4R8I

High Resolution Structure of a Mirror-Image RNA Oligonucleotide Aptamer in Complex with the Chemokine CCL2

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Interleukin 8-like chemokines	8034307	3001955	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	IL8	e4r8iA1	A: beta barrels	X: IL8-related (From Homology)	H: IL8-related	T: IL8	F: IL8	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.50.40	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00048	Small cytokines (intecrine/chemokine), interleukin-8 like (IL8)	Small cytokines (intecrine/chemokine), interleukin-8 like	Includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity. Structure contains two highly conserved disulfide bonds.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	C-C motif chemokine 2	CCR chemokine receptor binding protein binding binding signaling receptor binding cytokine receptor binding G protein-coupled receptor binding chemokine receptor binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups CCR chemokine receptor binding protein binding binding signaling receptor binding cytokine receptor binding G protein-coupled receptor binding chemokine receptor binding catalytic activity, acting on a protein kinase activity protein kinase activity transferase activity catalytic activity phosphotransferase activity, alcohol group as acceptor transferase activity, transferring phosphorus-containing groups CCR2 chemokine receptor binding molecular function activator activity signaling receptor activator activity chemokine activity molecular function regulator activity cytokine activity signaling receptor regulator activity receptor ligand activity	cellular response to stimulus 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 response to peptide response to chemical cellular response to cytokine stimulus cellular process cellular response to stimulus 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 response to peptide response to chemical cellular response to cytokine stimulus cellular process signal transduction developmental process multicellular organismal process cellular developmental process glial cell migration nervous system development neurogenesis multicellular organism development gliogenesis cell differentiation anatomical structure development astrocyte cell migration cell migration cell motility system development helper T cell extravasation T cell extravasation lymphocyte migration leukocyte migration immune system process mononuclear cell migration cellular extravasation T cell migration response to fibroblast growth factor cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus response to growth factor cellular response to fibroblast growth factor stimulus chemotaxis taxis response to external stimulus locomotion cellular component organization organelle organization cellular component organization or biogenesis cytoskeleton organization cell surface receptor signaling pathway via STAT cell surface receptor signaling pathway via JAK-STAT protein phosphorylation phosphorylation primary metabolic process macromolecule modification phosphate-containing compound metabolic process metabolic process protein metabolic process macromolecule metabolic process protein modification process phosphorus metabolic process regulation of calcium ion import regulation of calcium ion transport regulation of localization positive regulation of calcium ion transport positive regulation of calcium ion import transport regulation of transport regulation of monoatomic ion transport positive regulation of biological process establishment of localization calcium ion transport metal ion transport localization positive regulation of transport positive regulation of monoatomic ion transport monoatomic ion transport calcium ion import monoatomic cation transport regulation of metal ion transport cell adhesion negative regulation of cell population proliferation cell population proliferation endothelial cell proliferation negative regulation of biological process regulation of vascular endothelial cell proliferation negative regulation of endothelial cell proliferation negative regulation of vascular endothelial cell proliferation regulation of endothelial cell proliferation regulation of cell population proliferation negative regulation of cellular process vascular endothelial cell proliferation regulation of epithelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation cell chemotaxis eosinophil chemotaxis granulocyte migration cellular response to chemical stimulus eosinophil migration granulocyte chemotaxis myeloid leukocyte migration leukocyte chemotaxis regulation of glial cell apoptotic process negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death negative regulation of glial cell apoptotic process cell death glial cell apoptotic process negative regulation of apoptotic process apoptotic process programmed cell death cellular response to interleukin-1 response to interleukin-1 G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger G protein-coupled receptor signaling pathway cellular homeostasis homeostatic process negative regulation of mononuclear cell migration negative regulation of locomotion regulation of cell motility negative regulation of chemotaxis regulation of lymphocyte chemotaxis natural killer cell chemotaxis regulation of immune system process negative regulation of lymphocyte migration regulation of mononuclear cell migration negative regulation of cell migration regulation of leukocyte chemotaxis regulation of leukocyte migration negative regulation of leukocyte migration regulation of response to stimulus regulation of locomotion negative regulation of response to external stimulus negative regulation of cell motility negative regulation of leukocyte chemotaxis regulation of natural killer cell chemotaxis regulation of response to external stimulus lymphocyte chemotaxis regulation of lymphocyte migration regulation of cell migration negative regulation of lymphocyte chemotaxis negative regulation of response to stimulus regulation of chemotaxis negative regulation of immune system process negative regulation of natural killer cell chemotaxis anatomical structure morphogenesis animal organ development animal organ morphogenesis blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development tube morphogenesis anatomical structure formation involved in morphogenesis blood vessel development humoral immune response immune response positive regulation of cell communication modulation of chemical synaptic transmission synaptic transmission, glutamatergic regulation of synaptic transmission, glutamatergic synaptic signaling positive regulation of cellular process trans-synaptic signaling regulation of signaling positive regulation of synaptic transmission cell-cell signaling positive regulation of synaptic transmission, glutamatergic chemical synaptic transmission regulation of trans-synaptic signaling anterograde trans-synaptic signaling regulation of cell communication positive regulation of signaling viral genome replication viral process viral life cycle response to chemokine cellular response to chemokine chemokine-mediated signaling pathway biological process involved in interspecies interaction between organisms response to lipid response to other organism cellular response to lipopolysaccharide response to oxygen-containing compound cellular response to molecule of bacterial origin response to lipopolysaccharide cellular response to oxygen-containing compound response to biotic stimulus cellular response to biotic stimulus response to bacterium cellular response to lipid response to external biotic stimulus response to molecule of bacterial origin neuron apoptotic process negative regulation of neuron apoptotic process regulation of neuron apoptotic process regulation of biosynthetic process regulation of macromolecule metabolic process macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process regulation of nitric-oxide synthase biosynthetic process biosynthetic process positive regulation of biosynthetic process regulation of macromolecule biosynthetic process positive regulation of macromolecule metabolic process positive regulation of nitric-oxide synthase biosynthetic process regulation of metabolic process nitric-oxide synthase biosynthetic process regulation of developmental process regulation of cell shape cell morphogenesis regulation of cell morphogenesis regulation of biological quality regulation of anatomical structure morphogenesis cellular response to tumor necrosis factor response to tumor necrosis factor defense response response to type II interferon defense response to symbiont cellular response to type II interferon defense response to other organism response to stress innate immune response monocyte chemotaxis regulation of cell cycle phase transition negative regulation of cell cycle cell cycle phase transition regulation of cell cycle G1/S phase transition cell cycle G1/S phase transition mitotic cell cycle negative regulation of mitotic cell cycle regulation of mitotic cell cycle negative regulation of cell cycle phase transition cell cycle regulation of cell cycle cell cycle process negative regulation of G1/S transition of mitotic cell cycle negative regulation of mitotic cell cycle phase transition regulation of cell cycle process negative regulation of cell cycle G1/S phase transition negative regulation of cell cycle process regulation of mitotic cell cycle phase transition mitotic cell cycle process regulation of G1/S transition of mitotic cell cycle G1/S transition of mitotic cell cycle mitotic cell cycle phase transition positive regulation of NMDA glutamate receptor activity regulation of signaling receptor activity monoatomic ion transmembrane transport regulation of transmembrane transporter activity regulation of signal transduction regulation of monoatomic ion transmembrane transport regulation of transporter activity positive regulation of molecular function positive regulation of transmembrane transport positive regulation of monoatomic ion transmembrane transport regulation of NMDA receptor activity regulation of monoatomic ion transmembrane transporter activity positive regulation of signaling receptor activity transmembrane transport regulation of molecular function regulation of transmembrane transport positive regulation of transporter activity regulation of neurotransmitter receptor activity positive regulation of ion transmembrane transporter activity antimicrobial humoral response antimicrobial humoral immune response mediated by antimicrobial peptide positive regulation of locomotion positive regulation of cell migration positive regulation of cell motility macrophage chemotaxis macrophage migration positive regulation of endothelial cell apoptotic process positive regulation of programmed cell death positive regulation of apoptotic process endothelial cell apoptotic process regulation of endothelial cell apoptotic process inflammatory response system process sensory perception nervous system process sensory perception of pain import into cell positive regulation of cellular component organization regulation of cellular component organization positive regulation of apoptotic cell clearance vesicle-mediated transport positive regulation of endocytosis phagocytosis apoptotic cell clearance regulation of endocytosis regulation of phagocytosis regulation of vesicle-mediated transport positive regulation of phagocytosis endocytosis regulation of apoptotic cell clearance regulation of leukocyte activation regulation of cell activation positive regulation of leukocyte cell-cell adhesion lymphocyte activation leukocyte cell-cell adhesion leukocyte activation positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation cell-cell adhesion T cell activation positive regulation of leukocyte activation regulation of multicellular organismal process regulation of cell-cell adhesion positive regulation of immune system process positive regulation of T cell activation positive regulation of cell adhesion regulation of cell adhesion cell activation regulation of T cell activation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process regulation of lymphocyte activation	cellular anatomical structure extracellular region extracellular space
B	Mirror-Image RNA Oligonucleotide Aptamer NOXE36	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001811	Chemokine interleukin-8-like domain	Domain
A	IPR000827	CC chemokine, conserved site	Conserved Site
A	IPR036048	Chemokine interleukin-8-like superfamily	Homologous Superfamily
A	IPR039809	Chemokine beta/gamma/delta	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: P13500	plasma cell myeloma pneumonia asthma status epilepticus Crohn disease silicosis squamous cell carcinoma Duchenne muscular dystrophy adult acute respiratory distress syndrome atherosclerosis glomerulonephritis liver disease hypertensive disorder influenza autoimmune hepatitis plasma cell myeloma pneumonia asthma status epilepticus Crohn disease silicosis squamous cell carcinoma Duchenne muscular dystrophy adult acute respiratory distress syndrome atherosclerosis glomerulonephritis liver disease hypertensive disorder influenza autoimmune hepatitis pulmonary tuberculosis calcinosis metabolic syndrome X cirrhosis of liver coronary artery disease heart valve disease retinal degeneration Liver Cirrhosis, Experimental brain ischemia spina bifida carotid artery disease inflammatory bowel disease chronic kidney disease pulmonary hypertension neural tube defect cutaneous leishmaniasis endometrial carcinoma allergic disease thyroid gland carcinoma interstitial nephritis schizophrenia HIV infectious disease cardiovascular disease middle cerebral artery infarction tethered spinal cord syndrome pleural disease thyroid adenoma congestive heart failure thyroid gland disease pulmonary fibrosis neural tube defects, susceptibility to cystic fibrosis diastematomyelia obesity disorder lung carcinoma ovarian cancer cancer malignant ependymoma pancreatic intraductal papillary-mucinous neoplasm endometrial cancer ileocolitis cerebrovascular disorder alopecia areata thrombotic disease eye disease arthritic joint disease thyroid cancer primary hyperoxaluria interstitial lung disease type 2 diabetes mellitus autoimmune disease ischemia reperfusion injury COVID-19 head and neck cancer bipolar disorder Crohn's colitis neurenteric cyst hematologic disease diabetic kidney disease lung adenocarcinoma drug-induced liver injury hyperglycemia malignant glioma adrenal cortex adenoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia susceptibility to HIV infection pilocytic astrocytoma inborn carbohydrate metabolic disorder plasma cell neoplasm pneumonitis myeloid neoplasm Gaucher disease atopic eczema psoriasis tuberculosis ulcerative colitis nasopharyngeal carcinoma juvenile dermatomyositis craniorachischisis ureteral obstruction heart disease bipolar I disorder cutaneous lupus erythematosus neurodegenerative disease brain injury non-small cell lung carcinoma breast disease skin disease lung cancer oral cavity neoplasm major depressive disorder Duchenne and Becker muscular dystrophy pancreatic intraductal papillary-mucinous carcinoma Emery-Dreifuss muscular dystrophy adrenal cortex carcinoma pancreatitis idiopathic interstitial pneumonia systemic lupus erythematosus pituitary cancer arteriosclerosis disorder iniencephaly mycobacterium tuberculosis, susceptibility to fatty liver disease interstitial cystitis myocardial ischemia glioblastoma atypical teratoid rhabdoid tumor invasive ductal breast carcinoma Becker muscular dystrophy kidney disease

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.