This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.

3d38

From Proteopedia

(Difference between revisions)

Jump to: navigation, search

Revision as of 12:25, 25 December 2014

Crystal structure of new trigonal form of photosynthetic reaction center from Blastochloris viridis. Crystals grown in microfluidics by detergent capture.

Structural highlights

3d38 is a 4 chain structure with sequence from Blastochloris viridis. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , , , , , , ,
NonStd Res:
Resources:	FirstGlance, OCA, RCSB, PDBsum

Function

[RCEM_RHOVI] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis. [CYCR_RHOVI] The reaction center of purple bacteria contains a tightly bound cytochrome molecule which re-reduces the photo oxidized primary electron donor. [RCEL_RHOVI] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis. [RCEH_RHOVI] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis.

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

This paper utilizes cyclodextrin-based host-guest chemistry in a microfluidic device to modulate the crystallization of membrane proteins and the process of concentration of membrane protein samples. Methyl-beta-cyclodextrin (MBCD) can efficiently capture a wide variety of detergents commonly used for the stabilization of membrane proteins by sequestering detergent monomers. Reaction Center (RC) from Blastochloris viridis was used here as a model system. In the process of concentrating membrane protein samples, MBCD was shown to break up free detergent micelles and prevent them from being concentrated. The addition of an optimal amount of MBCD to the RC sample captured loosely bound detergent from the protein-detergent complex and improved sample homogeneity, as characterized by dynamic light scattering. Using plug-based microfluidics, RC crystals were grown in the presence of MBCD, giving a different morphology and space group than crystals grown without MBCD. The crystal structure of RC crystallized in the presence of MBCD was consistent with the changes in packing and crystal contacts hypothesized for removal of loosely bound detergent. The incorporation of MBCD into a plug-based microfluidic crystallization method allows efficient use of limited membrane protein sample by reducing the amount of protein required and combining sparse matrix screening and optimization in one experiment. The use of MBCD for detergent capture can be expanded to develop cyclodextrin-derived molecules for fine-tuned detergent capture and thus modulate membrane protein crystallization in an even more controllable way.

Simple host-guest chemistry to modulate the process of concentration and crystallization of membrane proteins by detergent capture in a microfluidic device.,Li L, Nachtergaele S, Seddon AM, Tereshko V, Ponomarenko N, Ismagilov RF J Am Chem Soc. 2008 Oct 29;130(43):14324-8. Epub 2008 Oct 3. PMID:18831551^[1]

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

References

↑ Li L, Nachtergaele S, Seddon AM, Tereshko V, Ponomarenko N, Ismagilov RF. Simple host-guest chemistry to modulate the process of concentration and crystallization of membrane proteins by detergent capture in a microfluidic device. J Am Chem Soc. 2008 Oct 29;130(43):14324-8. Epub 2008 Oct 3. PMID:18831551 doi:10.1021/ja805361j

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/3d38"

@@ Line 3: / Line 3: @@
 == Structural highlights ==
 <table><tr><td colspan='2'>[[3d38]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Blastochloris_viridis Blastochloris viridis]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3D38 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3D38 FirstGlance]. <br>
-</td></tr><tr><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCB:BACTERIOCHLOROPHYLL+B'>BCB</scene>, <scene name='pdbligand=BPB:BACTERIOPHEOPHYTIN+B'>BPB</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HTO:HEPTANE-1,2,3-TRIOL'>HTO</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=MQ9:MENAQUINONE-9'>MQ9</scene>, <scene name='pdbligand=NS5:15-CIS-1,2-DIHYDRONEUROSPORENE'>NS5</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UQ1:UBIQUINONE-1'>UQ1</scene><br>
+</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCB:BACTERIOCHLOROPHYLL+B'>BCB</scene>, <scene name='pdbligand=BPB:BACTERIOPHEOPHYTIN+B'>BPB</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HTO:HEPTANE-1,2,3-TRIOL'>HTO</scene>, <scene name='pdbligand=LDA:LAURYL+DIMETHYLAMINE-N-OXIDE'>LDA</scene>, <scene name='pdbligand=MQ9:MENAQUINONE-9'>MQ9</scene>, <scene name='pdbligand=NS5:15-CIS-1,2-DIHYDRONEUROSPORENE'>NS5</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=UQ1:UBIQUINONE-1'>UQ1</scene></td></tr>
-<tr><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene></td></tr>
+<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=FME:N-FORMYLMETHIONINE'>FME</scene></td></tr>
-<tr><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=3d38 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d38 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d38 RCSB], [http://www.ebi.ac.uk/pdbsum/3d38 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=3d38 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3d38 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=3d38 RCSB], [http://www.ebi.ac.uk/pdbsum/3d38 PDBsum]</span></td></tr>
-<table>
+</table>
+== Function ==
+[[http://www.uniprot.org/uniprot/RCEM_RHOVI RCEM_RHOVI]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis. [[http://www.uniprot.org/uniprot/CYCR_RHOVI CYCR_RHOVI]] The reaction center of purple bacteria contains a tightly bound cytochrome molecule which re-reduces the photo oxidized primary electron donor. [[http://www.uniprot.org/uniprot/RCEL_RHOVI RCEL_RHOVI]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis. [[http://www.uniprot.org/uniprot/RCEH_RHOVI RCEH_RHOVI]] The reaction center is a membrane-bound complex that mediates the initial photochemical event in the electron transfer process of photosynthesis.
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 33: / Line 35: @@
 </StructureSection>
 [[Category: Blastochloris viridis]]
-[[Category: ATCG3D, Accelerated Technologies Center for Gene to 3D Structure.]]
+[[Category: ATCG3D, Accelerated Technologies Center for Gene to 3D Structure]]
-[[Category: Ismagilov, R F.]]
+[[Category: Ismagilov, R F]]
-[[Category: Li, L.]]
+[[Category: Li, L]]
-[[Category: Nachtergaele, S H.M.]]
+[[Category: Nachtergaele, S H.M]]
-[[Category: Ponomarenko, N.]]
+[[Category: Ponomarenko, N]]
-[[Category: Seddon, A M.]]
+[[Category: Seddon, A M]]
-[[Category: Tereshko, V.]]
+[[Category: Tereshko, V]]
 [[Category: Accelerated technologies center for gene to 3d structure]]
 [[Category: Atcg3d]]
@@ Line 57: / Line 59: @@
 [[Category: Photosynthesis]]
 [[Category: Plug]]
-[[Category: Protein structure initiative]]
+[[Category: PSI, Protein structure initiative]]
-[[Category: Psi-2]]
 [[Category: Reaction center]]
 [[Category: Structural genomic]]
 [[Category: Transmembrane]]
 [[Category: Transport]]

3d38

From Proteopedia

Revision as of 12:25, 25 December 2014

Crystal structure of new trigonal form of photosynthetic reaction center from Blastochloris viridis. Crystals grown in microfluidics by detergent capture.

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox