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.


3a0h

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (14:06, 1 November 2023) (edit) (undo)
 
(7 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:3a0h.png|left|200px]]
 
-
{{STRUCTURE_3a0h| PDB=3a0h | SCENE= }}
+
==Crystal structure of I-substituted Photosystem II complex==
 +
<StructureSection load='3a0h' size='340' side='right'caption='[[3a0h]], [[Resolution|resolution]] 4.00&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[3a0h]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermostichus_vulcanus Thermostichus vulcanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A0H OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3A0H FirstGlance]. <br>
 +
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 4&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BCR:BETA-CAROTENE'>BCR</scene>, <scene name='pdbligand=CLA:CHLOROPHYLL+A'>CLA</scene>, <scene name='pdbligand=DGD:DIGALACTOSYL+DIACYL+GLYCEROL+(DGDG)'>DGD</scene>, <scene name='pdbligand=FE2:FE+(II)+ION'>FE2</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=IOD:IODIDE+ION'>IOD</scene>, <scene name='pdbligand=LHG:1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE'>LHG</scene>, <scene name='pdbligand=MGE:(1S)-2-(ALPHA-L-ALLOPYRANOSYLOXY)-1-[(TRIDECANOYLOXY)METHYL]ETHYL+PALMITATE'>MGE</scene>, <scene name='pdbligand=OEC:OXYGEN+EVOLVING+SYSTEM'>OEC</scene>, <scene name='pdbligand=PHO:PHEOPHYTIN+A'>PHO</scene>, <scene name='pdbligand=PQ9:5-[(2E,6E,10E,14E,18E,22E)-3,7,11,15,19,23,27-HEPTAMETHYLOCTACOSA-2,6,10,14,18,22,26-HEPTAENYL]-2,3-DIMETHYLBENZO-1,4-QUINONE'>PQ9</scene></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=3a0h FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3a0h OCA], [https://pdbe.org/3a0h PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3a0h RCSB], [https://www.ebi.ac.uk/pdbsum/3a0h PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3a0h ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/PSBA_THEVL PSBA_THEVL] D1 (PsbA) and D2 (PsbD) bind P680, the primary electron donor of photosystem II (PSII) as well as electron acceptors. PSII is a light-driven water plastoquinone oxidoreductase, using light energy to abstract electrons from H(2)O, generating a proton gradient subsequently used for ATP formation.[HAMAP-Rule:MF_01379]
 +
== 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/a0/3a0h_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=3a0h ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
The chloride ion, Cl(-), is an essential cofactor for oxygen evolution of photosystem II (PSII) and is closely associated with the Mn(4)Ca cluster. Its detailed location and function have not been identified, however. We substituted Cl(-) with a bromide ion (Br(-)) or an iodide ion (I(-)) in PSII and analyzed the crystal structures of PSII with Br(-) and I(-) substitutions. Substitution of Cl(-) with Br(-) did not inhibit oxygen evolution, whereas substitution of Cl(-) with I(-) completely inhibited oxygen evolution, indicating the efficient replacement of Cl(-) by I(-). PSII with Br(-) and I(-) substitutions were crystallized, and their structures were analyzed. The results showed that there are 2 anion-binding sites in each PSII monomer; they are located on 2 sides of the Mn(4)Ca cluster at equal distances from the metal cluster. Anion-binding site 1 is close to the main chain of D1-Glu-333, and site 2 is close to the main chain of CP43-Glu-354; these 2 residues are coordinated directly with the Mn(4)Ca cluster. In addition, site 1 is located in the entrance of a proton exit channel. These results indicate that these 2 Cl(-) anions are required to maintain the coordination structure of the Mn(4)Ca cluster as well as the proposed proton channel, thereby keeping the oxygen-evolving complex fully active.
-
===Crystal structure of I-substituted Photosystem II complex===
+
Location of chloride and its possible functions in oxygen-evolving photosystem II revealed by X-ray crystallography.,Kawakami K, Umena Y, Kamiya N, Shen JR Proc Natl Acad Sci U S A. 2009 May 26;106(21):8567-72. Epub 2009 May 11. PMID:19433803<ref>PMID:19433803</ref>
-
{{ABSTRACT_PUBMED_19433803}}
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
 
+
</div>
-
==About this Structure==
+
<div class="pdbe-citations 3a0h" style="background-color:#fffaf0;"></div>
-
[[3a0h]] is a 40 chain structure of [[Cytochrome c]] and [[Photosystem II]] with sequence from [http://en.wikipedia.org/wiki/Thermosynechococcus_vulcanus Thermosynechococcus vulcanus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3A0H OCA].
+
==See Also==
==See Also==
-
*[[Cytochrome c|Cytochrome c]]
+
*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
-
*[[Photosystem II|Photosystem II]]
+
*[[Photosystem II 3D structures|Photosystem II 3D structures]]
-
 
+
== References ==
-
==Reference==
+
<references/>
-
<ref group="xtra">PMID:019433803</ref><references group="xtra"/>
+
__TOC__
-
[[Category: Thermosynechococcus vulcanus]]
+
</StructureSection>
-
[[Category: Kamiya, N.]]
+
[[Category: Large Structures]]
-
[[Category: Kawakami, K.]]
+
[[Category: Thermostichus vulcanus]]
-
[[Category: Shen, J R.]]
+
[[Category: Kamiya N]]
-
[[Category: Umena, Y.]]
+
[[Category: Kawakami K]]
-
[[Category: Electron transport]]
+
[[Category: Shen J-R]]
-
[[Category: Heme]]
+
[[Category: Umena Y]]
-
[[Category: Herbicide resistance]]
+
-
[[Category: Iron]]
+
-
[[Category: Membrane]]
+
-
[[Category: Metal-binding]]
+
-
[[Category: Multi-membrane protein complex]]
+
-
[[Category: Photosynthesis]]
+
-
[[Category: Photosystem ii]]
+
-
[[Category: Reaction center]]
+
-
[[Category: Thylakoid]]
+
-
[[Category: Transmembrane]]
+
-
[[Category: Transport]]
+

Current revision

Crystal structure of I-substituted Photosystem II complex

PDB ID 3a0h

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/3a0h"
Personal tools