1ooa: Difference between revisions

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

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

caption="1ooa, resolution 2.45Å" />

'''CRYSTAL STRUCTURE OF NF-kB(p50)2 COMPLEXED TO A HIGH-AFFINITY RNA APTAMER'''<br />

==Overview==

We have recently identified an RNA aptamer for the transcription factor, NF-kappaB p50 homodimer [(p50)2], which exhibits little sequence, resemblance to the consensus DNA target for (p50)2, but binds (p50)2 with, an affinity similar to that of the optimal DNA target. We describe here, the 2.45-A resolution x-ray crystal structure of the p50 RHR/RNA aptamer, complex. The structure reveals that two RNA molecules bind independent of, each other to the p50 N-terminal Ig-like domains. The RNA secondary, structure is comprised of a stem and a stem-loop separated by an internal, loop folded into a kinked helix because of the cross-strand stacking of, three internal loop guanines. These guanines, placed at the edge of the 3', helix, together with the major groove of the irregular 3' helix, form the, binding surface for p50. Each p50 monomer uses the same surface to, recognize the distorted RNA major groove as observed in the kappaB DNA/p50, RHR complex, resulting in strikingly similar interfaces. The structure, reveals how the aptamer specifically selects p50 and discriminates against, p65. We also discuss the physiological implications of RNA binding by, (p50)2.

We have recently identified an RNA aptamer for the transcription factor NF-kappaB p50 homodimer [(p50)2], which exhibits little sequence resemblance to the consensus DNA target for (p50)2, but binds (p50)2 with an affinity similar to that of the optimal DNA target. We describe here the 2.45-A resolution x-ray crystal structure of the p50 RHR/RNA aptamer complex. The structure reveals that two RNA molecules bind independent of each other to the p50 N-terminal Ig-like domains. The RNA secondary structure is comprised of a stem and a stem-loop separated by an internal loop folded into a kinked helix because of the cross-strand stacking of three internal loop guanines. These guanines, placed at the edge of the 3' helix, together with the major groove of the irregular 3' helix, form the binding surface for p50. Each p50 monomer uses the same surface to recognize the distorted RNA major groove as observed in the kappaB DNA/p50 RHR complex, resulting in strikingly similar interfaces. The structure reveals how the aptamer specifically selects p50 and discriminates against p65. We also discuss the physiological implications of RNA binding by (p50)2.

==About this Structure==

1OOA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://~~ispc~~.weizmann.ac.il/oca-bin/ocashort?id=1OOA OCA].

1OOA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OOA OCA].

==Reference==

Line 13:

[[Category: Mus musculus]]

[[Category: Single protein]]

[[Category: Cassiday, L.A.]]

[[Category: Cassiday, L A.]]

[[Category: Ghosh, G.]]

[[Category: Huang, D.B.]]

[[Category: Huang, D B.]]

[[Category: III, L.J.Maher.]]

[[Category: III, L J.Maher.]]

[[Category: Vu, D.]]

[[Category: Zimmerman, J.M.]]

[[Category: Zimmerman, J M.]]

[[Category: crystal structure]]

[[Category: protein-rna complex]]

[[Category: transcription factor nf-kb]]

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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:19:53 2008''

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@@ Line 1: / Line 1: @@
-[[Image:1ooa.gif|left|200px]]<br /><applet load="1ooa" size="450" color="white" frame="true" align="right" spinBox="true"
+[[Image:1ooa.gif|left|200px]]<br /><applet load="1ooa" size="350" color="white" frame="true" align="right" spinBox="true"
 caption="1ooa, resolution 2.45&Aring;" />
 '''CRYSTAL STRUCTURE OF NF-kB(p50)2 COMPLEXED TO A HIGH-AFFINITY RNA APTAMER'''<br />
 ==Overview==
-We have recently identified an RNA aptamer for the transcription factor, NF-kappaB p50 homodimer [(p50)2], which exhibits little sequence, resemblance to the consensus DNA target for (p50)2, but binds (p50)2 with, an affinity similar to that of the optimal DNA target. We describe here, the 2.45-A resolution x-ray crystal structure of the p50 RHR/RNA aptamer, complex. The structure reveals that two RNA molecules bind independent of, each other to the p50 N-terminal Ig-like domains. The RNA secondary, structure is comprised of a stem and a stem-loop separated by an internal, loop folded into a kinked helix because of the cross-strand stacking of, three internal loop guanines. These guanines, placed at the edge of the 3', helix, together with the major groove of the irregular 3' helix, form the, binding surface for p50. Each p50 monomer uses the same surface to, recognize the distorted RNA major groove as observed in the kappaB DNA/p50, RHR complex, resulting in strikingly similar interfaces. The structure, reveals how the aptamer specifically selects p50 and discriminates against, p65. We also discuss the physiological implications of RNA binding by, (p50)2.
+We have recently identified an RNA aptamer for the transcription factor NF-kappaB p50 homodimer [(p50)2], which exhibits little sequence resemblance to the consensus DNA target for (p50)2, but binds (p50)2 with an affinity similar to that of the optimal DNA target. We describe here the 2.45-A resolution x-ray crystal structure of the p50 RHR/RNA aptamer complex. The structure reveals that two RNA molecules bind independent of each other to the p50 N-terminal Ig-like domains. The RNA secondary structure is comprised of a stem and a stem-loop separated by an internal loop folded into a kinked helix because of the cross-strand stacking of three internal loop guanines. These guanines, placed at the edge of the 3' helix, together with the major groove of the irregular 3' helix, form the binding surface for p50. Each p50 monomer uses the same surface to recognize the distorted RNA major groove as observed in the kappaB DNA/p50 RHR complex, resulting in strikingly similar interfaces. The structure reveals how the aptamer specifically selects p50 and discriminates against p65. We also discuss the physiological implications of RNA binding by (p50)2.
 ==About this Structure==
-OOA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1OOA OCA].
+OOA is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OOA OCA].
 ==Reference==
@@ Line 13: / Line 13: @@
 [[Category: Mus musculus]]
 [[Category: Single protein]]
-[[Category: Cassiday, L.A.]]
+[[Category: Cassiday, L A.]]
 [[Category: Ghosh, G.]]
-[[Category: Huang, D.B.]]
+[[Category: Huang, D B.]]
-[[Category: III, L.J.Maher.]]
+[[Category: III, L J.Maher.]]
 [[Category: Vu, D.]]
-[[Category: Zimmerman, J.M.]]
+[[Category: Zimmerman, J M.]]
 [[Category: crystal structure]]
 [[Category: protein-rna complex]]
 [[Category: transcription factor nf-kb]]
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Tue Nov 20 23:03:41 2007''
+''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 14:19:53 2008''