	3000157	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ubiquitin-like	8035116	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8035116	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8035114	3000157	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)
B	Flavin_Reduct	e3r66B1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Flavin_Reduct	ECOD (develop294)
A	M20_dimer	e3r66A1	A: alpha bundles	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: M20_dimer	ECOD (develop294)
D	Flavin_Reduct	e3r66D1	A: alpha bundles	X: Lipocalins/Streptavidin	H: Zn-dependent exopeptidases	T: Zn-dependent exopeptidases	F: Flavin_Reduct	ECOD (develop294)
C	Anemone_cytotox	e3r66C1	A: alpha bundles	X: EF-hand	H: Insect pheromone/odorant-binding proteins	T: Insect pheromone/odorant-binding proteins	F: Anemone_cytotox	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.287.10	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	S15/NS1, RNA-binding	CATH (4.3.0)
A	1.10.287.10	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	S15/NS1, RNA-binding	CATH (4.3.0)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C, D	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Non-structural protein 1	enzyme regulator activity protein kinase inhibitor activity molecular function inhibitor activity molecular function regulator activity enzyme inhibitor activity protein kinase regulator activity protein serine/threonine kinase inhibitor activity kinase inhibitor activity kinase regulator activity RNA binding binding nucleic acid binding	symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host ISG15-protein conjugation biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host immune response biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host process symbiont-mediated perturbation of host innate immune response modulation of process of another organism symbiont-mediated perturbation of host cellular process response to stimulus response to other organism symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host ISG15-protein conjugation biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host immune response biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host process symbiont-mediated perturbation of host innate immune response modulation of process of another organism symbiont-mediated perturbation of host cellular process response to stimulus response to other organism symbiont-mediated perturbation of host defenses symbiont-mediated suppression of host PKR/eIFalpha signaling symbiont-mediated response to host defenses response to external stimulus response to biotic stimulus symbiont-mediated suppression of host signal transduction pathway symbiont-mediated suppression of host-directed shutoff of host translation symbiont-mediated suppression of host defenses response to host response to external biotic stimulus symbiont-mediated perturbation of host signal transduction pathway symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated suppression of host type I interferon-mediated signaling pathway	host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus other organism part host intracellular organelle host cell cytoplasm
C, D	Ubiquitin-like protein ISG15	cell adhesion molecule binding protein-containing complex binding protein binding binding integrin binding signaling receptor binding protein tag activity molecular tag activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding	negative regulation of post-translational protein modification regulation of cellular process regulation of protein modification process negative regulation of biological process regulation of protein ubiquitination regulation of primary metabolic process protein ubiquitination negative regulation of protein modification process negative regulation of cellular process protein metabolic process negative regulation of protein ubiquitination regulation of protein modification by small protein conjugation or removal protein modification process negative regulation of protein metabolic process negative regulation of post-translational protein modification regulation of cellular process regulation of protein modification process negative regulation of biological process regulation of protein ubiquitination regulation of primary metabolic process protein ubiquitination negative regulation of protein modification process negative regulation of cellular process protein metabolic process negative regulation of protein ubiquitination regulation of protein modification by small protein conjugation or removal protein modification process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biological process negative regulation of protein modification by small protein conjugation or removal regulation of post-translational protein modification regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process macromolecule modification metabolic process cellular process macromolecule metabolic process post-translational protein modification regulation of metabolic process protein modification by small protein conjugation protein modification by small protein conjugation or removal cellular response to stimulus response to stimulus regulation of type I interferon-mediated signaling pathway response to cytokine regulation of signal transduction response to biotic stimulus cell communication interferon-mediated signaling pathway cellular response to type I interferon cellular response to cytokine stimulus regulation of immune system process signal transduction immune response response to other organism regulation of innate immune response negative regulation of immune response response to external stimulus regulation of response to cytokine stimulus negative regulation of response to cytokine stimulus regulation of response to stimulus response to chemical defense response to other organism negative regulation of response to external stimulus negative regulation of defense response regulation of immune response response to type I interferon regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of response to external stimulus negative regulation of response to biotic stimulus negative regulation of signaling signaling negative regulation of cell communication cytokine-mediated signaling pathway response to stress regulation of response to stress innate immune response response to external biotic stimulus regulation of signaling cell surface receptor signaling pathway negative regulation of response to stimulus defense response regulation of cytokine-mediated signaling pathway defense response to symbiont negative regulation of signal transduction response to peptide negative regulation of immune system process negative regulation of cytokine-mediated signaling pathway immune system process type I interferon-mediated signaling pathway regulation of cell communication negative regulation of type I interferon-mediated signaling pathway negative regulation of innate immune response catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process protein catabolic process macromolecule catabolic process integrin-mediated signaling pathway regulation of biosynthetic process multicellular organismal process regulation of type II interferon production type II interferon production gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process cytokine production regulation of cytokine production regulation of macromolecule biosynthetic process regulation of multicellular organismal process ISG15-protein conjugation regulation of developmental process positive regulation of biological process regulation of biomineral tissue development regulation of bone mineralization positive regulation of ossification positive regulation of developmental process multicellular organism development positive regulation of biomineral tissue development ossification anatomical structure development biomineral tissue development developmental process regulation of multicellular organismal development bone mineralization animal organ development tissue development positive regulation of bone mineralization positive regulation of multicellular organismal process regulation of ossification defense response to bacterium response to bacterium positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of interferon-beta production interferon-beta production positive regulation of cellular process positive regulation of type I interferon production type I interferon production positive regulation of gene expression positive regulation of interferon-beta production positive regulation of cytokine production regulation of type I interferon production regulation of cellular component organization positive regulation of cellular component organization protein-containing complex organization positive regulation of cellular component biogenesis regulation of protein oligomerization regulation of cellular component biogenesis cellular component biogenesis cellular component organization regulation of protein-containing complex assembly positive regulation of protein-containing complex assembly cellular component assembly positive regulation of protein oligomerization protein complex oligomerization protein-containing complex assembly cellular component organization or biogenesis cellular developmental process homeostatic process cell development regulation of cell differentiation regulation of cell development positive regulation of cell differentiation cell differentiation myeloid cell homeostasis erythrocyte homeostasis hemopoiesis regulation of myeloid cell differentiation erythrocyte differentiation regulation of erythrocyte differentiation positive regulation of erythrocyte differentiation multicellular organismal-level homeostasis myeloid cell differentiation positive regulation of myeloid cell differentiation regulation of hemopoiesis homeostasis of number of cells interleukin-10 production regulation of interleukin-10 production positive regulation of interleukin-10 production localization protein localization to organelle macromolecule localization protein localization to mitochondrion intracellular protein localization negative regulation of viral genome replication viral life cycle negative regulation of viral process regulation of viral process regulation of viral life cycle viral genome replication viral process regulation of viral genome replication response to virus defense response to virus positive regulation of type II interferon production	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR009068	uS15/NS1, RNA-binding domain superfamily	Homologous Superfamily
A, B	IPR004208	Influenza non-structural protein (NS1)	Family
C, D	IPR000626	Ubiquitin-like domain	Domain
C, D	IPR015496	Ubiquilin	Family
C, D	IPR019956	Ubiquitin domain	Domain
C, D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
C, D	Pharos: P05161	mendelian susceptibility to mycobacterial diseases due to complete ISG15 deficiency influenza malignant mesothelioma ovarian cancer pilocytic astrocytoma atopic eczema Sjogren syndrome breast carcinoma tuberculosis cystic fibrosis exocrine pancreatic carcinoma juvenile dermatomyositis lung adenocarcinoma malignant pancreatic neoplasm microphthalmia with limb anomalies mendelian susceptibility to mycobacterial diseases due to complete ISG15 deficiency influenza malignant mesothelioma ovarian cancer pilocytic astrocytoma atopic eczema Sjogren syndrome breast carcinoma tuberculosis cystic fibrosis exocrine pancreatic carcinoma juvenile dermatomyositis lung adenocarcinoma malignant pancreatic neoplasm microphthalmia with limb anomalies pancreatic ductal adenocarcinoma plasma cell myeloma Barrett esophagus subependymal giant cell astrocytoma Crohn disease ulcerative colitis dermatomyositis glioblastoma interstitial cystitis large cell medulloblastoma malignant ependymoma medulloblastoma multiple sclerosis pancreatic intraductal papillary-mucinous neoplasm psoriasis breast cancer systemic lupus erythematosus cutaneous lupus erythematosus esophageal adenocarcinoma hepatocellular carcinoma invasive ductal breast carcinoma Liver carcinoma

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C, D	CSD	Parent Component: CYS RESID: AA0262 PSI-MOD : L-cysteine sulfinic acid MOD:00267

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.