8irc - Revision history

OCA at 15:25, 13 August 2026

2026-08-13T15:25:12Z

← Older revision		Revision as of 15:25, 13 August 2026
Line 5:		Line 5:
	<table><tr><td colspan='2'>[[8irc]] 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=8IRC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8IRC FirstGlance]. <br>		<table><tr><td colspan='2'>[[8irc]] 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=8IRC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8IRC 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]] 2.25Å</td></tr>		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.25Å</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=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=HTG:HEPTYL+1-THIOHEXOPYRANOSIDE'>HTG</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=MG:MAGNESIUM+ION'>MG~~</scene>, <scene name='pdbligand=OEX:CA-MN4-O5+CLUSTER'>OEX~~</scene>, <scene name='pdbligand=PHO:PHEOPHYTIN+A'>PHO</scene>, <scene name='pdbligand=PL9:2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE'>PL9</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=UNL:UNKNOWN+LIGAND'>UNL~~</scene></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=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=HTG:HEPTYL+1-THIOHEXOPYRANOSIDE'>HTG</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=PHO:PHEOPHYTIN+A'>PHO</scene>, <scene name='pdbligand=PL9:2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE'>PL9</scene>, <scene name='pdbligand=SQD:1,2-DI-O-ACYL-3-O-[6-DEOXY-6-SULFO-ALPHA-D-GLUCOPYRANOSYL]-SN-GLYCEROL'>SQD</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=8irc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8irc OCA], [https://pdbe.org/8irc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8irc RCSB], [https://www.ebi.ac.uk/pdbsum/8irc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8irc ProSAT]</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=8irc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8irc OCA], [https://pdbe.org/8irc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8irc RCSB], [https://www.ebi.ac.uk/pdbsum/8irc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8irc ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== 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]		[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]
			<div style="background-color:#fffaf0;">
			== Publication Abstract from PubMed ==
			Photosystem II (PSII) catalyses the oxidation of water through a four-step cycle of S(i) states (i = 0-4) at the Mn(4)CaO(5) cluster(1-3), during which an extra oxygen (O6) is incorporated at the S(3) state to form a possible dioxygen(4-7). Structural changes of the metal cluster and its environment during the S-state transitions have been studied on the microsecond timescale. Here we use pump-probe serial femtosecond crystallography to reveal the structural dynamics of PSII from nanoseconds to milliseconds after illumination with one flash (1F) or two flashes (2F). Y(Z), a tyrosine residue that connects the reaction centre P680 and the Mn(4)CaO(5) cluster, showed structural changes on a nanosecond timescale, as did its surrounding amino acid residues and water molecules, reflecting the fast transfer of electrons and protons after flash illumination. Notably, one water molecule emerged in the vicinity of Glu189 of the D1 subunit of PSII (D1-E189), and was bound to the Ca(2+) ion on a sub-microsecond timescale after 2F illumination. This water molecule disappeared later with the concomitant increase of O6, suggesting that it is the origin of O6. We also observed concerted movements of water molecules in the O1, O4 and Cl-1 channels and their surrounding amino acid residues to complete the sequence of electron transfer, proton release and substrate water delivery. These results provide crucial insights into the structural dynamics of PSII during S-state transitions as well as O-O bond formation.

			Oxygen-evolving photosystem II structures during S(1)-S(2)-S(3) transitions.,Li H, Nakajima Y, Nango E, Owada S, Yamada D, Hashimoto K, Luo F, Tanaka R, Akita F, Kato K, Kang J, Saitoh Y, Kishi S, Yu H, Matsubara N, Fujii H, Sugahara M, Suzuki M, Masuda T, Kimura T, Thao TN, Yonekura S, Yu LJ, Tosha T, Tono K, Joti Y, Hatsui T, Yabashi M, Kubo M, Iwata S, Isobe H, Yamaguchi K, Suga M, Shen JR Nature. 2024 Feb;626(7999):670-677. doi: 10.1038/s41586-023-06987-5. Epub 2024 , Jan 31. PMID:38297122<ref>PMID:38297122</ref>

			From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
			</div>
			<div class="pdbe-citations 8irc" style="background-color:#fffaf0;"></div>
			== References ==
			<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>

OCA at 10:06, 17 January 2024

2024-01-17T10:06:19Z

← Older revision		Revision as of 10:06, 17 January 2024
Line 1:		Line 1:
	~~'''Unreleased structure'''~~

	~~The entry~~ 8irc is ~~ON HOLD until Paper Publication~~		==XFEL structure of cyanobacterial photosystem II following one flash (1F) with a 5-millisecond delay (Single conformation)==
			<StructureSection load='8irc' size='340' side='right'caption='[[8irc]], [[Resolution\|resolution]] 2.25Å' scene=''>
	~~Authors~~: Li, H., ~~Suga~~, M., ~~Shen~~, J.R.		== Structural highlights ==
			<table><tr><td colspan='2'>[[8irc]] 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=8IRC OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8IRC FirstGlance]. <br>
	~~Description~~: ~~XFEL structure~~ of ~~cyanobacterial~~ photosystem II ~~following one flash~~ (1F) ~~with~~ a 5-~~millisecond delay~~ (~~Single conformation~~)		</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution\|Resolution]] 2.25Å</td></tr>
	[[Category: ~~Unreleased~~ Structures]]		<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=BCT:BICARBONATE+ION'>BCT</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</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=FME:N-FORMYLMETHIONINE'>FME</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HEC:HEME+C'>HEC</scene>, <scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=HTG:HEPTYL+1-THIOHEXOPYRANOSIDE'>HTG</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=OEX:CA-MN4-O5+CLUSTER'>OEX</scene>, <scene name='pdbligand=PHO:PHEOPHYTIN+A'>PHO</scene>, <scene name='pdbligand=PL9:2,3-DIMETHYL-5-(3,7,11,15,19,23,27,31,35-NONAMETHYL-2,6,10,14,18,22,26,30,34-HEXATRIACONTANONAENYL-2,5-CYCLOHEXADIENE-1,4-DIONE-2,3-DIMETHYL-5-SOLANESYL-1,4-BENZOQUINONE'>PL9</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=UNL:UNKNOWN+LIGAND'>UNL</scene></td></tr>
	[[Category: Li, H]]		<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=8irc FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8irc OCA], [https://pdbe.org/8irc PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8irc RCSB], [https://www.ebi.ac.uk/pdbsum/8irc PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8irc ProSAT]</span></td></tr>
	[[Category: Shen~~, J.R~~]]		</table>
	[[Category: Suga, M]]		== 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]
			__TOC__
			</StructureSection>
			[[Category: Large Structures]]
			[[Category: Thermostichus vulcanus]]
			[[Category: Li H]]
			[[Category: Shen JR]]
			[[Category: Suga M]]

OCA at 05:27, 18 May 2023

2023-05-18T05:27:43Z

← Older revision		Revision as of 05:27, 18 May 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

	The entry 8irc is ON HOLD		The entry 8irc is ON HOLD until Paper Publication

	Authors: Li, H., Suga, M., Shen, J.R.		Authors: Li, H., Suga, M., Shen, J.R.

OCA: Protected "8irc" [edit=sysop:move=sysop]

2023-03-29T04:57:54Z

Protected "8irc" [edit=sysop:move=sysop]

← Older revision	Revision as of 04:57, 29 March 2023
(No difference)

OCA: New page: '''Unreleased structure''' The entry 8irc is ON HOLD Authors: Li, H., Suga, M., Shen, J.R. Description: XFEL structure of cyanobacterial photosystem II following one flash (1F) with a ...

2023-03-29T04:57:53Z

New page: '''Unreleased structure''' The entry 8irc is ON HOLD Authors: Li, H., Suga, M., Shen, J.R. Description: XFEL structure of cyanobacterial photosystem II following one flash (1F) with a ...

New page

'''Unreleased structure'''

The entry 8irc is ON HOLD

Authors: Li, H., Suga, M., Shen, J.R.

Description: XFEL structure of cyanobacterial photosystem II following one flash (1F) with a 5-millisecond delay (Single conformation)
[[Category: Unreleased Structures]]
[[Category: Li, H]]
[[Category: Shen, J.R]]
[[Category: Suga, M]]