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Article ; Online: RNA structure-based ribosome recruitment: lessons from the Dicistroviridae intergenic region IRESes.

Pfingsten, Jennifer S / Kieft, Jeffrey S

2008 Volume 14, Issue 7, Page(s) 1255–1263

Abstract: In eukaryotes, the canonical process of initiating protein synthesis on an mRNA depends on many large protein factors and the modified nucleotide cap on the 5' end of the mRNA. However, certain RNA sequences can bypass the need for these proteins and cap, ...

Abstract	In eukaryotes, the canonical process of initiating protein synthesis on an mRNA depends on many large protein factors and the modified nucleotide cap on the 5' end of the mRNA. However, certain RNA sequences can bypass the need for these proteins and cap, using an RNA structure-based mechanism called internal initiation of translation. These RNAs are called internal ribosome entry sites (IRESes), and the cap-independent initiation pathway they support is critical for successful infection by many viruses of medical and economic importance. In this review, we briefly describe and compare mechanistic and structural groups of viral IRES RNAs, focusing on those IRESes that are capable of direct ribosome recruitment using specific RNA structures. We then discuss in greater detail some recent advances in our understanding of the intergenic region IRESes of the Dicistroviridae, which use the most streamlined ribosome-recruitment mechanism yet discovered. By combining these findings with knowledge of canonical translation and the behavior of other IRESes, mechanistic models of this RNA structure-based process are emerging.
MeSH term(s)	Models, Molecular ; Protein Biosynthesis ; RNA Viruses/chemistry ; RNA Viruses/genetics ; RNA Viruses/physiology ; RNA, Viral/chemistry ; RNA, Viral/genetics ; Ribosomes/physiology
Chemical Substances	RNA, Viral
Language	English
Publishing date	2008-05-30
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	1241540-6
ISSN	1469-9001 ; 1355-8382
ISSN (online)	1469-9001
ISSN	1355-8382
DOI	10.1261/rna.987808
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Article: Weapons in the molecular arms race.

Kieft, Jeffrey S / Pfingsten, Jennifer S

Nature structural & molecular biology

2006 Volume 12, Issue 11, Page(s) 938–939

MeSH term(s)	Dimerization ; Evolution, Molecular ; Models, Molecular ; Nodaviridae/chemistry ; Protein Conformation ; RNA Interference ; RNA-Binding Proteins/chemistry ; RNA-Binding Proteins/metabolism ; Tombusvirus/chemistry ; Viral Proteins/chemistry ; Viral Proteins/metabolism
Chemical Substances	RNA-Binding Proteins ; Viral Proteins
Language	English
Publishing date	2006-01-06
Publishing country	United States
Document type	News
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/nsmb1105-938
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Article ; Online: RNA recognition by the DNA end-binding Ku heterodimer.

Dalby, Andrew B / Goodrich, Karen J / Pfingsten, Jennifer S / Cech, Thomas R

RNA (New York, N.Y.)

2013 Volume 19, Issue 6, Page(s) 841–851

Abstract: Most nucleic acid-binding proteins selectively bind either DNA or RNA, but not both nucleic acids. The Saccharomyces cerevisiae Ku heterodimer is unusual in that it has two very different biologically relevant binding modes: (1) Ku is a sequence- ... ...

Abstract	Most nucleic acid-binding proteins selectively bind either DNA or RNA, but not both nucleic acids. The Saccharomyces cerevisiae Ku heterodimer is unusual in that it has two very different biologically relevant binding modes: (1) Ku is a sequence-nonspecific double-stranded DNA end-binding protein with prominent roles in nonhomologous end-joining and telomeric capping, and (2) Ku associates with a specific stem-loop of TLC1, the RNA subunit of budding yeast telomerase, and is necessary for proper nuclear localization of this ribonucleoprotein enzyme. TLC1 RNA-binding and dsDNA-binding are mutually exclusive, so they may be mediated by the same site on Ku. Although dsDNA binding by Ku is well studied, much less is known about what features of an RNA hairpin enable specific recognition by Ku. To address this question, we localized the Ku-binding site of the TLC1 hairpin with single-nucleotide resolution using phosphorothioate footprinting, used chemical modification to identify an unpredicted motif within the hairpin secondary structure, and carried out mutagenesis of the stem-loop to ascertain the critical elements within the RNA that permit Ku binding. Finally, we provide evidence that the Ku-binding site is present in additional budding yeast telomerase RNAs and discuss the possibility that RNA binding is a conserved function of the Ku heterodimer.
MeSH term(s)	Base Sequence ; Binding Sites ; CME-Carbodiimide/analogs & derivatives ; CME-Carbodiimide/chemistry ; Cell Nucleus/chemistry ; Cell Nucleus/genetics ; DNA Footprinting/methods ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/genetics ; Electrophoresis, Polyacrylamide Gel ; Inverted Repeat Sequences ; Mutation ; Nucleic Acid Conformation ; Nucleotide Motifs ; Phosphorothioate Oligonucleotides/chemistry ; Protein Interaction Mapping ; RNA/genetics ; RNA/metabolism ; RNA Cleavage ; RNA, Fungal/chemistry ; RNA, Fungal/genetics ; RNA-Binding Proteins/genetics ; RNA-Binding Proteins/metabolism ; Saccharomyces cerevisiae/chemistry ; Saccharomyces cerevisiae/genetics ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/genetics ; Sulfuric Acid Esters/chemistry ; Telomerase/chemistry ; Telomerase/genetics ; Telomerase/metabolism
Chemical Substances	DNA-Binding Proteins ; Phosphorothioate Oligonucleotides ; RNA, Fungal ; RNA-Binding Proteins ; Saccharomyces cerevisiae Proteins ; Sulfuric Acid Esters ; high affinity DNA-binding factor, S cerevisiae ; telomerase RNA ; 1-cyclohexyl-3-(2-(4-morpholinyl)ethyl)carbodiimide (15580-20-8) ; CME-Carbodiimide (2491-17-0) ; RNA (63231-63-0) ; Telomerase (EC 2.7.7.49) ; dimethyl sulfate (JW5CW40Z50)
Language	English
Publishing date	2013-04-22
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1241540-6
ISSN	1469-9001 ; 1355-8382
ISSN (online)	1469-9001
ISSN	1355-8382
DOI	10.1261/rna.038703.113
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Article ; Online: Mechanistic role of structurally dynamic regions in Dicistroviridae IGR IRESs.

Pfingsten, Jennifer S / Castile, Alice E / Kieft, Jeffrey S

Journal of molecular biology

2009 Volume 395, Issue 1, Page(s) 205–217

Abstract: Dicistroviridae intergenic region (IGR) internal ribosome entry site(s) (IRES) RNAs drive a cap ...

Abstract	Dicistroviridae intergenic region (IGR) internal ribosome entry site(s) (IRES) RNAs drive a cap-independent pathway of translation initiation, recruiting both small and large ribosomal subunits to viral RNA without the use of any canonical translation initiation factors. This ability is conferred by the folded three-dimensional structure of the IRES RNA, which has been solved by X-ray crystallography. Here, we report the chemical probing of Plautia stali intestine virus IGR IRES in the unbound form, in the 40S-subunit-bound form, and in the 80S-ribosome-bound form. The results, when combined with an analysis of crystal structures, suggest that parts of the IRES RNA change structure as the preinitiation complex forms. Using mutagenesis coupled with native gel electrophoresis, preinitiation complex assembly assays, and translation initiation assays, we show that these potentially structurally dynamic elements of the IRES are involved in different steps in the pathway of ribosome recruitment and translation initiation. Like tRNAs, it appears that the IGR IRES undergoes local structural changes that are coordinated with structural changes in the ribosome, and these are critical for the IRES mechanism of action.
MeSH term(s)	Base Sequence ; Crystallography, X-Ray ; DNA, Intergenic/chemistry ; DNA, Intergenic/genetics ; Dicistroviridae/chemistry ; Models, Molecular ; Molecular Sequence Data ; Mutation/genetics ; Nucleic Acid Conformation ; Pliability ; Protein Biosynthesis ; Protein Structure, Tertiary ; Ribosomes/chemistry
Chemical Substances	DNA, Intergenic
Language	English
Publishing date	2009-10-28
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2009.10.047
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Article: Conservation and diversity among the three-dimensional folds of the Dicistroviridae intergenic region IRESes.

Pfingsten, Jennifer S / Costantino, David A / Kieft, Jeffrey S

Journal of molecular biology

2007 Volume 370, Issue 5, Page(s) 856–869

Abstract: Internal ribosome entry site (IRES) RNAs are necessary for successful infection of many pathogenic viruses, but the details of the RNA structure-based mechanism used to bind and manipulate the ribosome remain poorly understood. The IRES RNAs from the ... ...

Abstract	Internal ribosome entry site (IRES) RNAs are necessary for successful infection of many pathogenic viruses, but the details of the RNA structure-based mechanism used to bind and manipulate the ribosome remain poorly understood. The IRES RNAs from the Dicistroviridae intergenic region (IGR) are an excellent model system to understand the fundamental tenets of IRES function, requiring no protein factors to manipulate the ribosome and initiate translation. Here, we explore the architecture of four members of the IGR IRESes, representative of the two divergent classes of these IRES RNAs. Using biochemical and structural probing methods, we show that despite sequence variability they contain a common three-dimensional fold. The three-dimensional architecture of the ribosome binding domain from these IRESes is organized around a core helical scaffold, around which the rest of the RNA molecule folds. However, subtle variation in the folds of these IRESes and the presence of an additional secondary structure element suggest differences in the details of their manipulation of the large ribosomal subunit. Overall, the results demonstrate how a conserved three-dimensional RNA fold governs ribosome binding and manipulation.
MeSH term(s)	Base Sequence ; Models, Molecular ; Molecular Sequence Data ; Nucleic Acid Conformation ; RNA Viruses/genetics ; RNA, Viral/chemistry ; Ribosomes/genetics
Chemical Substances	RNA, Viral
Language	English
Publishing date	2007-07-27
Publishing country	England
Document type	Journal Article
ZDB-ID	80229-3
ISSN	1089-8638 ; 0022-2836
ISSN (online)	1089-8638
ISSN	0022-2836
DOI	10.1016/j.jmb.2007.04.076
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Mutually exclusive binding of telomerase RNA and DNA by Ku alters telomerase recruitment model.

Pfingsten, Jennifer S / Goodrich, Karen J / Taabazuing, Cornelius / Ouenzar, Faissal / Chartrand, Pascal / Cech, Thomas R

Cell

2012 Volume 148, Issue 5, Page(s) 922–932

Abstract: In Saccharomyces cerevisiae, the Ku heterodimer contributes to telomere maintenance as a component of telomeric chromatin and as an accessory subunit of telomerase. How Ku binding to double-stranded DNA (dsDNA) and to telomerase RNA (TLC1) promotes Ku's ... ...

Abstract	In Saccharomyces cerevisiae, the Ku heterodimer contributes to telomere maintenance as a component of telomeric chromatin and as an accessory subunit of telomerase. How Ku binding to double-stranded DNA (dsDNA) and to telomerase RNA (TLC1) promotes Ku's telomeric functions is incompletely understood. We demonstrate that deletions designed to constrict the DNA-binding ring of Ku80 disrupt nonhomologous end-joining (NHEJ), telomeric gene silencing, and telomere length maintenance, suggesting that these functions require Ku's DNA end-binding activity. Contrary to the current model, a mutant Ku with low affinity for dsDNA also loses affinity for TLC1 both in vitro and in vivo. Competition experiments reveal that wild-type Ku binds dsDNA and TLC1 mutually exclusively. Cells expressing the mutant Ku are deficient in nuclear accumulation of TLC1, as expected from the RNA-binding defect. These findings force reconsideration of the mechanisms by which Ku assists in recruiting telomerase to natural telomeres and broken chromosome ends. PAPERCLIP:
MeSH term(s)	Base Sequence ; DNA End-Joining Repair ; DNA-Binding Proteins/chemistry ; DNA-Binding Proteins/metabolism ; Models, Molecular ; Molecular Sequence Data ; Mutagenesis, Site-Directed ; RNA/metabolism ; Saccharomyces cerevisiae Proteins/chemistry ; Saccharomyces cerevisiae Proteins/metabolism ; Sequence Deletion ; Telomerase/chemistry ; Telomerase/metabolism ; Telomere/genetics ; Telomere/metabolism
Chemical Substances	DNA-Binding Proteins ; Saccharomyces cerevisiae Proteins ; high affinity DNA-binding factor, S cerevisiae ; telomerase RNA ; RNA (63231-63-0) ; Telomerase (EC 2.7.7.49)
Language	English
Publishing date	2012-02-23
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2012.01.033
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Article ; Online: Structural basis for ribosome recruitment and manipulation by a viral IRES RNA.

Pfingsten, Jennifer S / Costantino, David A / Kieft, Jeffrey S

Science (New York, N.Y.)

2006 Volume 314, Issue 5804, Page(s) 1450–1454

Abstract: Canonical cap-dependent translation initiation requires a large number of protein factors that act in a stepwise assembly process. In contrast, internal ribosomal entry sites (IRESs) are cis-acting RNAs that in some cases completely supplant these ... ...

Abstract	Canonical cap-dependent translation initiation requires a large number of protein factors that act in a stepwise assembly process. In contrast, internal ribosomal entry sites (IRESs) are cis-acting RNAs that in some cases completely supplant these factors by recruiting and activating the ribosome using a single structured RNA. Here we present the crystal structures of the ribosome-binding domain from a Dicistroviridae intergenic region IRES at 3.1 angstrom resolution, providing a view of the prefolded architecture of an all-RNA translation initiation apparatus. Docking of the structure into cryo-electron microscopy reconstructions of an IRES-ribosome complex suggests a model for ribosome manipulation by a dynamic IRES RNA.
MeSH term(s)	Binding Sites ; Cryoelectron Microscopy ; Crystallization ; Crystallography, X-Ray ; Models, Molecular ; Mutation ; Nucleic Acid Conformation ; Protein Biosynthesis ; RNA Viruses/genetics ; RNA, Viral/chemistry ; RNA, Viral/genetics ; RNA, Viral/metabolism ; Regulatory Sequences, Ribonucleic Acid/genetics ; Ribosomes/metabolism
Chemical Substances	RNA, Viral ; Regulatory Sequences, Ribonucleic Acid
Language	English
Publishing date	2006-12-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.1133281
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Article ; Online: The 5' leader of the mRNA encoding the mouse neurotrophin receptor TrkB contains two internal ribosomal entry sites that are differentially regulated.

Timmerman, Stephanie L / Pfingsten, Jennifer S / Kieft, Jeffrey S / Krushel, Les A

PloS one

2007 Volume 3, Issue 9, Page(s) e3242

Abstract: A single internal ribosomal entry site (IRES) in conjunction with IRES transactivating factors (ITAFs) is sufficient to recruit the translational machinery to a eukaryotic mRNA independent of the cap structure. However, we demonstrate that the mouse TrkB ...

Abstract	A single internal ribosomal entry site (IRES) in conjunction with IRES transactivating factors (ITAFs) is sufficient to recruit the translational machinery to a eukaryotic mRNA independent of the cap structure. However, we demonstrate that the mouse TrkB mRNA contains two independent IRESes. The mouse TrkB mRNA consists of one of two 5' leaders (1428 nt and 448 nt), both of which include the common 3' exon (Ex2, 344 nt). Dicistronic RNA transfections and in vitro translation of monocistronic RNA demonstrated that both full-length 5' leaders, as well as Ex2, exhibit IRES activity indicating the IRES is located within Ex2. Additional analysis of the upstream sequences demonstrated that the first 260 nt of exon 1 (Ex1a) also contains an IRES. Dicistronic RNA transfections into SH-SY5Y cells showed the Ex1a IRES is constitutively active. However, the Ex2 IRES is only active in response to retinoic acid induced neural differentiation, a state which correlates with the synthesis of the ITAF polypyrimidine tract binding protein (PTB1). Correspondingly, addition or knock-down of PTB1 altered Ex2, but not Ex1a IRES activity in vitro and ex vivo, respectively. These results demonstrate that the two functionally independent IRESes within the mouse TrkB 5' leader are differentially regulated, in part by PTB1.
MeSH term(s)	5' Untranslated Regions/genetics ; Animals ; Cell Line, Tumor ; Exons ; Fireflies/metabolism ; Gene Expression Regulation ; Genes ; Luciferases/metabolism ; Mice ; Models, Biological ; Polypyrimidine Tract-Binding Protein/metabolism ; Protein Binding ; Receptor, trkB/metabolism ; Receptor, trkB/physiology ; Renilla/metabolism ; Ribosomes/metabolism
Chemical Substances	5' Untranslated Regions ; Polypyrimidine Tract-Binding Protein (139076-35-0) ; Luciferases (EC 1.13.12.-) ; Receptor, trkB (EC 2.7.10.1)
Language	English
Publishing date	2007-09-19
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0003242
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: tRNA-mRNA mimicry drives translation initiation from a viral IRES.

Costantino, David A / Pfingsten, Jennifer S / Rambo, Robert P / Kieft, Jeffrey S

Nature structural & molecular biology

2007 Volume 15, Issue 1, Page(s) 57–64

Abstract: Internal ribosome entry site (IRES) RNAs initiate protein synthesis in eukaryotic cells by a noncanonical cap-independent mechanism. IRESes are critical for many pathogenic viruses, but efforts to understand their function are complicated by the ... ...

Abstract	Internal ribosome entry site (IRES) RNAs initiate protein synthesis in eukaryotic cells by a noncanonical cap-independent mechanism. IRESes are critical for many pathogenic viruses, but efforts to understand their function are complicated by the diversity of IRES sequences as well as by limited high-resolution structural information. The intergenic region (IGR) IRESes of the Dicistroviridae viruses are powerful model systems to begin to understand IRES function. Here we present the crystal structure of a Dicistroviridae IGR IRES domain that interacts with the ribosome's decoding groove. We find that this RNA domain precisely mimics the transfer RNA anticodon-messenger RNA codon interaction, and its modeled orientation on the ribosome helps explain translocation without peptide bond formation. When combined with a previous structure, this work completes the first high-resolution description of an IRES RNA and provides insight into how RNAs can manipulate complex biological machines.
MeSH term(s)	Anticodon/genetics ; Binding Sites ; Hepacivirus/genetics ; Models, Genetic ; Models, Molecular ; Nucleic Acid Conformation ; Protein Biosynthesis ; RNA, Messenger/chemistry ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; RNA, Transfer/chemistry ; RNA, Transfer/genetics ; RNA, Transfer/metabolism ; RNA, Viral/chemistry ; RNA, Viral/genetics ; RNA, Viral/metabolism ; Ribosomes/genetics ; Ribosomes/physiology
Chemical Substances	Anticodon ; RNA, Messenger ; RNA, Viral ; RNA, Transfer (9014-25-9)
Language	English
Publishing date	2007-12-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2126708-X
ISSN	1545-9985 ; 1545-9993
ISSN (online)	1545-9985
ISSN	1545-9993
DOI	10.1038/nsmb1351
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Article: Structural Basis for Ribosome Recruitment and Manipulation by a Viral IRES RNA

Pfingsten, Jennifer S / Costantino, David A / Kieft, Jeffrey S

Science. 2006 Dec. 1, v. 314, no. 5804

2006

Abstract	Canonical cap-dependent translation initiation requires a large number of protein factors that act in a stepwise assembly process. In contrast, internal ribosomal entry sites (IRESs) are cis-acting RNAs that in some cases completely supplant these factors by recruiting and activating the ribosome using a single structured RNA. Here we present the crystal structures of the ribosome-binding domain from a Dicistroviridae intergenic region IRES at 3.1 angstrom resolution, providing a view of the prefolded architecture of an all-RNA translation initiation apparatus. Docking of the structure into cryo-electron microscopy reconstructions of an IRES-ribosome complex suggests a model for ribosome manipulation by a dynamic IRES RNA.
Keywords	cryo-electron microscopy ; crystal structure ; Dicistroviridae ; intergenic DNA ; models ; ribosomes ; RNA
Language	English
Dates of publication	2006-1201
Size	p. 1450-1454.
Publishing place	American Association for the Advancement of Science
Document type	Article
ZDB-ID	128410-1
ISSN	1095-9203 ; 0036-8075
ISSN (online)	1095-9203
ISSN	0036-8075
DOI	10.1126/science.1133281
Database	NAL-Catalogue (AGRICOLA)

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