6kmx: Difference between revisions

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 <SX load='6kmx' size='340' side='right' viewer='molstar' caption='[[6kmx]], [[Resolution|resolution]] 2.41&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6kmx]] is a 27 chain structure with sequence from [http://en.wikipedia.org/wiki/Halomicronema_hongdechloris_c2206 Halomicronema hongdechloris c2206]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KMX OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6KMX FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6kmx]] is a 27 chain structure with sequence from [https://en.wikipedia.org/wiki/Halomicronema_hongdechloris_C2206 Halomicronema hongdechloris C2206]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6KMX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6KMX FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=BCR:BETA-CAROTENE'>BCR</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL0:CHLOROPHYLL+A+ISOMER'>CL0</scene>, <scene name='pdbligand=CLA:CHLOROPHYLL+A'>CLA</scene>, <scene name='pdbligand=F6C:Chlorophyll+F'>F6C</scene>, <scene name='pdbligand=LHG:1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE'>LHG</scene>, <scene name='pdbligand=LMG:1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE'>LMG</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=PQN:PHYLLOQUINONE'>PQN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 2.41&#8491;</td></tr>
-<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6kmw|6kmw]]</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=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL0:CHLOROPHYLL+A+ISOMER'>CL0</scene>, <scene name='pdbligand=CLA:CHLOROPHYLL+A'>CLA</scene>, <scene name='pdbligand=F6C:Chlorophyll+F'>F6C</scene>, <scene name='pdbligand=LHG:1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE'>LHG</scene>, <scene name='pdbligand=LMG:1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE'>LMG</scene>, <scene name='pdbligand=LMT:DODECYL-BETA-D-MALTOSIDE'>LMT</scene>, <scene name='pdbligand=PQN:PHYLLOQUINONE'>PQN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene>, <scene name='pdbligand=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photosystem_I Photosystem I], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.97.1.12 1.97.1.12] </span></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=6kmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kmx OCA], [https://pdbe.org/6kmx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6kmx RCSB], [https://www.ebi.ac.uk/pdbsum/6kmx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6kmx ProSAT]</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=6kmx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6kmx OCA], [http://pdbe.org/6kmx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6kmx RCSB], [http://www.ebi.ac.uk/pdbsum/6kmx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6kmx ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/A0A1Z3HPE3_9CYAN A0A1Z3HPE3_9CYAN]] Apoprotein for the two 4Fe-4S centers FA and FB of photosystem I (PSI); essential for photochemical activity. FB is the terminal electron acceptor of PSI, donating electrons to ferredoxin. The C-terminus interacts with PsaA/B/D and helps assemble the protein into the PSI complex. Required for binding of PsaD and PsaE to PSI. PSI is a plastocyanin/cytochrome c6-ferredoxin oxidoreductase, converting photonic excitation into a charge separation, which transfers an electron from the donor P700 chlorophyll pair to the spectroscopically characterized acceptors A0, A1, FX, FA and FB in turn.[HAMAP-Rule:MF_01303] [[http://www.uniprot.org/uniprot/A0A1Z3HIL0_9CYAN A0A1Z3HIL0_9CYAN]] PsaA and PsaB bind P700, the primary electron donor of photosystem I (PSI), as well as the electron acceptors A0, A1 and FX. PSI is a plastocyanin/cytochrome c6-ferredoxin oxidoreductase, converting photonic excitation into a charge separation, which transfers an electron from the donor P700 chlorophyll pair to the spectroscopically characterized acceptors A0, A1, FX, FA and FB in turn. Oxidized P700 is reduced on the lumenal side of the thylakoid membrane by plastocyanin or cytochrome c6.[HAMAP-Rule:MF_00482]  PsaA and psaB bind P700, the primary electron donor of photosystem I (PSI), as well as the electron acceptors A0, A1 and FX.[RuleBase:RU003775] [[http://www.uniprot.org/uniprot/A0A1Z3HIN6_9CYAN A0A1Z3HIN6_9CYAN]] PsaA and PsaB bind P700, the primary electron donor of photosystem I (PSI), as well as the electron acceptors A0, A1 and FX. PSI is a plastocyanin/cytochrome c6-ferredoxin oxidoreductase, converting photonic excitation into a charge separation, which transfers an electron from the donor P700 chlorophyll pair to the spectroscopically characterized acceptors A0, A1, FX, FA and FB in turn. Oxidized P700 is reduced on the lumenal side of the thylakoid membrane by plastocyanin or cytochrome c6.[HAMAP-Rule:MF_00458]  PsaA and psaB bind P700, the primary electron donor of photosystem I (PSI), as well as the electron acceptors A0, A1 and FX.[RuleBase:RU003775] [[http://www.uniprot.org/uniprot/A0A1Z3HI16_9CYAN A0A1Z3HI16_9CYAN]] Stabilizes the interaction between PsaC and the PSI core, assists the docking of the ferredoxin to PSI and interacts with ferredoxin-NADP oxidoreductase.[HAMAP-Rule:MF_00613]
+[https://www.uniprot.org/uniprot/A0A1Z3HIN6_9CYAN A0A1Z3HIN6_9CYAN] PsaA and PsaB bind P700, the primary electron donor of photosystem I (PSI), as well as the electron acceptors A0, A1 and FX. PSI is a plastocyanin/cytochrome c6-ferredoxin oxidoreductase, converting photonic excitation into a charge separation, which transfers an electron from the donor P700 chlorophyll pair to the spectroscopically characterized acceptors A0, A1, FX, FA and FB in turn. Oxidized P700 is reduced on the lumenal side of the thylakoid membrane by plastocyanin or cytochrome c6.[HAMAP-Rule:MF_00458]  PsaA and psaB bind P700, the primary electron donor of photosystem I (PSI), as well as the electron acceptors A0, A1 and FX.[RuleBase:RU003775]
-<div style="background-color:#fffaf0;">
-== Publication Abstract from PubMed ==
-Chlorophylls (Chl) play pivotal roles in energy capture, transfer and charge separation in photosynthesis. Among Chls functioning in oxygenic photosynthesis, Chl f is the most red-shifted type first found in a cyanobacterium Halomicronema hongdechloris. The location and function of Chl f in photosystems are not clear. Here we analyzed the high-resolution structures of photosystem I (PSI) core from H. hongdechloris grown under white or far-red light by cryo-electron microscopy. The structure showed that, far-red PSI binds 83 Chl a and 7 Chl f, and Chl f are associated at the periphery of PSI but not in the electron transfer chain. The appearance of Chl f is well correlated with the expression of PSI genes induced under far-red light. These results indicate that Chl f functions to harvest the far-red light and enhance uphill energy transfer, and changes in the gene sequences are essential for the binding of Chl f.
-Structural basis for the adaptation and function of chlorophyll f in photosystem I.,Kato K, Shinoda T, Nagao R, Akimoto S, Suzuki T, Dohmae N, Chen M, Allakhverdiev SI, Shen JR, Akita F, Miyazaki N, Tomo T Nat Commun. 2020 Jan 13;11(1):238. doi: 10.1038/s41467-019-13898-5. PMID:31932639<ref>PMID:31932639</ref>
+==See Also==
+*[[Photosystem I 3D structures|Photosystem I 3D structures]]
-From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-</div>
-<div class="pdbe-citations 6kmx" style="background-color:#fffaf0;"></div>
-== References ==
-<references/>
 __TOC__
 </SX>
-[[Category: Halomicronema hongdechloris c2206]]
+[[Category: Halomicronema hongdechloris C2206]]
 [[Category: Large Structures]]
-[[Category: Photosystem I]]
+[[Category: Akita F]]
-[[Category: Akita, F]]
+[[Category: Kato K]]
-[[Category: Kato, K]]
+[[Category: Miyazaki N]]
-[[Category: Miyazaki, N]]
+[[Category: Nagao R]]
-[[Category: Nagao, R]]
+[[Category: Shen JR]]
-[[Category: Shen, J R]]
-[[Category: Electron transport]]
-[[Category: Photosystem i]]