9es7: Difference between revisions
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==Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with water molecules at 1.94 A resolution== | |||
<StructureSection load='9es7' size='340' side='right'caption='[[9es7]], [[Resolution|resolution]] 1.94Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[9es7]] is a 18 chain structure with sequence from [https://en.wikipedia.org/wiki/Spinacia_oleracea Spinacia oleracea]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9ES7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9ES7 FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 1.94Å</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=FES:FE2/S2+(INORGANIC)+CLUSTER'>FES</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=LMG:1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE'>LMG</scene>, <scene name='pdbligand=SQD:1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL'>SQD</scene>, <scene name='pdbligand=UMQ:UNDECYL-MALTOSIDE'>UMQ</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=9es7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9es7 OCA], [https://pdbe.org/9es7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9es7 RCSB], [https://www.ebi.ac.uk/pdbsum/9es7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9es7 ProSAT]</span></td></tr> | |||
</table> | |||
== Function == | |||
[https://www.uniprot.org/uniprot/CYB6_SPIOL CYB6_SPIOL] Component of the cytochrome b6-f complex, which mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions.[HAMAP-Rule:MF_00633] | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
A multi-subunit enzyme, cytochrome b(6)f (cytb(6)f), provides the crucial link between photosystems I and II in the photosynthetic membranes of higher plants, transferring electrons between plastoquinone (PQ) and plastocyanin. The atomic structure of cytb(6)f is known, but its detailed catalytic mechanism remains elusive. Here we present cryogenic electron microscopy structures of spinach cytb(6)f at 1.9 A and 2.2 A resolution, revealing an unexpected orientation of the substrate PQ in the haem ligand niche that forms the PQ reduction site (Q(n)). PQ, unlike Q(n) inhibitors, is not in direct contact with the haem. Instead, a water molecule is coordinated by one of the carbonyl groups of PQ and can act as the immediate proton donor for PQ. In addition, we identify water channels that connect Q(n) with the aqueous exterior of the enzyme, suggesting that the binding of PQ in Q(n) displaces water through these channels. The structures confirm large movements of the head domain of the iron-sulfur protein (ISP-HD) towards and away from the plastoquinol oxidation site (Q(p)) and define the unique position of ISP-HD when a Q(p) inhibitor (2,5-dibromo-3-methyl-6-isopropylbenzoquinone) is bound. This work identifies key conformational states of cytb(6)f, highlights fundamental differences between substrates and inhibitors and proposes a quinone-water exchange mechanism. | |||
Molecular basis of plastoquinone reduction in plant cytochrome b(6)f.,Pintscher S, Pietras R, Mielecki B, Szwalec M, Wojcik-Augustyn A, Indyka P, Rawski M, Koziej L, Jaciuk M, Wazny G, Glatt S, Osyczka A Nat Plants. 2024 Oct 3. doi: 10.1038/s41477-024-01804-x. PMID:39362993<ref>PMID:39362993</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 9es7" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Large Structures]] | |||
[[Category: Spinacia oleracea]] | |||
[[Category: Glatt S]] | |||
[[Category: Indyka P]] | |||
[[Category: Jaciuk M]] | |||
[[Category: Koziej L]] | |||
[[Category: Mielecki B]] | |||
[[Category: Osyczka A]] | |||
[[Category: Pietras R]] | |||
[[Category: Pintscher S]] | |||
[[Category: Rawski M]] | |||
[[Category: Szwalec M]] | |||
[[Category: Wazny G]] | |||
[[Category: Wojcik-Augustyn A]] | |||
Latest revision as of 07:18, 17 October 2024
Cryo-EM structure of Spinacia oleracea cytochrome b6f complex with water molecules at 1.94 A resolutionCryo-EM structure of Spinacia oleracea cytochrome b6f complex with water molecules at 1.94 A resolution
Structural highlights
FunctionCYB6_SPIOL Component of the cytochrome b6-f complex, which mediates electron transfer between photosystem II (PSII) and photosystem I (PSI), cyclic electron flow around PSI, and state transitions.[HAMAP-Rule:MF_00633] Publication Abstract from PubMedA multi-subunit enzyme, cytochrome b(6)f (cytb(6)f), provides the crucial link between photosystems I and II in the photosynthetic membranes of higher plants, transferring electrons between plastoquinone (PQ) and plastocyanin. The atomic structure of cytb(6)f is known, but its detailed catalytic mechanism remains elusive. Here we present cryogenic electron microscopy structures of spinach cytb(6)f at 1.9 A and 2.2 A resolution, revealing an unexpected orientation of the substrate PQ in the haem ligand niche that forms the PQ reduction site (Q(n)). PQ, unlike Q(n) inhibitors, is not in direct contact with the haem. Instead, a water molecule is coordinated by one of the carbonyl groups of PQ and can act as the immediate proton donor for PQ. In addition, we identify water channels that connect Q(n) with the aqueous exterior of the enzyme, suggesting that the binding of PQ in Q(n) displaces water through these channels. The structures confirm large movements of the head domain of the iron-sulfur protein (ISP-HD) towards and away from the plastoquinol oxidation site (Q(p)) and define the unique position of ISP-HD when a Q(p) inhibitor (2,5-dibromo-3-methyl-6-isopropylbenzoquinone) is bound. This work identifies key conformational states of cytb(6)f, highlights fundamental differences between substrates and inhibitors and proposes a quinone-water exchange mechanism. Molecular basis of plastoquinone reduction in plant cytochrome b(6)f.,Pintscher S, Pietras R, Mielecki B, Szwalec M, Wojcik-Augustyn A, Indyka P, Rawski M, Koziej L, Jaciuk M, Wazny G, Glatt S, Osyczka A Nat Plants. 2024 Oct 3. doi: 10.1038/s41477-024-01804-x. PMID:39362993[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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