9M6M | pdb_00009m6m

Atomic-Level Architecture and Assembly Mechanism of High-order Structures of RIPK1 Fibril Network Revealed by Integrated Structural Biology

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E	PF12721	RIP homotypic interaction motif (RHIM)	RIP homotypic interaction motif	-	Motif

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E	Receptor-interacting serine/threonine-protein kinase 1	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule 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-containing complex binding protein binding signaling receptor binding cytokine receptor binding tumor necrosis factor receptor superfamily binding death receptor binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity death domain binding protein domain specific binding protein serine kinase activity identical protein binding protein homodimerization activity protein dimerization activity protein serine/threonine kinase activity	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process response to cytokine regulation of signal transduction positive regulation of response to cytokine stimulus cytokine-mediated signaling pathway cell communication positive regulation of tumor necrosis factor-mediated signaling pathway positive regulation of response to stimulus cellular response to tumor necrosis factor cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process response to cytokine regulation of signal transduction positive regulation of response to cytokine stimulus cytokine-mediated signaling pathway cell communication positive regulation of tumor necrosis factor-mediated signaling pathway positive regulation of response to stimulus cellular response to tumor necrosis factor tumor necrosis factor-mediated signaling pathway cellular response to cytokine stimulus signal transduction positive regulation of cellular process regulation of biological process regulation of signaling cell surface receptor signaling pathway regulation of tumor necrosis factor-mediated signaling pathway regulation of cytokine-mediated signaling pathway biological regulation response to peptide regulation of response to cytokine stimulus regulation of response to stimulus response to chemical regulation of cell communication cellular process response to tumor necrosis factor positive regulation of cytokine-mediated signaling pathway positive regulation of signaling regulation of defense response regulation of response to external stimulus defense response response to external stimulus regulation of inflammatory response positive regulation of response to external stimulus positive regulation of inflammatory response regulation of response to stress response to stress positive regulation of defense response inflammatory response protein-containing complex organization necroptotic process ripoptosome assembly involved in necroptotic process programmed necrotic cell death cell death ripoptosome assembly cellular component organization cellular component biogenesis cellular component assembly protein-containing complex assembly cellular component organization or biogenesis programmed cell death apoptotic process positive regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death positive regulation of apoptotic process catabolic process metabolic process primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process neuron apoptotic process positive regulation of neuron apoptotic process regulation of neuron apoptotic process regulation of execution phase of apoptosis positive regulation of execution phase of apoptosis execution phase of apoptosis necroptotic signaling pathway extrinsic apoptotic signaling pathway via death domain receptors extrinsic apoptotic signaling pathway apoptotic signaling pathway protein phosphorylation protein autophosphorylation phosphorylation macromolecule modification phosphate-containing compound metabolic process protein modification process phosphorus metabolic process multicellular organismal process positive regulation of interleukin-8 production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process cytokine production regulation of cytokine production positive regulation of macromolecule metabolic process regulation of multicellular organismal process regulation of biosynthetic process interleukin-8 production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process positive regulation of cytokine production regulation of metabolic process regulation of interleukin-8 production intracellular signal transduction positive regulation of JNK cascade regulation of intracellular signal transduction JNK cascade intracellular signaling cassette positive regulation of MAPK cascade regulation of JNK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade MAPK cascade negative regulation of biological process positive regulation of post-transcriptional gene silencing regulation of primary metabolic process nucleobase-containing compound metabolic process post-transcriptional regulation of gene expression positive regulation of post-transcriptional gene silencing by RNA RNA processing negative regulation of metabolic process regulation of miRNA processing miRNA-mediated post-transcriptional gene silencing negative regulation of gene expression negative regulation of macromolecule biosynthetic process post-transcriptional gene silencing miRNA processing RNA metabolic process regulation of miRNA-mediated gene silencing RNA biosynthetic process nucleic acid biosynthetic process positive regulation of miRNA-mediated gene silencing regulation of regulatory ncRNA processing regulation of gene silencing by regulatory ncRNA negative regulation of cellular process regulation of post-transcriptional gene silencing by regulatory ncRNA positive regulation of miRNA processing negative regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process regulatory ncRNA-mediated post-transcriptional gene silencing nucleic acid metabolic process regulatory ncRNA-mediated gene silencing regulatory ncRNA processing regulation of post-transcriptional gene silencing negative regulation of biosynthetic process positive regulation of DNA-binding transcription factor activity positive regulation of NF-kappaB transcription factor activity positive regulation of molecular function DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of molecular function regulation of DNA-binding transcription factor activity regulation of DNA-templated transcription myeloid leukocyte differentiation regulation of leukocyte differentiation cellular developmental process regulation of developmental process cell development regulation of cell differentiation mononuclear cell differentiation regulation of cell development positive regulation of developmental process multicellular organism development positive regulation of cell differentiation positive regulation of hemopoiesis cell differentiation anatomical structure development regulation of immune system process regulation of macrophage differentiation positive regulation of immune system process developmental process regulation of multicellular organismal development hemopoiesis regulation of myeloid cell differentiation positive regulation of cell development macrophage differentiation regulation of myeloid leukocyte differentiation positive regulation of myeloid leukocyte differentiation positive regulation of macrophage differentiation myeloid cell differentiation immune system process positive regulation of myeloid cell differentiation regulation of hemopoiesis positive regulation of leukocyte differentiation leukocyte differentiation negative regulation of signaling negative regulation of cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of response to stimulus negative regulation of programmed cell death negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic process regulation of apoptotic signaling pathway interleukin-6-mediated signaling pathway cellular response to interleukin-6 positive regulation of interleukin-6-mediated signaling pathway response to interleukin-6 regulation of interleukin-6-mediated signaling pathway positive regulation of DNA-templated transcription transcription by RNA polymerase II regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process positive regulation of canonical NF-kappaB signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction negative regulation of extrinsic apoptotic signaling pathway in absence of ligand signal transduction in absence of ligand negative regulation of signal transduction in absence of ligand extrinsic apoptotic signaling pathway in absence of ligand regulation of extrinsic apoptotic signaling pathway in absence of ligand lymphocyte apoptotic process leukocyte apoptotic process T cell apoptotic process negative regulation of intracellular signal transduction negative regulation of canonical NF-kappaB signal transduction supramolecular fiber organization amyloid fibril formation positive regulation of apoptotic signaling pathway positive regulation of extrinsic apoptotic signaling pathway negative regulation of necroptotic process regulation of necroptotic process negative regulation of programmed necrotic cell death regulation of programmed necrotic cell death cellular response to oxidative stress response to oxygen-containing compound cellular response to chemical stress cellular response to oxygen-containing compound cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species cellular response to chemical stimulus cellular response to stress cellular response to endogenous stimulus cellular response to growth factor stimulus response to endogenous stimulus response to growth factor regulation of non-canonical NF-kappaB signal transduction non-canonical NF-kappaB signal transduction positive regulation of non-canonical NF-kappaB signal transduction peptidyl-serine modification peptidyl-serine phosphorylation peptidyl-amino acid modification peptidyl-serine autophosphorylation positive regulation of necroptotic process positive regulation of programmed necrotic cell death positive regulation of phosphorylation positive regulation of phosphorus metabolic process positive regulation of phosphate metabolic process regulation of phosphorus metabolic process regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of protein modification process positive regulation of protein phosphorylation regulation of protein metabolic process regulation of tumor necrosis factor production positive regulation of tumor necrosis factor superfamily cytokine production tumor necrosis factor superfamily cytokine production positive regulation of tumor necrosis factor production tumor necrosis factor production regulation of tumor necrosis factor superfamily cytokine production reactive oxygen species metabolic process regulation of reactive oxygen species metabolic process	protein-containing complex receptor complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cell periphery plasma membrane protein complex membrane plasma membrane protein-containing complex receptor complex membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle cell periphery plasma membrane protein complex membrane plasma membrane death-inducing signaling complex membrane protein complex ripoptosome catalytic complex cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E	IPR000719	Protein kinase domain	Domain
A, B, C, D, E	IPR025735	RIP homotypic interaction motif	Binding Site
A, B, C, D, E	IPR000488	Death domain	Domain
A, B, C, D, E	IPR051681	Serine/Threonine Kinases and Pseudokinases	Family
A, B, C, D, E	IPR001245	Serine-threonine/tyrosine-protein kinase, catalytic domain	Domain
A, B, C, D, E	IPR011029	Death-like domain superfamily	Homologous Superfamily
A, B, C, D, E	IPR011009	Protein kinase-like domain superfamily	Homologous Superfamily
A, B, C, D, E	IPR037934	RIP1, Death domain	Domain
A, B, C, D, E	IPR008271	Serine/threonine-protein kinase, active site	Active Site

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.