4ixr: Difference between revisions

Latest revision as of 09:36, 17 October 2024

RT fs X-ray diffraction of Photosystem II, first illuminated stateRT fs X-ray diffraction of Photosystem II, first illuminated state

Structural highlights

4ixr is a 20 chain structure with sequence from Thermosynechococcus vestitus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 5.9Å
Ligands:	, , , , , , , , , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PSBA1_THEVB Photosystem II (PSII) is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. The D1/D2 (PsbA/PsbD) reaction center heterodimer binds P680, the primary electron donor of PSII as well as several subsequent electron acceptors.[HAMAP-Rule:MF_01379]^[1] ^[2] ^[3]

Publication Abstract from PubMed

Intense femtosecond x-ray pulses produced at the Linac Coherent Light Source (LCLS) were used for simultaneous x-ray diffraction (XRD) and x-ray emission spectroscopy (XES) of microcrystals of Photosystem II (PS II) at room temperature. This method probes the overall protein structure and the electronic structure of the Mn(4)CaO(5) cluster in the oxygen-evolving complex of PS II. XRD data are presented from both the dark state (S(1)) and the first illuminated state (S(2)) of PS II. Our simultaneous XRD/XES study shows that the PS II crystals are intact during our measurements at the LCLS, not only with respect to the structure of PS II, but also with regard to the electronic structure of the highly radiation-sensitive Mn(4)CaO(5) cluster, opening new directions for future dynamics studies.

Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature.,Kern J, Alonso-Mori R, Tran R, Hattne J, Gildea RJ, Echols N, Glockner C, Hellmich J, Laksmono H, Sierra RG, Lassalle-Kaiser B, Koroidov S, Lampe A, Han G, Gul S, Difiore D, Milathianaki D, Fry AR, Miahnahri A, Schafer DW, Messerschmidt M, Seibert MM, Koglin JE, Sokaras D, Weng TC, Sellberg J, Latimer MJ, Grosse-Kunstleve RW, Zwart PH, White WE, Glatzel P, Adams PD, Bogan MJ, Williams GJ, Boutet S, Messinger J, Zouni A, Sauter NK, Yachandra VK, Bergmann U, Yano J Science. 2013 Feb 14. PMID:23413188^[4]

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

References

↑ Broser M, Gabdulkhakov A, Kern J, Guskov A, Muh F, Saenger W, Zouni A. Crystal structure of monomeric photosystem II from Thermosynechococcus elongatus at 3.6-a resolution. J Biol Chem. 2010 Aug 20;285(34):26255-62. Epub 2010 Jun 17. PMID:20558739 doi:10.1074/jbc.M110.127589
↑ Broser M, Glockner C, Gabdulkhakov A, Guskov A, Buchta J, Kern J, Muh F, Dau H, Saenger W, Zouni A. Structural basis of cyanobacterial photosystem II Inhibition by the herbicide terbutryn. J Biol Chem. 2011 May 6;286(18):15964-72. Epub 2011 Mar 2. PMID:21367867 doi:http://dx.doi.org/10.1074/jbc.M110.215970
↑ Kern J, Tran R, Alonso-Mori R, Koroidov S, Echols N, Hattne J, Ibrahim M, Gul S, Laksmono H, Sierra RG, Gildea RJ, Han G, Hellmich J, Lassalle-Kaiser B, Chatterjee R, Brewster AS, Stan CA, Glockner C, Lampe A, DiFiore D, Milathianaki D, Fry AR, Seibert MM, Koglin JE, Gallo E, Uhlig J, Sokaras D, Weng TC, Zwart PH, Skinner DE, Bogan MJ, Messerschmidt M, Glatzel P, Williams GJ, Boutet S, Adams PD, Zouni A, Messinger J, Sauter NK, Bergmann U, Yano J, Yachandra VK. Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. Nat Commun. 2014 Jul 9;5:4371. doi: 10.1038/ncomms5371. PMID:25006873 doi:http://dx.doi.org/10.1038/ncomms5371
↑ Kern J, Alonso-Mori R, Tran R, Hattne J, Gildea RJ, Echols N, Glockner C, Hellmich J, Laksmono H, Sierra RG, Lassalle-Kaiser B, Koroidov S, Lampe A, Han G, Gul S, Difiore D, Milathianaki D, Fry AR, Miahnahri A, Schafer DW, Messerschmidt M, Seibert MM, Koglin JE, Sokaras D, Weng TC, Sellberg J, Latimer MJ, Grosse-Kunstleve RW, Zwart PH, White WE, Glatzel P, Adams PD, Bogan MJ, Williams GJ, Boutet S, Messinger J, Zouni A, Sauter NK, Yachandra VK, Bergmann U, Yano J. Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature. Science. 2013 Feb 14. PMID:23413188 doi:http://dx.doi.org/10.1126/science.1234273

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OCA

[1] Broser M, Gabdulkhakov A, Kern J, Guskov A, Muh F, Saenger W, Zouni A. Crystal structure of monomeric photosystem II from Thermosynechococcus elongatus at 3.6-a resolution. J Biol Chem. 2010 Aug 20;285(34):26255-62. Epub 2010 Jun 17. PMID:20558739 doi:10.1074/jbc.M110.127589

[2] Broser M, Glockner C, Gabdulkhakov A, Guskov A, Buchta J, Kern J, Muh F, Dau H, Saenger W, Zouni A. Structural basis of cyanobacterial photosystem II Inhibition by the herbicide terbutryn. J Biol Chem. 2011 May 6;286(18):15964-72. Epub 2011 Mar 2. PMID:21367867 doi:http://dx.doi.org/10.1074/jbc.M110.215970

[3] Kern J, Tran R, Alonso-Mori R, Koroidov S, Echols N, Hattne J, Ibrahim M, Gul S, Laksmono H, Sierra RG, Gildea RJ, Han G, Hellmich J, Lassalle-Kaiser B, Chatterjee R, Brewster AS, Stan CA, Glockner C, Lampe A, DiFiore D, Milathianaki D, Fry AR, Seibert MM, Koglin JE, Gallo E, Uhlig J, Sokaras D, Weng TC, Zwart PH, Skinner DE, Bogan MJ, Messerschmidt M, Glatzel P, Williams GJ, Boutet S, Adams PD, Zouni A, Messinger J, Sauter NK, Bergmann U, Yano J, Yachandra VK. Taking snapshots of photosynthetic water oxidation using femtosecond X-ray diffraction and spectroscopy. Nat Commun. 2014 Jul 9;5:4371. doi: 10.1038/ncomms5371. PMID:25006873 doi:http://dx.doi.org/10.1038/ncomms5371

[4] Kern J, Alonso-Mori R, Tran R, Hattne J, Gildea RJ, Echols N, Glockner C, Hellmich J, Laksmono H, Sierra RG, Lassalle-Kaiser B, Koroidov S, Lampe A, Han G, Gul S, Difiore D, Milathianaki D, Fry AR, Miahnahri A, Schafer DW, Messerschmidt M, Seibert MM, Koglin JE, Sokaras D, Weng TC, Sellberg J, Latimer MJ, Grosse-Kunstleve RW, Zwart PH, White WE, Glatzel P, Adams PD, Bogan MJ, Williams GJ, Boutet S, Messinger J, Zouni A, Sauter NK, Yachandra VK, Bergmann U, Yano J. Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature. Science. 2013 Feb 14. PMID:23413188 doi:http://dx.doi.org/10.1126/science.1234273

[1]

[2]

[3]

[4]

@@ Line 1: / Line 1: @@
-{{STRUCTURE_4ixr|  PDB=4ixr  |  SCENE=  }}
-===RT fs X-ray diffraction of Photosystem II, first illuminated state===
-{{ABSTRACT_PUBMED_23413188}}
-==Function==
+==RT fs X-ray diffraction of Photosystem II, first illuminated state==
-[[http://www.uniprot.org/uniprot/PSBF_THEEB PSBF_THEEB]] This b-type cytochrome is tightly associated with the reaction center of photosystem II and possibly is part of the water-oxidation complex (By similarity).[HAMAP-Rule:MF_00643] [[http://www.uniprot.org/uniprot/PSBL_THEEB PSBL_THEEB]] Required for PSII activity (By similarity). [[http://www.uniprot.org/uniprot/PSBJ_THEEB PSBJ_THEEB]] This protein is a component of the reaction center of photosystem II (By similarity). [[http://www.uniprot.org/uniprot/YCF12_THEEB YCF12_THEEB]] A core subunit of photosystem II (PSII).[HAMAP-Rule:MF_01329] [[http://www.uniprot.org/uniprot/PSBU_THEEB PSBU_THEEB]] Stabilizes the structure of photosystem II oxygen-evolving complex (OEC), the ion environment of oxygen evolution and protects the OEC against heat-induced inactivation (By similarity).[HAMAP-Rule:MF_00589] [[http://www.uniprot.org/uniprot/PSBT_THEEB PSBT_THEEB]] Seems to play a role in the dimerization of PSII.<ref>PMID:15653799</ref>  [[http://www.uniprot.org/uniprot/PSBI_THEEB PSBI_THEEB]] This protein is a component of the reaction center of photosystem II.[HAMAP-Rule:MF_01316] [[http://www.uniprot.org/uniprot/PSBA1_THEEB PSBA1_THEEB]] This is one of the two reaction center proteins of photosystem II. [[http://www.uniprot.org/uniprot/PSBX_THEEB PSBX_THEEB]] Involved in the binding and/or turnover of quinones at the Q(B) site of Photosystem II.<ref>PMID:11230572</ref>  [[http://www.uniprot.org/uniprot/PSBZ_THEEB PSBZ_THEEB]] Controls the interaction of photosystem II (PSII) cores with the light-harvesting antenna. May also aid in binding of PsbK, Ycf12 and the oxygen-evolving complex to PSII, at least in vitro.<ref>PMID:17967798</ref>  [[http://www.uniprot.org/uniprot/PSBK_THEEB PSBK_THEEB]] This protein is a component of the reaction center of photosystem II.[HAMAP-Rule:MF_00441] [[http://www.uniprot.org/uniprot/PSBO_THEEB PSBO_THEEB]] MSP binds to a putative Mn-binding protein and keeps 2 of the 4 Mn-atoms associated with PSII (By similarity). [[http://www.uniprot.org/uniprot/CY550_THEEB CY550_THEEB]] Low-potential cytochrome c that plays a role in the oxygen-evolving complex of photosystem II. It is not essential for growth under normal conditions but is required under low CO(2) concentrations.[HAMAP-Rule:MF_01378] [[http://www.uniprot.org/uniprot/PSBE_THEEB PSBE_THEEB]] This b-type cytochrome is tightly associated with the reaction center of photosystem II and possibly is part of the water-oxidation complex.[HAMAP-Rule:MF_00642]
+<StructureSection load='4ixr' size='340' side='right'caption='[[4ixr]], [[Resolution|resolution]] 5.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4ixr]] is a 20 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermosynechococcus_vestitus Thermosynechococcus vestitus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IXR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=4IXR 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]] 5.9&#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=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=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</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=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=4ixr FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ixr OCA], [https://pdbe.org/4ixr PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=4ixr RCSB], [https://www.ebi.ac.uk/pdbsum/4ixr PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=4ixr ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/PSBA1_THEVB PSBA1_THEVB] Photosystem II (PSII) is a light-driven water:plastoquinone oxidoreductase that uses light energy to abstract electrons from H(2)O, generating O(2) and a proton gradient subsequently used for ATP formation. It consists of a core antenna complex that captures photons, and an electron transfer chain that converts photonic excitation into a charge separation. The D1/D2 (PsbA/PsbD) reaction center heterodimer binds P680, the primary electron donor of PSII as well as several subsequent electron acceptors.[HAMAP-Rule:MF_01379]<ref>PMID:20558739</ref> <ref>PMID:21367867</ref> <ref>PMID:25006873</ref>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Intense femtosecond x-ray pulses produced at the Linac Coherent Light Source (LCLS) were used for simultaneous x-ray diffraction (XRD) and x-ray emission spectroscopy (XES) of microcrystals of Photosystem II (PS II) at room temperature. This method probes the overall protein structure and the electronic structure of the Mn(4)CaO(5) cluster in the oxygen-evolving complex of PS II. XRD data are presented from both the dark state (S(1)) and the first illuminated state (S(2)) of PS II. Our simultaneous XRD/XES study shows that the PS II crystals are intact during our measurements at the LCLS, not only with respect to the structure of PS II, but also with regard to the electronic structure of the highly radiation-sensitive Mn(4)CaO(5) cluster, opening new directions for future dynamics studies.
-==About this Structure==
+Simultaneous Femtosecond X-ray Spectroscopy and Diffraction of Photosystem II at Room Temperature.,Kern J, Alonso-Mori R, Tran R, Hattne J, Gildea RJ, Echols N, Glockner C, Hellmich J, Laksmono H, Sierra RG, Lassalle-Kaiser B, Koroidov S, Lampe A, Han G, Gul S, Difiore D, Milathianaki D, Fry AR, Miahnahri A, Schafer DW, Messerschmidt M, Seibert MM, Koglin JE, Sokaras D, Weng TC, Sellberg J, Latimer MJ, Grosse-Kunstleve RW, Zwart PH, White WE, Glatzel P, Adams PD, Bogan MJ, Williams GJ, Boutet S, Messinger J, Zouni A, Sauter NK, Yachandra VK, Bergmann U, Yano J Science. 2013 Feb 14. PMID:23413188<ref>PMID:23413188</ref>
-[[4ixr]] is a 40 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermosynechococcus_elongatus Thermosynechococcus elongatus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=4IXR OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<references group="xtra"/><references/>
+</div>
-[[Category: Photosystem II]]
+<div class="pdbe-citations 4ixr" style="background-color:#fffaf0;"></div>
-[[Category: Thermosynechococcus elongatus]]
-[[Category: Adams, P D.]]
+==See Also==
-[[Category: Alonso-Mori, R.]]
+*[[Cytochrome C 3D structures|Cytochrome C 3D structures]]
-[[Category: Bergmann, U.]]
+*[[Photosystem II 3D structures|Photosystem II 3D structures]]
-[[Category: Bogan, M J.]]
+== References ==
-[[Category: Boutet, S.]]
+<references/>
-[[Category: DiFiore, D.]]
+__TOC__
-[[Category: Echols, N.]]
+</StructureSection>
-[[Category: Fry, A R.]]
+[[Category: Large Structures]]
-[[Category: Gildea, R J.]]
+[[Category: Thermosynechococcus vestitus]]
-[[Category: Glatzel, P.]]
+[[Category: Adams PD]]
-[[Category: Gloeckner, C.]]
+[[Category: Alonso-Mori R]]
-[[Category: Grosse-Kunstleve, R W.]]
+[[Category: Bergmann U]]
-[[Category: Gul, S.]]
+[[Category: Bogan MJ]]
-[[Category: Han, G.]]
+[[Category: Boutet S]]
-[[Category: Hattne, J.]]
+[[Category: DiFiore D]]
-[[Category: Hellmich, J.]]
+[[Category: Echols N]]
-[[Category: Kern, J.]]
+[[Category: Fry AR]]
-[[Category: Koglin, J E.]]
+[[Category: Gildea RJ]]
-[[Category: Koroidov, S.]]
+[[Category: Glatzel P]]
-[[Category: Laksmono, H.]]
+[[Category: Gloeckner C]]
-[[Category: Lampe, A.]]
+[[Category: Grosse-Kunstleve RW]]
-[[Category: Lassalle-Kaiser, B.]]
+[[Category: Gul S]]
-[[Category: Latimer, M J.]]
+[[Category: Han G]]
-[[Category: Messerschmidt, M.]]
+[[Category: Hattne J]]
-[[Category: Messinger, J.]]
+[[Category: Hellmich J]]
-[[Category: Miahnahri, A.]]
+[[Category: Kern J]]
-[[Category: Milathianaki, D.]]
+[[Category: Koglin JE]]
-[[Category: Sauter, N K.]]
+[[Category: Koroidov S]]
-[[Category: Schafer, D W.]]
+[[Category: Laksmono H]]
-[[Category: Seibert, M M.]]
+[[Category: Lampe A]]
-[[Category: Sellberg, J.]]
+[[Category: Lassalle-Kaiser B]]
-[[Category: Sierra, R G.]]
+[[Category: Latimer MJ]]
-[[Category: Sokaras, D.]]
+[[Category: Messerschmidt M]]
-[[Category: Tran, R.]]
+[[Category: Messinger J]]
-[[Category: Weng, T C.]]
+[[Category: Miahnahri A]]
-[[Category: White, W E.]]
+[[Category: Milathianaki D]]
-[[Category: Williams, G J.]]
+[[Category: Sauter NK]]
-[[Category: Yachandra, V K.]]
+[[Category: Schafer DW]]
-[[Category: Yano, J.]]
+[[Category: Seibert MM]]
-[[Category: Zouni, A.]]
+[[Category: Sellberg J]]
-[[Category: Zwart, P H.]]
+[[Category: Sierra RG]]
-[[Category: Electron transport]]
+[[Category: Sokaras D]]
-[[Category: Iron]]
+[[Category: Tran R]]
-[[Category: Manganese]]
+[[Category: Weng T-C]]
-[[Category: Membrane complex]]
+[[Category: White WE]]
-[[Category: Photosynthesis]]
+[[Category: Williams GJ]]
-[[Category: Ps ii]]
+[[Category: Yachandra VK]]
-[[Category: Ps2]]
+[[Category: Yano J]]
-[[Category: Reaction center]]
+[[Category: Zouni A]]
-[[Category: Thylakoid membrane]]
+[[Category: Zwart PH]]
-[[Category: Transmembrane alpha-helix]]
-[[Category: Water oxidation]]

4ixr: Difference between revisions

Latest revision as of 09:36, 17 October 2024

RT fs X-ray diffraction of Photosystem II, first illuminated stateRT fs X-ray diffraction of Photosystem II, first illuminated state

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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4ixr: Difference between revisions

Latest revision as of 09:36, 17 October 2024

RT fs X-ray diffraction of Photosystem II, first illuminated stateRT fs X-ray diffraction of Photosystem II, first illuminated state

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

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