2jsv

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px <!-- The line below this paragraph, containing "STRUCTURE_2jsv", creates the "Structure Box" on the page. You may change the PDB parameter (which sets the PD...)
Current revision (19:04, 29 May 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:2jsv.jpg|left|200px]]
 
-
<!--
+
==Dipole tensor-based refinement for atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR spectroscopy==
-
The line below this paragraph, containing "STRUCTURE_2jsv", creates the "Structure Box" on the page.
+
<StructureSection load='2jsv' size='340' side='right'caption='[[2jsv]]' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[2jsv]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Streptococcus_sp._'group_G' Streptococcus sp. 'group G']. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JSV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2JSV FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solid-state 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=2jsv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2jsv OCA], [https://pdbe.org/2jsv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2jsv RCSB], [https://www.ebi.ac.uk/pdbsum/2jsv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2jsv ProSAT]</span></td></tr>
-
{{STRUCTURE_2jsv| PDB=2jsv | SCENE= }}
+
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/SPG2_STRSG SPG2_STRSG]
 +
== 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/js/2jsv_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.spt</scriptWhenUnchecked>
 +
<text>to colour the structure by Evolutionary Conservation</text>
 +
</jmolCheckbox>
 +
</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=2jsv ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Magic-angle spinning (MAS) solid-state NMR (SSNMR) techniques have emerged in recent years for solving complete structures of uniformly labeled proteins lacking macroscopic order. Strategies used thus far have relied primarily on semiquantitative distance restraints, analogous to the nuclear Overhauser effect (NOE) routinely used in solution NMR. Here, we present a complementary approach for using relative orientations of molecular fragments, determined from dipolar line shapes. Whereas SSNMR distance restraints typically have an uncertainty of approximately 1 A, the tensor-based experiments report on relative vector (pseudobond) angles with precision of a few degrees. By using 3D techniques of this type, vector angle (VEAN) restraints were determined for the majority of the 56-residue B1 immunoglobulin binding domain of protein G [protein GB1 (a total of 47 HN-HN, 49 HN-HC, and 12 HA-HB restraints)]. By using distance restraints alone in the structure calculations, the overall backbone root-mean-square deviation (bbRMSD) was 1.01 +/- 0.13 A (1.52 +/- 0.12 A for all heavy atoms), which improved to 0.49 +/- 0.05 A (1.19 +/- 0.07 A) on the addition of empirical chemical shift [torsion angle likelihood obtained from shift and sequence similarity (TALOS)] restraints. VEAN restraints further improved the ensemble to 0.31 +/- 0.06 A bbRMSD (1.06 +/- 0.07 A); relative to the structure with distances alone, most of the improvement remained (bbRMSD 0.64 +/- 0.09 A; 1.29 +/- 0.07 A) when TALOS restraints were removed before refinement. These results represent significant progress toward atomic-resolution protein structure determination by SSNMR, capabilities that can be applied to a large range of membrane proteins and fibrils, which are often not amenable to solution NMR or x-ray crystallography.
-
'''Dipole tensor-based refinement for atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR spectroscopy'''
+
Dipole tensor-based atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR.,Franks WT, Wylie BJ, Schmidt HL, Nieuwkoop AJ, Mayrhofer RM, Shah GJ, Graesser DT, Rienstra CM Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4621-6. Epub 2008 Mar 14. PMID:18344321<ref>PMID:18344321</ref>
-
 
+
-
 
+
-
==Overview==
+
-
Magic-angle spinning (MAS) solid-state NMR (SSNMR) techniques have emerged in recent years for solving complete structures of uniformly labeled proteins lacking macroscopic order. Strategies used thus far have relied primarily on semiquantitative distance restraints, analogous to the nuclear Overhauser effect (NOE) routinely used in solution NMR. Here, we present a complementary approach for using relative orientations of molecular fragments, determined from dipolar line shapes. Whereas SSNMR distance restraints typically have an uncertainty of approximately 1 A, the tensor-based experiments report on relative vector (pseudobond) angles with precision of a few degrees. By using 3D techniques of this type, vector angle (VEAN) restraints were determined for the majority of the 56-residue B1 immunoglobulin binding domain of protein G [protein GB1 (a total of 47 HN-HN, 49 HN-HC, and 12 HA-HB restraints)]. By using distance restraints alone in the structure calculations, the overall backbone root-mean-square deviation (bbRMSD) was 1.01 +/- 0.13 A (1.52 +/- 0.12 A for all heavy atoms), which improved to 0.49 +/- 0.05 A (1.19 +/- 0.07 A) on the addition of empirical chemical shift [torsion angle likelihood obtained from shift and sequence similarity (TALOS)] restraints. VEAN restraints further improved the ensemble to 0.31 +/- 0.06 A bbRMSD (1.06 +/- 0.07 A); relative to the structure with distances alone, most of the improvement remained (bbRMSD 0.64 +/- 0.09 A; 1.29 +/- 0.07 A) when TALOS restraints were removed before refinement. These results represent significant progress toward atomic-resolution protein structure determination by SSNMR, capabilities that can be applied to a large range of membrane proteins and fibrils, which are often not amenable to solution NMR or x-ray crystallography.
+
-
==About this Structure==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
2JSV is a [[Single protein]] structure of sequence from [http://en.wikipedia.org/wiki/Bacteria Bacteria]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2JSV OCA].
+
</div>
 +
<div class="pdbe-citations 2jsv" style="background-color:#fffaf0;"></div>
-
==Reference==
+
==See Also==
-
Dipole tensor-based atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR., Franks WT, Wylie BJ, Schmidt HL, Nieuwkoop AJ, Mayrhofer RM, Shah GJ, Graesser DT, Rienstra CM, Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4621-6. Epub 2008 Mar 14. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/18344321 18344321]
+
*[[Protein G|Protein G]]
-
[[Category: Bacteria]]
+
== References ==
-
[[Category: Single protein]]
+
<references/>
-
[[Category: Franks, W.]]
+
__TOC__
-
[[Category: Frericks, H L.]]
+
</StructureSection>
-
[[Category: Graesser, D T.]]
+
[[Category: Large Structures]]
-
[[Category: Mayrhofer, R.]]
+
[[Category: Streptococcus sp. 'group G']]
-
[[Category: Nieuwkoop, A J.]]
+
[[Category: Franks W]]
-
[[Category: Rienstra, C M.]]
+
[[Category: Frericks HL]]
-
[[Category: Shah, G J.]]
+
[[Category: Graesser DT]]
-
[[Category: Wylie, B J.]]
+
[[Category: Mayrhofer R]]
-
[[Category: Cell wall]]
+
[[Category: Nieuwkoop AJ]]
-
[[Category: Gb1]]
+
[[Category: Rienstra CM]]
-
[[Category: Igg-binding protein]]
+
[[Category: Shah GJ]]
-
[[Category: Immune system]]
+
[[Category: Wylie BJ]]
-
[[Category: Peptidoglycan-anchor]]
+
-
[[Category: Ssnmr]]
+
-
[[Category: Tensor refinement]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Apr 16 23:01:53 2008''
+

Current revision

Dipole tensor-based refinement for atomic-resolution structure determination of a nanocrystalline protein by solid-state NMR spectroscopy

PDB ID 2jsv

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/2jsv"
Personal tools