2pea

From Proteopedia

(Difference between revisions)

Revision as of 10:33, 11 September 2015

NMR Based Structure of the Closed Conformation of LYS48-Linked Di-Ubiquitin Using Experimental Global Rotational Diffusion Tensor from NMR Relaxation Measurements

Structural highlights

2pea is a 2 chain structure with sequence from Human. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance.
Related:	1d3z, 1aar, 2bgf, 2pe9
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

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

We present a simple and robust approach that uses the overall rotational diffusion tensor as a structural constraint for domain positioning in multidomain proteins and protein-protein complexes. This method offers the possibility to use NMR relaxation data for detailed structure characterization of such systems provided the structures of individual domains are available. The proposed approach extends the concept of using long-range information contained in the overall rotational diffusion tensor. In contrast to the existing approaches, we use both the principal axes and principal values of protein's rotational diffusion tensor to determine not only the orientation but also the relative positioning of the individual domains in a protein. This is achieved by finding the domain arrangement in a molecule that provides the best possible agreement with all components of the overall rotational diffusion tensor derived from experimental data. The accuracy of the proposed approach is demonstrated for two protein systems with known domain arrangement and parameters of the overall tumbling: the HIV-1 protease homodimer and Maltose Binding Protein. The accuracy of the method and its sensitivity to domain positioning are also tested using computer-generated data for three protein complexes, for which the experimental diffusion tensors are not available. In addition, the proposed method is applied here to determine, for the first time, the structure of both open and closed conformations of a Lys48-linked diubiquitin chain, where domain motions render impossible accurate structure determination by other methods. The proposed method opens new avenues for improving structure characterization of proteins in solution.

Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor.,Ryabov Y, Fushman D J Am Chem Soc. 2007 Jun 27;129(25):7894-902. Epub 2007 Jun 6. PMID:17550252^[1]

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

References

↑ Ryabov Y, Fushman D. Structural assembly of multidomain proteins and protein complexes guided by the overall rotational diffusion tensor. J Am Chem Soc. 2007 Jun 27;129(25):7894-902. Epub 2007 Jun 6. PMID:17550252 doi:10.1021/ja071185d

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

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

@@ Line 2: / Line 2: @@
 <StructureSection load='2pea' size='340' side='right' caption='[[2pea]], [[NMR_Ensembles_of_Models | 1 NMR models]]' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[2pea]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2PEA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PEA FirstGlance]. <br>
+<table><tr><td colspan='2'>[[2pea]] is a 2 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=2PEA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2PEA FirstGlance]. <br>
 </td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1d3z|1d3z]], [[1aar|1aar]], [[2bgf|2bgf]], [[2pe9|2pe9]]</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=2pea FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pea OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2pea RCSB], [http://www.ebi.ac.uk/pdbsum/2pea PDBsum]</span></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=2pea FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2pea OCA], [http://pdbe.org/2pea PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2pea RCSB], [http://www.ebi.ac.uk/pdbsum/2pea PDBsum]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 24: / Line 24: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2pea" style="background-color:#fffaf0;"></div>
 ==See Also==
@@ Line 31: / Line 32: @@
 __TOC__
 </StructureSection>
-[[Category: Homo sapiens]]
+[[Category: Human]]
 [[Category: Fushman, D]]
 [[Category: Ryabov, Y]]

2pea

From Proteopedia

Revision as of 10:33, 11 September 2015

NMR Based Structure of the Closed Conformation of LYS48-Linked Di-Ubiquitin Using Experimental Global Rotational Diffusion Tensor from NMR Relaxation Measurements

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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