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Search results 2401 to 2500 out of 4706 for Coil

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Type Details Score
Protein Domain
Type: Family
Description: This entry represents the Envelope (E) small membrane protein of Middle East respiratory syndrome (MERS) coronavirus (CoV), as well as E proteins from related coronaviruses.E protein is the smallest of the major structural proteins. It is conserved among Coronavirus strains. It is an integral membrane protein involved in several aspects of the virus' life cycle, such as assembly, budding, envelope formation, and pathogenesis []. During the replication cycle, E is abundantly expressed inside the infected cell, but only a small portion is incorporated into the virus envelope. The majority of the protein participates in viral assembly and budding [, ]. It can act as a viroporin by oligomerizing after insertion in host membranes to create a hydrophilic pore that allows ion transport [, ]. Additionally, the E protein is thought to prevent M protein aggregation and induce membrane curvature [].SARS-CoV E protein forms a Ca2+ permeable channel in the endoplasmic reticulum Golgi apparatus intermediate compartment (ERGIC)/Golgi membranes. The E protein ion channel activity alters Ca2+ homeostasis within cells boosting the activation of the NLRP3 inflammasome, which leads to the overproduction of IL-1beta. SARS-CoV overstimulates the NF-kappaB inflammatory pathway and interacts with the cellular protein syntenin, triggering p38 MARK activation. These signalling cascades result in exacerbated inflammation and immunopathology [].Cov E proteins have a short hydrophilic N terminus, followed by a large hydrophobic transmembrane (TM) domain, and end with a long, hydrophilic C terminus, which comprises the majority of the protein. The hydrophobic region of the TM domain contains at least one predicted amphipathic α-helix that pentamerizes to form an ion-conductive pore in membranes. CoV E proteins have been proposed to have at least two roles. One is related to their TM channel domain. This would be active in the secretory pathway, altering lumenal environments and rearranging secretory organelles and leading to efficienttrafficking of virions. The other would be related to their extramembrane domains, particularly the C-terminal domain. This is involved in protein-protein interactions and targeting, among other roles [, , , ]. In the CoV E protein structure a longer α-helix encompasses the TM domain, which is connected to another shorter C-terminal α-helix by a flexible linker domain, forming an L-shape [Li]. The CoV E pentamer is a right handed α-helical bundle where the C-terminal tails coil around each other [].
Protein Domain
Type: Domain
Description: This entry represents the C-type lectin-like domain (CTLD) of the type found in human dendritic cell (DC)-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN), also known as CD209 antigen, and the related receptor, DC-SIGN receptor (DC-SIGNR), also known as CD209 antigen-like protein 1 or C-type lectin domain family 4 member M. This group also contains proteins similar to hepatic asialoglycoprotein receptor (ASGP-R) and langerin (also known as CD207 or C-type lectin domain family 4 member K) in human. These proteins are type II membrane proteins with a CTLD ectodomain. CTLD refers to a domain homologous to the carbohydrate-recognition domains (CRDs) of the C-type lectins [].DC-SIGN is thought to mediate the initial contact between dendritic cells and resting T cells, and may also mediate the rolling of DCs on epithelium []. DC-SIGN and DC-SIGNR bind to oligosaccharides present on human tissues, as well as on pathogens including parasites, bacteria, and viruses. DC-SIGN and DC-SIGNR bind to HIV, enhancing viral infection of T cells []. DC-SIGN and DC-SIGNR are homotetrameric, and contain four CTLDs stabilized by a coiled coil of alpha helices []. The hepatic ASGP-R is an endocytic recycling receptor which binds and internalizes desialylated glycoproteins having a terminal galactose or N-acetylgalactosamine residues on their N-linked carbohydrate chains, via the clathrin-coated pit mediated endocytic pathway, and delivers them to lysosomes for degradation. It has been proposed that glycoproteins bearing terminals 'Sia (sialic acid) alpha2, 6GalNAc' and 'Sia alpha2, 6Gal' are endogenous ligands for ASGP-R, and that ASGP-R participates in regulating the relative concentration of serum glycoproteins bearing alpha 2,6-linked Sia []. The human ASGP-R is a hetero-oligomer composed of two subunits, both of which are found within this group []. Langerin is expressed in a subset of dendritic leukocytes, the Langerhans cells (LC). Langerin induces the formation of Birbeck Granules (BGs) and associates with these BGs following internalization []. Langerin binds, in a calcium-dependent manner, to glyco-conjugates containing mannose and related sugars mediating their uptake and degradation. Langerin molecules oligomerize as trimers with three CTLDs held together by a coiled-coil of alpha helices [].
Protein Domain
Type: Domain
Description: This entry represents the C-lobe of FERM domain found in the ERM family members, including ezrin, radixin, moesin and merlin. They are composed of a N-terminal FERM (ERM) domain, a coiled coil region (CRR), and a C-terminal domain CERMAD (C-terminal ERM association domain) which has an F-actin-binding site (ABD). Two actin-binding sites have been identified in the middle and N-terminal domains. Merlin is structurally similar to the ERM proteins, but instead of an actin-binding domain (ABD), it contains a C-terminal domain (CTD), just like the proteins from the 4.1 family. Activated ezrin, radixin and moesin are thought to be involved in the linking of actin filaments to CD43, CD44, ICAM1-3 cell adhesion molecules, various membrane channels and receptors, such as the Na+/H+ exchanger-3 (NHE3), cystic fibrosis transmembrane conductance regulator (CFTR), and the beta2-adrenergic receptor [, ]. The ERM proteins exist in two states, a dormant state in which the FERM domain binds to its own C-terminal tail and thereby precludes binding of some partner proteins, and an activated state, in which the FERM domain binds to one of many membrane binding proteins and the C-terminal tail binds to F-actin [, ]. The FERM domain has a cloverleaf tripart structure composed of: (1) FERM_N (A-lobe or F1); (2) FERM_M (B-lobe, or F2); and (3) FERM_C (C-lobe or F3). The C-lobe/F3 within the FERM domain is part of the PH domain family. Like most other ERM members they have a phosphoinositide-binding site in their FERM domain. The FERM C domain is the third structural domain within the FERM domain. The FERM domain is found in the cytoskeletal-associated proteins such as ezrin, moesin, radixin, 4.1R, and merlin. These proteins provide a link between the membrane and cytoskeleton and are involved in signal transduction pathways. The FERM domain is also found in protein tyrosine phosphatases (PTPs) , the tyrosine kinases FAK and JAK, in addition to other proteins involved in signaling. This domain is structurally similar to the PH and PTB domains and consequently is capable of binding to both peptides and phospholipids at different sites [, ].
Protein Domain
Type: Homologous_superfamily
Description: The Krueppel-associated box (KRAB) is a domain of around 75 amino acids that is found in the N-terminal part of about one third of eukaryotic Krueppel-type C2H2 zinc finger proteins (ZFPs) []. It is enriched in charged amino acids and can be divided into subregions A and B, which are predicted to fold into two amphipathic α-helices. The KRAB A and B boxes can be separated by variable spacer segments and many KRAB proteins contain only the A box [].The functions currently known for members of the KRAB-containing protein family include transcriptional repression of RNA polymerase I, II and III promoters, binding and splicing of RNA, and control of nucleolus function. The KRAB domain functions as a transcriptional repressor when tethered to the template DNA by a DNA-binding domain. A sequence of 45 amino acids in the KRAB A subdomain has been shown to be necessary and sufficient for transcriptional repression. The B box does not repress by itself but does potentiate the repression exerted by the KRAB A subdomain [, ]. Gene silencing requires the binding of the KRAB domain to the RING-B box-coiled coil (RBCC) domain of the KAP-1/TIF1-beta corepressor. As KAP-1 binds to the heterochromatin proteins HP1, it has been proposed that the KRAB-ZFP-bound target gene could be silenced following recruitment to heterochromatin [, ].KRAB-ZFPs probably constitute the single largest class of transcription factors within the human genome []. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. Although the function of KRAB-ZFPs is largely unknown, they appear to play important roles during cell differentiation and development. These proteins have been shown to play important roles in cell differentiation and organ development, and in regulating viral replication and transcription. A KRAB domain may consist of an A-box, or of an A-box plus either a B-box, a divergent B-box (b), or a C-box. Only the A-box is included in this model. The A-box is needed for repression, the B- and C- boxes are not. KRAB-ZFPs have one or two KRAB domains at their amino-terminal end, and multiple C2H2 zinc finger motifs at their C-termini. Some KRAB-ZFPs also contain a SCAN domain which mediates homo- and hetero-oligomerization. The KRAB domain is a protein-protein interaction module which represses transcription through recruiting corepressors. A key mechanism appears to be the following: KRAB-AFPs tethered to DNA recruit, via their KRAB domain, the repressor KAP1 (KRAB-associated protein-1, also known as transcription intermediary factor 1 beta, KRAB-A interacting protein and tripartite motif protein 28). The KAP1/ KRAB-AFP complex in turn recruits the heterochromatin protein 1 (HP1) family, and other chromatin modulating proteins, leading to transcriptional repression through heterochromatin formation [].
Protein Domain
Type: Family
Description: The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms, including bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms. They function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression [, ].SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170kDa, and share a five-domain structure, with globular N- and C-terminal domains separated by a long(circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residuesthat are typical of flexible regionsin a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which has been shown by mutational studies to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases []. All SMC proteins appear to form dimers, either forming homodimers, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers form core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis. SMC dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains.Proteins in this entry include SMC1/2/3/4 from Saccharomyces cerevisiae. SMC1-SMC3 heterodimer is part of the cohesin complex, which is required for sister chromatid cohesion in mitosis and meiosis []. SMC2-SMC4 heterodimer is part of the condensin complex, which is required for chromosome condensation during both mitosis and meiosis [, ].
Protein Domain
Type: Family
Description: The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms, including bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms. They function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression [].SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170kDa, and share a five-domain structure, with globular N- and C-terminal domains separated by a long(circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residuesthat are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which has been shown by mutational studies to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases []. All SMC proteins appear to form dimers, either forming homodimers, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers form core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis. SMC dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains.This entry represents the SMC protein from bacteria and archaea [, , ].
Protein Domain
Type: Domain
Description: The Krueppel-associated box (KRAB) is a domain of around 75 amino acids that is found in the N-terminal part of about one third of eukaryotic Krueppel-type C2H2 zinc finger proteins (ZFPs) []. It is enriched in charged amino acids and can be divided into subregions A and B, which are predicted to fold into two amphipathic α-helices. The KRAB A and B boxes can be separated by variable spacer segments and many KRAB proteins contain only the A box [].The functions currently known for members of the KRAB-containing protein family include transcriptional repression of RNA polymerase I, II and III promoters, binding and splicing of RNA, and control of nucleolus function. The KRAB domain functions as a transcriptional repressor when tethered to the template DNA by a DNA-binding domain. A sequence of 45 amino acids in the KRAB A subdomain has been shown to be necessary and sufficient for transcriptional repression. The B box does not repress by itself but does potentiate the repression exerted by the KRAB A subdomain [, ]. Gene silencing requires the binding of the KRAB domain to the RING-B box-coiled coil (RBCC) domain of the KAP-1/TIF1-beta corepressor. As KAP-1 binds to the heterochromatin proteins HP1, it has been proposed that the KRAB-ZFP-bound target gene could be silenced following recruitment to heterochromatin [, ].KRAB-ZFPs probably constitute the single largest class of transcription factors within the human genome []. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B. Although the function of KRAB-ZFPs is largely unknown, they appear to play important roles during cell differentiation and development. These proteins have been shown to play important roles in cell differentiation and organ development, and in regulating viral replication and transcription. A KRAB domain may consist of an A-box, or of an A-box plus either a B-box, a divergent B-box (b), or a C-box. Only the A-box is included in this model. The A-box is needed for repression, the B- and C- boxes are not. KRAB-ZFPs have one or two KRAB domains at their amino-terminal end, and multiple C2H2 zinc finger motifs at their C-termini. Some KRAB-ZFPs also contain a SCAN domain which mediates homo- and hetero-oligomerization. The KRAB domain is a protein-protein interaction module which represses transcription through recruiting corepressors. A key mechanism appears to be the following: KRAB-AFPs tethered to DNA recruit, via their KRAB domain, the repressor KAP1 (KRAB-associated protein-1, also known as transcription intermediary factor 1 beta, KRAB-A interacting protein and tripartite motif protein 28). The KAP1/ KRAB-AFP complex in turn recruits the heterochromatin protein 1 (HP1) family, and other chromatin modulating proteins, leading to transcriptional repression through heterochromatin formation [].
Publication
First Author: Araki K
Year: 1999
Journal: Cell Mol Biol (Noisy-le-grand)
Title: Exchangeable gene trap using the Cre/mutated lox system.
Volume: 45
Issue: 5
Pages: 737-50
Publication
First Author: Taniwaki T
Year: 2005
Journal: Dev Growth Differ
Title: Characterization of an exchangeable gene trap using pU-17 carrying a stop codon-beta geo cassette.
Volume: 47
Issue: 3
Pages: 163-72
Publication        
First Author: MGD Nomenclature Committee
Year: 1995
Title: Nomenclature Committee Use
Protein Coding Gene
Type: protein_coding_gene
Organism: mouse, laboratory
Protein Coding Gene
Type: protein_coding_gene
Organism: mouse, laboratory
Protein Coding Gene
Type: protein_coding_gene
Organism: mouse, laboratory
Protein Coding Gene
Type: protein_coding_gene
Organism: mouse, laboratory
Publication      
First Author: Mouse Genome Informatics and VEGA Genome Database Project
Year: 2006
Journal: Database Release
Title: Collaboration to Associate VEGA (Vertebrate Genome Annotation) Mouse Gene Models with MGI Markers
Protein
Organism: Mus musculus/domesticus
Length: 950  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 680  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 930  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 272  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 489  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 959  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 686  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 1233  
Fragment?: false
Publication
First Author: Mark C
Year: 1999
Journal: DNA Cell Biol
Title: Comparative analysis of KRAB zinc finger proteins in rodents and man: evidence for several evolutionarily distinct subfamilies of KRAB zinc finger genes.
Volume: 18
Issue: 5
Pages: 381-96
Protein
Organism: Mus musculus/domesticus
Length: 814  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 846  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 437  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 107  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 89  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 64  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 92  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 90  
Fragment?: true
Protein
Organism: Mus musculus/domesticus
Length: 104  
Fragment?: true
Protein
Organism: Mus musculus/domesticus
Length: 241  
Fragment?: true
Protein
Organism: Mus musculus/domesticus
Length: 133  
Fragment?: true
Protein
Organism: Mus musculus/domesticus
Length: 88  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 81  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 67  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 118  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 250  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 64  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 93  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 231  
Fragment?: true
Protein
Organism: Mus musculus/domesticus
Length: 118  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 98  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 72  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 95  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 64  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 102  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 98  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 106  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 72  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 65  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 80  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 114  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 64  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 128  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 86  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 63  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 64  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 64  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 64  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 181  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 64  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 64  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 156  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 272  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 150  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 118  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 136  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 119  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 105  
Fragment?: true
Protein
Organism: Mus musculus/domesticus
Length: 42  
Fragment?: true
Protein
Organism: Mus musculus/domesticus
Length: 165  
Fragment?: true
Protein
Organism: Mus musculus/domesticus
Length: 143  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 582  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 141  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 76  
Fragment?: true
Protein
Organism: Mus musculus/domesticus
Length: 85  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 87  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 211  
Fragment?: true
Protein
Organism: Mus musculus/domesticus
Length: 72  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 63  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 71  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 210  
Fragment?: true
Protein
Organism: Mus musculus/domesticus
Length: 81  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 98  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 154  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 74  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 99  
Fragment?: true
Protein
Organism: Mus musculus/domesticus
Length: 84  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 59  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 194  
Fragment?: true
Protein
Organism: Mus musculus/domesticus
Length: 105  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 68  
Fragment?: true
Protein
Organism: Mus musculus/domesticus
Length: 60  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 122  
Fragment?: true
Protein
Organism: Mus musculus/domesticus
Length: 136  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 81  
Fragment?: false
Protein
Organism: Mus musculus/domesticus
Length: 92  
Fragment?: false