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2at9

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Revision as of 13:06, 10 September 2015

STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM BY ELECTRON CRYSTALLOGRAPHY

Structural highlights

2at9 is a 1 chain structure with sequence from Halobacterium salinarum. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	,
NonStd Res:
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum

Function

[BACR_HALSA] Light-driven proton pump.

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

Electron crystallography has the potential to visualise the charge status of atoms. This is due to the significantly different scattering factors of neutral and ionised atoms for electrons in the low-resolution range (typically less than 5 A). In previous work, we observed two different types of densities around acidic residues in the experimental (|Fo|) map of bacteriorhodopsin (bR), a light-driven proton pump. We suggested that these might reflect different states of the acidic residues; namely, the protonated (neutral) and the deprotonated (negatively charged) state. To evaluate the observed charge more quantitatively, we refined the atomic model for bR and eight surrounding lipids using our electron crystallographic data set between 8.0 and 3.0 A resolution, where the charge effect is small. The refined model yielded an R-factor of 23.7% and a free R-factor of 33.0%. To evaluate the effect of charges on the density map, we calculated a difference (|Fo|-|Fc|) map including data of a resolution lower than 8.0 A resolution, where the charge effect is significant. We found strong peaks in the difference map mainly in the backbone region of the transmembrane helices. We interpreted these peaks to come from the polarisation of the polar groups in the main chain of the alpha-helices and we examined this by assuming a partial charge of 0.5 for the peptide carbonyl groups. The resulting R and free R-factors dropped from 0.250 and 0.341 to 0.246 and 0.336, respectively. Furthermore, we also observed some strong peaks around some side-chains, which could be assigned to positively charged atoms. Thus, we could show that Asp36 and Asp102 are likely to interact with cations nearby. In addition, peaks found around the acidic residues Glu74, Glu194 and Glu212 have different features and might represent positive charges on polarised water molecules or hydroxonium ions.

The structure of bacteriorhodopsin at 3.0 A resolution based on electron crystallography: implication of the charge distribution.,Mitsuoka K, Hirai T, Murata K, Miyazawa A, Kidera A, Kimura Y, Fujiyoshi Y J Mol Biol. 1999 Feb 26;286(3):861-82. PMID:10024456^[1]

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

References

↑ Mitsuoka K, Hirai T, Murata K, Miyazawa A, Kidera A, Kimura Y, Fujiyoshi Y. The structure of bacteriorhodopsin at 3.0 A resolution based on electron crystallography: implication of the charge distribution. J Mol Biol. 1999 Feb 26;286(3):861-82. PMID:10024456 doi:10.1006/jmbi.1998.2529

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/2at9"

@@ Line 5: / Line 5: @@
 </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=2DP:3-[[3-METHYLPHOSPHONO-GLYCEROLYL]PHOSPHONYL]-[1,2-DI[2,6,10,14-TETRAMETHYL-HEXADECAN-16-YL]GLYCEROL'>2DP</scene>, <scene name='pdbligand=RET:RETINAL'>RET</scene></td></tr>
 <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=PCA:PYROGLUTAMIC+ACID'>PCA</scene></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=2at9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2at9 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=2at9 RCSB], [http://www.ebi.ac.uk/pdbsum/2at9 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=2at9 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2at9 OCA], [http://pdbe.org/2at9 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2at9 RCSB], [http://www.ebi.ac.uk/pdbsum/2at9 PDBsum]</span></td></tr>
 </table>
+== Function ==
+[[http://www.uniprot.org/uniprot/BACR_HALSA BACR_HALSA]] Light-driven proton pump.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 25: / Line 27: @@
 From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 </div>
+<div class="pdbe-citations 2at9" style="background-color:#fffaf0;"></div>
 ==See Also==

2at9

From Proteopedia

Revision as of 13:06, 10 September 2015

STRUCTURE OF BACTERIORHODOPSIN AT 3.0 ANGSTROM BY ELECTRON CRYSTALLOGRAPHY

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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