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2a3j

From Proteopedia

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Current revision

Structure of URNdesign, a complete computational redesign of human U1A protein

Structural highlights

2a3j is a 1 chain structure with sequence from Homo sapiens. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Solution NMR
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

SNRPA_HUMAN Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.^[1]

Evolutionary Conservation

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

Achieving atomic-level resolution in the computational design of a protein structure remains a challenging problem despite recent progress. Rigorous experimental tests are needed to improve protein design algorithms, yet studies of the structure and dynamics of computationally designed proteins are very few. The NMR structure and backbone dynamics of a redesigned protein of 96 amino acids are compared here with the design target, human U1A protein. We demonstrate that the redesigned protein reproduces the target structure to within the uncertainty of the NMR coordinates, even as 65 out of 96 amino acids were simultaneously changed by purely computational methods. The dynamics of the backbone of the redesigned protein also mirror those of human U1A, suggesting that the protein design algorithm captures the shape of the potential energy landscape in addition to the local energy minimum.

High-resolution structural validation of the computational redesign of human U1A protein.,Dobson N, Dantas G, Baker D, Varani G Structure. 2006 May;14(5):847-56. PMID:16698546^[2]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Lutz CS, Cooke C, O'Connor JP, Kobayashi R, Alwine JC. The snRNP-free U1A (SF-A) complex(es): identification of the largest subunit as PSF, the polypyrimidine-tract binding protein-associated splicing factor. RNA. 1998 Dec;4(12):1493-9. PMID:9848648
↑ Dobson N, Dantas G, Baker D, Varani G. High-resolution structural validation of the computational redesign of human U1A protein. Structure. 2006 May;14(5):847-56. PMID:16698546 doi:10.1016/j.str.2006.02.011

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2a3j"

@@ Line 1: / Line 1: @@
 ==Structure of URNdesign, a complete computational redesign of human U1A protein==
-<StructureSection load='2a3j' size='340' side='right' caption='[[2a3j]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''>
+<StructureSection load='2a3j' size='340' side='right'caption='[[2a3j]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2a3j]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A3J OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2A3J FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2a3j]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2A3J OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2A3J FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2a3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a3j OCA], [http://pdbe.org/2a3j PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2a3j RCSB], [http://www.ebi.ac.uk/pdbsum/2a3j PDBsum]</span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
+<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2a3j FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2a3j OCA], [https://pdbe.org/2a3j PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2a3j RCSB], [https://www.ebi.ac.uk/pdbsum/2a3j PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2a3j ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN]] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>
+[https://www.uniprot.org/uniprot/SNRPA_HUMAN SNRPA_HUMAN] Binds stem loop II of U1 snRNA. It is the first snRNP to interact with pre-mRNA. This interaction is required for the subsequent binding of U2 snRNP and the U4/U6/U5 tri-snRNP. In a snRNP-free form (SF-A) may be involved in coupled pre-mRNA splicing and polyadenylation process. Binds preferentially to the 5'-UGCAC-3' motif in vitro.<ref>PMID:9848648</ref>
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
 Check<jmol>
   <jmolCheckbox>
-    <scriptWhenChecked>select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a3/2a3j_consurf.spt"</scriptWhenChecked>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/a3/2a3j_consurf.spt"</scriptWhenChecked>
     <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
@@ Line 28: / Line 30: @@
 ==See Also==
-*[[Nucleoprotein|Nucleoprotein]]
+*[[Nucleoprotein 3D structures|Nucleoprotein 3D structures]]
 == References ==
 <references/>
 __TOC__
 </StructureSection>
-[[Category: Human]]
+[[Category: Homo sapiens]]
-[[Category: Baker, D]]
+[[Category: Large Structures]]
-[[Category: Dantas, G]]
+[[Category: Baker D]]
-[[Category: Dobson, N]]
+[[Category: Dantas G]]
-[[Category: Varani, G]]
+[[Category: Dobson N]]
-[[Category: Computationally designed protein]]
+[[Category: Varani G]]
-[[Category: Rna binding protein]]
-[[Category: Rrm]]
-[[Category: U1a]]

2a3j

From Proteopedia

Current revision

Structure of URNdesign, a complete computational redesign of human U1A protein

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

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