1txs: Difference between revisions

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[[Image:1txs.gif|left|200px]]<br /><applet load="1txs" size="~~450~~" color="white" frame="true" align="right" spinBox="true"

[[Image:1txs.gif|left|200px]]<br /><applet load="1txs" size="350" color="white" frame="true" align="right" spinBox="true"

caption="1txs" />

'''STEM-LOOP D OF THE CLOVERLEAF DOMAIN OF ENTEROVIRAL 5'UTR RNA'''<br />

==Overview==

Stem-loop D from the cloverleaf RNA is a highly conserved domain within, the 5'-UTR of enteroviruses and rhinoviruses. Interaction between the, stem-loop D RNA and the viral 3C or 3CD proteins constitutes an essential, feature of a ribonucleoprotein complex that plays a critical role in, regulating viral translation and replication. Here we report the solution, NMR structure of a 38-nucleotide RNA with a sequence that encompasses the, entire stem-loop D domain and corresponds to the consensus sequence found, in enteroviruses and rhinoviruses. Sequence variants corresponding to, Poliovirus type 1 and Coxsackievirus B3 have virtually the same structure, based on small differences in chemical shifts. A substantial number (136), of (1)H-(13)C one-bond residual dipolar coupling (RDC) values were used in, the structure determination in addition to conventional distance and, torsion angle restraints. Inclusion of the RDC restraints was essential, for achieving well-defined structures, both globally and locally. The, structure of the consensus stem-loop D is an elongated A-type helical stem, capped by a UACG tetraloop with a wobble UG closing base pair. Three, consecutive pyrimidine base pairs (two UU and one CU pair) are present in, the middle of the helical stem, creating distinctive local structural, features such as a dramatically widened major groove. A dinucleotide bulge, is located near the base of the stem. The bulge itself is flexible and not, as well defined as the other parts of the molecule, but the flanking base, pairs are intact. The peculiar spatial arrangement of the distinctive, structural elements implies that they may work synergistically to achieve, optimal binding affinity and specificity toward the viral 3C or 3CD, proteins.

Stem-loop D from the cloverleaf RNA is a highly conserved domain within the 5'-UTR of enteroviruses and rhinoviruses. Interaction between the stem-loop D RNA and the viral 3C or 3CD proteins constitutes an essential feature of a ribonucleoprotein complex that plays a critical role in regulating viral translation and replication. Here we report the solution NMR structure of a 38-nucleotide RNA with a sequence that encompasses the entire stem-loop D domain and corresponds to the consensus sequence found in enteroviruses and rhinoviruses. Sequence variants corresponding to Poliovirus type 1 and Coxsackievirus B3 have virtually the same structure, based on small differences in chemical shifts. A substantial number (136) of (1)H-(13)C one-bond residual dipolar coupling (RDC) values were used in the structure determination in addition to conventional distance and torsion angle restraints. Inclusion of the RDC restraints was essential for achieving well-defined structures, both globally and locally. The structure of the consensus stem-loop D is an elongated A-type helical stem capped by a UACG tetraloop with a wobble UG closing base pair. Three consecutive pyrimidine base pairs (two UU and one CU pair) are present in the middle of the helical stem, creating distinctive local structural features such as a dramatically widened major groove. A dinucleotide bulge is located near the base of the stem. The bulge itself is flexible and not as well defined as the other parts of the molecule, but the flanking base pairs are intact. The peculiar spatial arrangement of the distinctive structural elements implies that they may work synergistically to achieve optimal binding affinity and specificity toward the viral 3C or 3CD proteins.

==About this Structure==

1TXS is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=1TXS OCA].

1TXS is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TXS OCA].

==Reference==

Line 14:

[[Category: Andino, R.]]

[[Category: Du, Z.]]

[[Category: James, T.L.]]

[[Category: James, T L.]]

[[Category: Ulyanov, N.B.]]

[[Category: Ulyanov, N B.]]

[[Category: Yu, J.]]

[[Category: closing wobble ug pair]]

Line 22:

[[Category: two-nucleotide bulge]]

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@@ Line 1: / Line 1: @@
-[[Image:1txs.gif|left|200px]]<br /><applet load="1txs" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1txs.gif|left|200px]]<br /><applet load="1txs" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1txs" />
 '''STEM-LOOP D OF THE CLOVERLEAF DOMAIN OF ENTEROVIRAL 5'UTR RNA'''<br />
 ==Overview==
-Stem-loop D from the cloverleaf RNA is a highly conserved domain within, the 5'-UTR of enteroviruses and rhinoviruses. Interaction between the, stem-loop D RNA and the viral 3C or 3CD proteins constitutes an essential, feature of a ribonucleoprotein complex that plays a critical role in, regulating viral translation and replication. Here we report the solution, NMR structure of a 38-nucleotide RNA with a sequence that encompasses the, entire stem-loop D domain and corresponds to the consensus sequence found, in enteroviruses and rhinoviruses. Sequence variants corresponding to, Poliovirus type 1 and Coxsackievirus B3 have virtually the same structure, based on small differences in chemical shifts. A substantial number (136), of (1)H-(13)C one-bond residual dipolar coupling (RDC) values were used in, the structure determination in addition to conventional distance and, torsion angle restraints. Inclusion of the RDC restraints was essential, for achieving well-defined structures, both globally and locally. The, structure of the consensus stem-loop D is an elongated A-type helical stem, capped by a UACG tetraloop with a wobble UG closing base pair. Three, consecutive pyrimidine base pairs (two UU and one CU pair) are present in, the middle of the helical stem, creating distinctive local structural, features such as a dramatically widened major groove. A dinucleotide bulge, is located near the base of the stem. The bulge itself is flexible and not, as well defined as the other parts of the molecule, but the flanking base, pairs are intact. The peculiar spatial arrangement of the distinctive, structural elements implies that they may work synergistically to achieve, optimal binding affinity and specificity toward the viral 3C or 3CD, proteins.
+Stem-loop D from the cloverleaf RNA is a highly conserved domain within the 5'-UTR of enteroviruses and rhinoviruses. Interaction between the stem-loop D RNA and the viral 3C or 3CD proteins constitutes an essential feature of a ribonucleoprotein complex that plays a critical role in regulating viral translation and replication. Here we report the solution NMR structure of a 38-nucleotide RNA with a sequence that encompasses the entire stem-loop D domain and corresponds to the consensus sequence found in enteroviruses and rhinoviruses. Sequence variants corresponding to Poliovirus type 1 and Coxsackievirus B3 have virtually the same structure, based on small differences in chemical shifts. A substantial number (136) of (1)H-(13)C one-bond residual dipolar coupling (RDC) values were used in the structure determination in addition to conventional distance and torsion angle restraints. Inclusion of the RDC restraints was essential for achieving well-defined structures, both globally and locally. The structure of the consensus stem-loop D is an elongated A-type helical stem capped by a UACG tetraloop with a wobble UG closing base pair. Three consecutive pyrimidine base pairs (two UU and one CU pair) are present in the middle of the helical stem, creating distinctive local structural features such as a dramatically widened major groove. A dinucleotide bulge is located near the base of the stem. The bulge itself is flexible and not as well defined as the other parts of the molecule, but the flanking base pairs are intact. The peculiar spatial arrangement of the distinctive structural elements implies that they may work synergistically to achieve optimal binding affinity and specificity toward the viral 3C or 3CD proteins.
 ==About this Structure==
-TXS is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1TXS OCA].
+TXS is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TXS OCA].
 ==Reference==
@@ Line 14: / Line 14: @@
 [[Category: Andino, R.]]
 [[Category: Du, Z.]]
-[[Category: James, T.L.]]
+[[Category: James, T L.]]
-[[Category: Ulyanov, N.B.]]
+[[Category: Ulyanov, N B.]]
 [[Category: Yu, J.]]
 [[Category: closing wobble ug pair]]
@@ Line 22: / Line 22: @@
 [[Category: two-nucleotide bulge]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 02:56:23 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 15:18:28 2008''