Affinage

COPE

Coatomer subunit epsilon · UniProt O14579

Length
308 aa
Mass
34.5 kDa
Annotated
2026-06-09
100 papers in source corpus 6 papers cited in narrative 6 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 4/4 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

COPE (epsilon-COP) is a structural subunit of the coatomer (COPI) complex that maintains coatomer integrity and is required for Golgi structure and ER-through-Golgi membrane transport (PMID:8207054). Its core molecular role is to stabilize alpha-COP and the assembled coatomer: in yeast, epsilon-COP overproduction rescues an alpha-COP mutant and its deletion causes rapid loss of alpha-COP and a block in ER-to-Golgi transport, with allele-specific synthetic lethality establishing a direct functional partnership (PMID:9463377). Structurally, epsilon-COP adopts a tetratricopeptide repeat (TPR) fold whose repeats form a circular bracelet that wraps around and interlocks with a beta-hairpin of the alpha-COP C-terminal domain, and the resulting heterodimer directly contacts the Dsl1 tethering complex, indicating exposure on the COPI vesicle surface (PMID:20534429). Loss of epsilon-COP function in mammalian ldlF cells vesiculates the Golgi, blocks ER-to-Golgi transport and endocytic recycling of the LDL receptor, and impairs canonical retrograde Golgi transport (PMID:8207054, PMID:12847103); a single Glu251Lys substitution renders the protein thermolabile, and its destabilization accounts for these transport and morphological defects (PMID:8626666). No COPE-linked human Mendelian disease appears in the available corpus.

Mechanistic history

Synthesis pass · year-by-year structured walk · 6 steps
  1. 1994 High

    Established that epsilon-COP/coatomer is functionally required in cells, linking it for the first time to Golgi maintenance, ER-Golgi transport, and endocytic recycling.

    Evidence CHO ldlF temperature-sensitive mutant rescued by hamster epsilon-COP cDNA, with Golgi morphology, ER-Golgi transport, and LDL receptor recycling assays

    PMID:8207054

    Open questions at the time
    • Did not define the molecular activity of epsilon-COP within coatomer
    • Did not identify which coatomer subunits epsilon-COP contacts
  2. 1996 High

    Pinpointed the molecular basis of the ldlF phenotype to a single thermolabile point mutation, showing protein instability—not loss of a catalytic function—drives the transport defects.

    Evidence Sequencing identified Glu251Lys; transfection rescue and pulse-chase stability analysis of the mutant protein

    PMID:8626666

    Open questions at the time
    • Did not establish how destabilized epsilon-COP affects the rest of the coatomer
    • Stability relationship to other subunits not directly linked
  3. 1998 High

    Defined epsilon-COP's primary molecular role as stabilizing alpha-COP and the coatomer complex, and demonstrated a direct functional interaction with alpha-COP.

    Evidence Yeast genetics: high-copy suppression of an alpha-COP ts mutant, sec28Δ phenotypes, gel filtration of coatomer, allele-specific synthetic lethality

    PMID:9463377

    Open questions at the time
    • Did not resolve the structural basis of the epsilon-COP/alpha-COP interaction
    • Mechanism by which stabilization preserves transport not detailed
  4. 1999 Medium

    Confirmed the yeast homologue acts in the early secretory pathway and linked its loss to ER membrane accumulation and nuclear morphology defects.

    Evidence Yeast ts mutant screen, ANU2 disruption, electron microscopy, CPY secretion assay

    PMID:10532354

    Open questions at the time
    • Mechanism connecting epsilon-COP loss to abnormal nuclear morphology unknown
    • Single lab, low sequence identity ortholog assignment
  5. 2003 Medium

    Showed that epsilon-COP/COPI function is required for canonical retrograde Golgi transport and that its loss unmasks an alternative direct endosome-to-ER route.

    Evidence ldlF cells at non-permissive temperature; ricin transport tracked by ER glycosylation and trans-Golgi sulfation, with brefeldin A treatment

    PMID:12847103

    Open questions at the time
    • Molecular components of the bypass route not identified
    • Single lab biochemical readouts
  6. 2010 High

    Resolved how epsilon-COP physically interlocks with alpha-COP and contacts the Dsl1 tethering complex, providing a structural basis for its stabilizing and vesicle-surface roles.

    Evidence 2.9 Å crystal structure of alpha-COP CTD bound to full-length epsilon-COP; solution heterodimer formation and Dsl1 pull-down assays

    PMID:20534429

    Open questions at the time
    • Structure of epsilon-COP within the full heptameric coatomer not determined
    • Functional consequence of the Dsl1 contact for tethering in vivo not established

Open questions

Synthesis pass · forward-looking unresolved questions
  • How the epsilon-COP/alpha-COP heterodimer integrates Dsl1-mediated tethering with COPI vesicle uncoating and fusion in intact cells remains unresolved.
  • No in vivo mechanism linking the Dsl1 contact to vesicle tethering
  • No human disease association in the corpus
  • No structure of the assembled coatomer with epsilon-COP in context

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0005198 structural molecule activity 3 GO:0140313 molecular sequestering activity 1
Localization
GO:0005783 endoplasmic reticulum 2 GO:0005794 Golgi apparatus 2 GO:0031410 cytoplasmic vesicle 1
Pathway
R-HSA-5653656 Vesicle-mediated transport 3 R-HSA-9609507 Protein localization 2
Partners
COPADSL1 COMPLEX
Complex memberships
COPI coatomer

Evidence

Reading pass · 6 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
1994 epsilon-COP (COPE) is a component of the coatomer complex required for maintaining Golgi structure and mediating ER-through-Golgi transport. In the CHO ldlF temperature-sensitive mutant, loss of epsilon-COP function at the non-permissive temperature caused Golgi dissociation into vesicles and tubules (resembling brefeldin A effects) and disrupted ER-to-Golgi transport and endocytic recycling of LDL receptors. A hamster cDNA encoding epsilon-COP specifically corrected all ts defects, providing the first genetic evidence that coatomer plays roles in Golgi structure maintenance, ER-through-Golgi transport, and endocytic recycling. Somatic cell genetics (CHO temperature-sensitive mutant ldlF), cDNA complementation cloning, immunofluorescence microscopy of Golgi morphology, functional assays for LDL receptor recycling and ER-Golgi transport The Journal of cell biology High 8207054
1996 A single point mutation (Glu251Lys) in epsilon-COP is responsible for all temperature-sensitive membrane-transport defects in ldlF cells. The mutant ts-epsilon-COP protein is synthesized normally but is thermolabile (t1/2 >6 h at 34°C, ~1-2 h at 39.5°C), and its instability accounts for the Golgi disintegration, ER-Golgi transport block, and LDL receptor degradation at the non-permissive temperature. The stability of beta-COP was not directly linked to that of epsilon-COP. Point mutation identification by sequencing, transfection rescue assays, pulse-chase stability analysis, immunochemical analysis, isoelectric focusing The Journal of biological chemistry High 8626666
1998 In yeast, epsilon-COP (Sec28p) is a structural component of coatomer whose primary function is to stabilize alpha-COP (Ret1p) and the coatomer complex. Overproduction of epsilon-COP suppresses temperature-sensitive defects of an alpha-COP mutant (ret1-3) by stabilizing alpha-COP levels. Deletion of epsilon-COP (sec28Δ) is not lethal but causes thermosensitivity; at 37°C, alpha-COP levels rapidly diminish and ER-to-Golgi transport (CPY maturation) is blocked. Allele-specific synthetic lethality between sec28Δ and alpha-COP mutations further supports a direct functional interaction. Yeast genetics (deletion, overexpression, high-copy suppressor screen), temperature-sensitive growth assays, carboxypeptidase Y trafficking assay, gel filtration of coatomer complex, synthetic lethality analysis The EMBO journal High 9463377
1999 The yeast gene ANU2 encodes the yeast homologue of mammalian epsilon-COP (sharing 20% sequence identity). Mutation or deletion of ANU2 causes defects in ER-to-Golgi vesicular transport, accumulation of ER membranes (shown by electron microscopy), and abnormal nuclear morphology (irregular, multi-lobed nuclei). These results place epsilon-COP in the early secretory pathway and link its loss to structural nuclear abnormalities. Yeast temperature-sensitive mutant screen using GFP-tagged nucleoplasmin, genetic mapping and sequencing of ANU2, gene disruption, electron microscopy, CPY secretion assay for ER-Golgi transport Cell structure and function Medium 10532354
2003 Depletion of epsilon-COP in ldlF cells (by shifting to non-permissive temperature) vesiculates the Golgi and induces a brefeldin A-resistant, direct endosome-to-ER transport pathway for ricin that bypasses the Golgi apparatus. Ricin reached the ER (shown by glycosylation and sulfation assays) while normal Golgi-mediated retrograde transport was severely inhibited, demonstrating that epsilon-COP/COPI function is required for canonical retrograde Golgi transport and that its loss reveals an alternative transport route. Temperature-sensitive ldlF cell system, ricin transport assay with modified ricin (ricin sulf-2), radioactive mannose incorporation into ER-glycosylated ricin, sulfate labeling of trans-Golgi-processed ricin, brefeldin A treatment, cytotoxicity assay The Journal of biological chemistry Medium 12847103
2010 The crystal structure of the alpha-COP C-terminal domain (CTD) in complex with full-length epsilon-COP was determined at 2.9 Å resolution. epsilon-COP adopts a tetratricopeptide repeat (TPR) fold that deviates substantially from canonical superhelical conformation; its TPRs form a circular bracelet that wraps around a protruding beta-hairpin of the alpha-COP CTD, interlocking the two proteins. The heterodimer forms in solution, and biochemical assays demonstrated that it directly interacts with the Dsl1 tethering complex, suggesting the heterodimer is exposed on the surface of COPI vesicles. X-ray crystallography (2.9 Å), biochemical solution studies (heterodimer formation), pull-down/binding assay with Dsl1 tethering complex Proceedings of the National Academy of Sciences of the United States of America High 20534429

Source papers

Stage 0 corpus · 100 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2010 Cryptic prophages help bacteria cope with adverse environments. Nature communications 496 21266997
2015 Physiological mechanisms used by fish to cope with salinity stress. The Journal of experimental biology 240 26085667
2006 How plants cope with complete submergence. The New phytologist 230 16608449
2006 Flavivirus infection activates the XBP1 pathway of the unfolded protein response to cope with endoplasmic reticulum stress. Journal of virology 221 16987981
2008 Ionizing radiation: how fungi cope, adapt, and exploit with the help of melanin. Current opinion in microbiology 213 18848901
2015 Mechanisms Used by Plants to Cope with DNA Damage. Annual review of plant biology 186 26653616
2011 Alternative splicing: enhancing ability to cope with stress via transcriptome plasticity. Plant science : an international journal of experimental plant biology 177 22325865
2015 An Aza-Cope Reactivity-Based Fluorescent Probe for Imaging Formaldehyde in Living Cells. Journal of the American Chemical Society 158 26306005
2006 ER stress: can the liver cope? Journal of hepatology 145 16797772
2017 How plants cope with UV-B: from perception to response. Current opinion in plant biology 143 28411583
1995 Regulation of the interferon-induced PKR: can viruses cope? Trends in microbiology 142 7537157
2019 How do cells cope with RNA damage and its consequences? The Journal of biological chemistry 140 31439666
2011 How sulphate-reducing microorganisms cope with stress: lessons from systems biology. Nature reviews. Microbiology 140 21572460
1994 Disruptions in Golgi structure and membrane traffic in a conditional lethal mammalian cell mutant are corrected by epsilon-COP. The Journal of cell biology 133 8207054
2008 How to cope with insect resistance to Bt toxins? Trends in biotechnology 129 18706722
2004 Stress and how bacteria cope with death and survival. Critical reviews in microbiology 117 15646400
2012 Genetic dissection of the zebrafish habenula, a possible switching board for selection of behavioral strategy to cope with fear and anxiety. Developmental neurobiology 111 21567982
2023 Cope with copper: From copper linked mechanisms to copper-based clinical cancer therapies. Cancer letters 102 37011869
2018 Immediate response mechanisms of Gram-negative solvent-tolerant bacteria to cope with environmental stress: cis-trans isomerization of unsaturated fatty acids and outer membrane vesicle secretion. Applied microbiology and biotechnology 102 29450619
2014 Combination of fluconazole with non-antifungal agents: a promising approach to cope with resistant Candida albicans infections and insight into new antifungal agent discovery. International journal of antimicrobial agents 99 24503221
2021 Nexus on climate change: agriculture and possible solution to cope future climate change stresses. Environmental science and pollution research international 96 33515149
2020 Nucleoid Associated Proteins: The Small Organizers That Help to Cope With Stress. Frontiers in microbiology 92 32373086
1999 How newborn mammals cope with hypoxia. Respiration physiology 91 10487295
2017 Development of a General Aza-Cope Reaction Trigger Applied to Fluorescence Imaging of Formaldehyde in Living Cells. Journal of the American Chemical Society 88 28375637
2021 A Critical Review on Communication Mechanism within Plant-Endophytic Fungi Interactions to Cope with Biotic and Abiotic Stresses. Journal of fungi (Basel, Switzerland) 78 34575757
2017 A 2-aza-Cope reactivity-based platform for ratiometric fluorescence imaging of formaldehyde in living cells. Chemical science 76 28580121
2017 Transcriptomic and microRNAomic profiling reveals multi-faceted mechanisms to cope with phosphate stress in a dinoflagellate. The ISME journal 72 28548660
1998 epsilon-COP is a structural component of coatomer that functions to stabilize alpha-COP. The EMBO journal 72 9463377
2006 Liver glyconeogenesis: a pathway to cope with postprandial amino acid excess in high-protein fed rats? American journal of physiology. Regulatory, integrative and comparative physiology 65 17158265
1996 A single point mutation in epsilon-COP results in temperature-sensitive, lethal defects in membrane transport in a Chinese hamster ovary cell mutant. The Journal of biological chemistry 65 8626666
2016 Pectinous cell wall thickenings formation - A common defense strategy of plants to cope with Pb. Environmental pollution (Barking, Essex : 1987) 64 27107260
2022 The hot science in rice research: How rice plants cope with heat stress. Plant, cell & environment 62 36478590
2022 How to Cope with the Challenges of Environmental Stresses in the Era of Global Climate Change: An Update on ROS Stave off in Plants. International journal of molecular sciences 60 35216108
2012 Prochlorococcus and Synechococcus have Evolved Different Adaptive Mechanisms to Cope with Light and UV Stress. Frontiers in microbiology 59 23024637
2014 Myc induced replicative stress response: How to cope with it and exploit it. Biochimica et biophysica acta 58 24735945
2000 Family care-giving and chronic illness: how parents cope with a child with a sickle cell disorder or thalassaemia. Health & social care in the community 58 11560675
2001 A better enzyme to cope with cold. Comparative flexibility studies on psychrotrophic, mesophilic, and thermophilic IPMDHs. The Journal of biological chemistry 55 11369782
2006 Excretion and conservation of glycerol, and expression of aquaporins and glyceroporins, during cold acclimation in Cope's gray tree frog Hyla chrysoscelis. American journal of physiology. Regulatory, integrative and comparative physiology 52 16973932
2024 Stress salinity in plants: New strategies to cope with in the foreseeable scenario. Plant physiology and biochemistry : PPB 50 38467083
2017 How do individuals cope with stress? Behavioural, physiological and neuronal differences between proactive and reactive coping styles in fish. The Journal of experimental biology 50 28167808
2015 Hapalindole/Ambiguine Biogenesis Is Mediated by a Cope Rearrangement, C-C Bond-Forming Cascade. Journal of the American Chemical Society 48 26629885
2023 How Do Plants Cope with DNA Damage? A Concise Review on the DDR Pathway in Plants. International journal of molecular sciences 44 36768727
2006 How high G+C Gram-positive bacteria and in particular bifidobacteria cope with heat stress: protein players and regulators. FEMS microbiology reviews 44 16911042
2022 An Insight into Abiotic Stress and Influx Tolerance Mechanisms in Plants to Cope in Saline Environments. Biology 43 35453796
2021 The selective advantage of facultative anaerobes relies on their unique ability to cope with changing oxygen levels during infection. Cellular microbiology 43 33813807
2018 Drinking to cope mediates the relationship between depression and alcohol risk: Different pathways for college and non-college young adults. Addictive behaviors 43 29407681
2010 Crystal structure of alpha-COP in complex with epsilon-COP provides insight into the architecture of the COPI vesicular coat. Proceedings of the National Academy of Sciences of the United States of America 42 20534429
2009 How plants cope with biotic interactions. Plant biology (Stuttgart, Germany) 42 19121108
2005 The combination therapy of hypertension to prevent cardiovascular events (COPE) trial: rationale and design. Hypertension research : official journal of the Japanese Society of Hypertension 42 16138563
2023 Insights into nanoparticles-induced neurotoxicity and cope up strategies. Frontiers in neuroscience 40 37214389
2018 Into the breach: how cells cope with wounds. Open biology 40 30282661
2001 Eukaryotic ribonuclease P: increased complexity to cope with the nuclear pre-tRNA pathway. Journal of cellular physiology 39 11241345
2021 Metabolomics combined with physiology and transcriptomics reveals how Citrus grandis leaves cope with copper-toxicity. Ecotoxicology and environmental safety 36 34352583
2003 Induction of direct endosome to endoplasmic reticulum transport in Chinese hamster ovary (CHO) cells (LdlF) with a temperature-sensitive defect in epsilon-coatomer protein (epsilon-COP). The Journal of biological chemistry 36 12847103
2019 Snails in the sun: Strategies of terrestrial gastropods to cope with hot and dry conditions. Ecology and evolution 34 31788227
2018 Neural stem cells from a mouse model of Rett syndrome are prone to senescence, show reduced capacity to cope with genotoxic stress, and are impaired in the differentiation process. Experimental & molecular medicine 31 29563495
2018 The Association between Distress Tolerance and Alcohol Related Problems: The Pathway of Drinking to Cope. Substance use & misuse 29 29708456
2009 Retractions: guidance from the Committee on Publication Ethics (COPE). Croatian medical journal 29 20017220
2011 The Chromobacterium violaceum type III effector CopE, a guanine nucleotide exchange factor for Rac1 and Cdc42, is involved in bacterial invasion of epithelial cells and pathogenesis. Molecular microbiology 28 21435035
2018 Structural basis of the Cope rearrangement and cyclization in hapalindole biogenesis. Nature chemical biology 27 29531360
2024 Cope with copper: From molecular mechanisms of cuproptosis to copper-related kidney diseases. International immunopharmacology 26 38663316
2022 Cavefish cope with environmental hypoxia by developing more erythrocytes and overexpression of hypoxia-inducible genes. eLife 26 34984980
2016 Contrasting strategies used by lichen microalgae to cope with desiccation-rehydration stress revealed by metabolite profiling and cell wall analysis. Environmental microbiology 26 26914009
2024 The ABCF proteins in Escherichia coli individually cope with 'hard-to-translate' nascent peptide sequences. Nucleic acids research 25 38661232
2023 Bacterial Communication Coordinated Behaviors of Whole Communities to Cope with Environmental Changes. Environmental science & technology 25 36862939
2022 Solutions: how adaptive changes in cellular fluids enable marine life to cope with abiotic stressors. Marine life science & technology 25 37073170
2021 Bioorthogonal Retro-Cope Elimination Reaction of N,N-Dialkylhydroxylamines and Strained Alkynes. Journal of the American Chemical Society 25 33829777
2008 How to cope with pathogenic long-lived plasma cells in autoimmune diseases. Annals of the rheumatic diseases 24 19022822
1999 Patterns of gene flow and population genetic structure in the canyon treefrog, Hyla arenicolor (Cope). Molecular ecology 24 10327657
2004 A comparative study of claisen and cope rearrangements catalyzed by chorismate mutase. An insight into enzymatic efficiency: transition state stabilization or substrate preorganization? Journal of the American Chemical Society 23 14709097
2023 Newly isolated Lactobacillus paracasei strain modulates lung immunity and improves the capacity to cope with influenza virus infection. Microbiome 21 37996951
2021 The genome of the extremophile Artemia provides insight into strategies to cope with extreme environments. BMC genomics 21 34465293
2021 ATG8ylation of proteins: A way to cope with cell stress? The Journal of cell biology 21 34671813
2010 Expression and immunolocalization of aquaporins HC-1, -2, and -3 in Cope's gray treefrog, Hyla chrysoscelis. Comparative biochemistry and physiology. Part A, Molecular & integrative physiology 21 20416391
2022 Chaperones and Catalysts: How Antigen Presentation Pathways Cope With Biological Necessity. Frontiers in immunology 20 35464465
2015 The expression of proteins involved in digestion and detoxification are regulated in Helicoverpa armigera to cope up with chlorpyrifos insecticide. Insect science 20 25284010
2023 Plants cope with fluctuating light by frequency-dependent nonphotochemical quenching and cyclic electron transport. The New phytologist 19 37429324
2020 Hepatic transcriptome of the freeze-tolerant Cope's gray treefrog, Dryophytes chrysoscelis: responses to cold acclimation and freezing. BMC genomics 19 32164545
2016 Tools to cope with difficult-to-express proteins. Applied microbiology and biotechnology 19 27079572
2012 A Mexican way to cope with stem cell grafting. Hematology (Amsterdam, Netherlands) 19 22507819
2008 A serotonin transporter gene polymorphism (5-HTTLPR), drinking-to-cope motivation, and negative life events among college students. Journal of studies on alcohol and drugs 19 18925339
2003 Running into problems: how cells cope with replicating damaged DNA. Mutation research 19 14643430
2021 FKBP5 expression is related to HPA flexibility and the capacity to cope with stressors in female and male house sparrows. Hormones and behavior 18 34280702
2021 TaFDL2-1A interacts with TabZIP8-7A protein to cope with drought stress via the abscisic acid signaling pathway. Plant science : an international journal of experimental plant biology 18 34482905
1999 Mutation of the yeast epsilon-COP gene ANU2 causes abnormal nuclear morphology and defects in intracellular vesicular transport. Cell structure and function 18 10532354
2019 HA-Dependent Tropism of H5N1 and H7N9 Influenza Viruses to Human Endothelial Cells Is Determined by Reduced Stability of the HA, Which Allows the Virus To Cope with Inefficient Endosomal Acidification and Constitutively Expressed IFITM3. Journal of virology 17 31597765
2019 Mechanisms used by DNA MMR system to cope with Cadmium-induced DNA damage in plants. Chemosphere 17 31883478
2020 Functional and Dysfunctional Neuroplasticity in Learning to Cope with Stress. Brain sciences 16 32102272
2016 Inhibiting ethylene perception with 1-methylcyclopropene triggers molecular responses aimed to cope with cell toxicity and increased respiration in citrus fruits. Plant physiology and biochemistry : PPB 16 26990405
2015 DNA barcode and evolutionary relationship within Laemolyta Cope 1872 (Characiformes: Anostomidae) through molecular analyses. Molecular phylogenetics and evolution 16 26238459
2007 Quality of life, drinking to cope, alcohol consumption and smoking in successfully treated HNSCC patients. Acta oto-laryngologica 16 17851968
2023 Comparative transcriptome and antioxidant biomarker response reveal molecular mechanisms to cope with zinc ion exposure in the unicellular eukaryote Paramecium. Journal of hazardous materials 15 37080029
2023 Integrative physiological, transcriptomic and metabolomic analysis reveals how the roots of two ornamental Hydrangea macrophylla cultivars cope with lead (Pb) toxicity. The Science of the total environment 15 37984650
2020 The antioxidant defense system in Chinese jujube is triggered to cope with phytoplasma invasion. Tree physiology 15 32483619
2021 From "Aha!" to "Haha!" Using Humor to Cope with Negative Stimuli. Cerebral cortex (New York, N.Y. : 1991) 14 33258955
2019 Alginates along the filament of the brown alga Ectocarpus help cells cope with stress. Scientific reports 14 31506545
2019 iTRAQ-Based Proteomic Analysis Reveals Several Strategies to Cope with Drought Stress in Maize Seedlings. International journal of molecular sciences 14 31779286
2023 Human Microglia Synthesize Neurosteroids to Cope with Rotenone-Induced Oxidative Stress. Antioxidants (Basel, Switzerland) 13 37107338
2020 Loss of TAZ Boosts PPARγ to Cope with Insulin Resistance. Cell metabolism 13 31951568
2021 [GO System, a DNA Repair Pathway to Cope with Oxidative Damage]. Molekuliarnaia biologiia 12 33871437

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