4R8I | pdb_00004r8i

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		e4r8iA1	A: HTH	X: HTH	H: Three-helical HTH	T: Ribosom_S12_S23	F:	ECOD (20:10:01)

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
B	Mirror-Image RNA Oligonucleotide Aptamer NOXE36	-	-	-
A	C-C motif chemokine 2	protein binding binding signaling receptor binding cytokine receptor binding G protein-coupled receptor binding chemokine receptor binding CCR 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 protein binding binding signaling receptor binding cytokine receptor binding G protein-coupled receptor binding chemokine receptor binding CCR 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 chemoattractant activity	cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication response to peptide response to chemical cellular process cellular response to cytokine stimulus cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation response to cytokine cytokine-mediated signaling pathway cell communication response to peptide response to chemical cellular process cellular response to cytokine stimulus 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 regulation of biosynthetic process positive regulation of biological process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process positive regulation of macromolecule biosynthetic process regulation of gene expression positive regulation of metabolic process biosynthetic process positive regulation of gene expression positive regulation of biosynthetic process regulation of macromolecule biosynthetic process metabolic process positive regulation of macromolecule metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular process 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 positive regulation of locomotion regulation of cell motility macrophage migration positive regulation of chemotaxis positive regulation of cell migration taxis regulation of immune system process regulation of mononuclear cell migration positive regulation of immune system process chemotaxis regulation of leukocyte chemotaxis regulation of leukocyte migration positive regulation of macrophage migration response to external stimulus positive regulation of leukocyte chemotaxis granulocyte migration regulation of response to stimulus regulation of locomotion regulation of response to external stimulus macrophage chemotaxis positive regulation of response to stimulus regulation of granulocyte chemotaxis regulation of macrophage migration positive regulation of response to external stimulus positive regulation of cell motility regulation of cell migration myeloid leukocyte migration positive regulation of mononuclear cell migration locomotion cell chemotaxis regulation of macrophage chemotaxis positive regulation of leukocyte migration regulation of chemotaxis cellular response to chemical stimulus granulocyte chemotaxis positive regulation of macrophage chemotaxis leukocyte chemotaxis 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 protein 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 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 regulation of epithelial cell proliferation vascular endothelial cell proliferation epithelial cell proliferation negative regulation of epithelial cell proliferation eosinophil chemotaxis eosinophil migration 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 positive regulation of cytosolic calcium ion concentration regulation of biological quality negative regulation of mononuclear cell migration negative regulation of locomotion negative regulation of chemotaxis regulation of lymphocyte chemotaxis natural killer cell chemotaxis negative regulation of lymphocyte migration negative regulation of cell migration negative regulation of leukocyte migration negative regulation of response to external stimulus negative regulation of cell motility negative regulation of leukocyte chemotaxis regulation of natural killer cell chemotaxis lymphocyte chemotaxis regulation of lymphocyte migration negative regulation of lymphocyte chemotaxis negative regulation of response to stimulus 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 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 positive regulation of signal transduction regulation of signal transduction glutamate receptor signaling pathway positive regulation of glutamate receptor signaling pathway regulation of glutamate receptor signaling pathway regulation of developmental process regulation of cell shape cell morphogenesis regulation of cell morphogenesis 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 chemokine (C-C motif) ligand 2 signaling pathway 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 antimicrobial humoral response antimicrobial humoral immune response mediated by antimicrobial peptide 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 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 membrane extracellular region extracellular space

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 retinal degeneration Liver Cirrhosis, Experimental heart valve disease 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 tethered spinal cord syndrome middle cerebral artery infarction pleural disease thyroid adenoma congestive heart failure thyroid gland disease pulmonary fibrosis neural tube defects, susceptibility to cystic fibrosis lung carcinoma diastematomyelia obesity disorder cancer malignant ependymoma ovarian cancer pancreatic intraductal papillary-mucinous neoplasm ileocolitis cerebrovascular disorder endometrial cancer thrombotic disease alopecia areata thyroid cancer eye disease arthritic joint disease primary hyperoxaluria interstitial lung disease autoimmune disease ischemia reperfusion injury COVID-19 type 2 diabetes mellitus bipolar disorder Crohn's colitis head and neck cancer neurenteric cyst hematologic disease lung adenocarcinoma diabetic kidney disease hyperglycemia malignant glioma drug-induced liver injury susceptibility to HIV infection adrenal cortex adenoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia pilocytic astrocytoma inborn carbohydrate metabolic disorder plasma cell neoplasm pneumonitis atopic eczema psoriasis tuberculosis myeloid neoplasm Gaucher disease juvenile dermatomyositis craniorachischisis ulcerative colitis nasopharyngeal carcinoma bipolar I disorder ureteral obstruction heart disease brain injury cutaneous lupus erythematosus neurodegenerative disease breast disease skin disease lung cancer non-small cell lung carcinoma major depressive disorder oral cavity neoplasm Duchenne and Becker muscular dystrophy pancreatic intraductal papillary-mucinous carcinoma idiopathic interstitial pneumonia systemic lupus erythematosus Emery-Dreifuss muscular dystrophy adrenal cortex carcinoma pancreatitis pituitary cancer iniencephaly arteriosclerosis disorder interstitial cystitis mycobacterium tuberculosis, susceptibility to fatty liver disease atypical teratoid rhabdoid tumor invasive ductal breast carcinoma myocardial ischemia glioblastoma 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.