4ixq: Difference between revisions

Revision as of 07:28, 25 December 2014

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

Structural highlights

4ixq is a 40 chain structure with sequence from Thermosynechococcus elongatus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Ligands:	, , , , , , , , , , , , , ,
NonStd Res:
Related:	4ixr
Activity:	Photosystem II, with EC number 1.10.3.9
Resources:	FirstGlance, OCA, RCSB, PDBsum

Function

[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] [PSBL_THEEB] Required for PSII activity (By similarity). [PSBJ_THEEB] This protein is a component of the reaction center of photosystem II (By similarity). [YCF12_THEEB] A core subunit of photosystem II (PSII).[HAMAP-Rule:MF_01329] [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] [PSBT_THEEB] Seems to play a role in the dimerization of PSII.^[1] [PSBI_THEEB] This protein is a component of the reaction center of photosystem II.[HAMAP-Rule:MF_01316] [PSBA1_THEEB] This is one of the two reaction center proteins of photosystem II. [PSBX_THEEB] Involved in the binding and/or turnover of quinones at the Q(B) site of Photosystem II.^[2] [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.^[3] [PSBK_THEEB] This protein is a component of the reaction center of photosystem II.[HAMAP-Rule:MF_00441] [PSBO_THEEB] MSP binds to a putative Mn-binding protein and keeps 2 of the 4 Mn-atoms associated with PSII (By similarity). [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] [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]

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

↑ Iwai M, Katoh H, Katayama M, Ikeuchi M. PSII-Tc protein plays an important role in dimerization of photosystem II. Plant Cell Physiol. 2004 Dec;45(12):1809-16. PMID:15653799 doi:45/12/1809
↑ Katoh H, Ikeuchi M. Targeted disruption of psbX and biochemical characterization of photosystem II complex in the thermophilic cyanobacterium Synechococcus elongatus. Plant Cell Physiol. 2001 Feb;42(2):179-88. PMID:11230572
↑ Iwai M, Suzuki T, Dohmae N, Inoue Y, Ikeuchi M. Absence of the PsbZ subunit prevents association of PsbK and Ycf12 with the PSII complex in the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. Plant Cell Physiol. 2007 Dec;48(12):1758-63. Epub 2007 Oct 28. PMID:17967798 doi:pcm148
↑ 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] Iwai M, Katoh H, Katayama M, Ikeuchi M. PSII-Tc protein plays an important role in dimerization of photosystem II. Plant Cell Physiol. 2004 Dec;45(12):1809-16. PMID:15653799 doi:45/12/1809

[2] Katoh H, Ikeuchi M. Targeted disruption of psbX and biochemical characterization of photosystem II complex in the thermophilic cyanobacterium Synechococcus elongatus. Plant Cell Physiol. 2001 Feb;42(2):179-88. PMID:11230572

[3] Iwai M, Suzuki T, Dohmae N, Inoue Y, Ikeuchi M. Absence of the PsbZ subunit prevents association of PsbK and Ycf12 with the PSII complex in the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. Plant Cell Physiol. 2007 Dec;48(12):1758-63. Epub 2007 Oct 28. PMID:17967798 doi:pcm148

[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_4ixq|  PDB=4ixq  |  SCENE=  }}
+==RT fs X-ray diffraction of Photosystem II, dark state==
-===RT fs X-ray diffraction of Photosystem II, dark state===
+<StructureSection load='4ixq' size='340' side='right' caption='[[4ixq]], [[Resolution|resolution]] 5.70&Aring;' scene=''>
-{{ABSTRACT_PUBMED_23413188}}
+== Structural highlights ==
+<table><tr><td colspan='2'>[[4ixq]] 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=4IXQ OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=4IXQ 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=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=OEC:OXYGEN+EVOLVING+SYSTEM'>OEC</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='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=UNK:UNKNOWN'>UNK</scene></td></tr>
+<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[4ixr|4ixr]]</td></tr>
+<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Photosystem_II Photosystem II], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.10.3.9 1.10.3.9] </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=4ixq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=4ixq OCA], [http://www.rcsb.org/pdb/explore.do?structureId=4ixq RCSB], [http://www.ebi.ac.uk/pdbsum/4ixq PDBsum]</span></td></tr>
+</table>
+== Function ==
+[[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]
+<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.
-==Function==
+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>
-[[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]
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[4ixq]] 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=4IXQ OCA].
+</div>
-==Reference==
+==See Also==
-<references group="xtra"/><references/>
+*[[Photosystem II|Photosystem II]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Photosystem II]]
 [[Category: Thermosynechococcus elongatus]]
-[[Category: Adams, P D.]]
+[[Category: Adams, P D]]
-[[Category: Alonso-Mori, R.]]
+[[Category: Alonso-Mori, R]]
-[[Category: Bergmann, U.]]
+[[Category: Bergmann, U]]
-[[Category: Bogan, M J.]]
+[[Category: Bogan, M J]]
-[[Category: Boutet, S.]]
+[[Category: Boutet, S]]
-[[Category: DiFiore, D.]]
+[[Category: DiFiore, D]]
-[[Category: Echols, N.]]
+[[Category: Echols, N]]
-[[Category: Fry, A R.]]
+[[Category: Fry, A R]]
-[[Category: Gildea, R J.]]
+[[Category: Gildea, R J]]
-[[Category: Glatzel, P.]]
+[[Category: Glatzel, P]]
-[[Category: Gloeckner, C.]]
+[[Category: Gloeckner, C]]
-[[Category: Grosse-Kunstleve, R W.]]
+[[Category: Grosse-Kunstleve, R W]]
-[[Category: Gul, S.]]
+[[Category: Gul, S]]
-[[Category: Han, G.]]
+[[Category: Han, G]]
-[[Category: Hattne, J.]]
+[[Category: Hattne, J]]
-[[Category: Hellmich, J.]]
+[[Category: Hellmich, J]]
-[[Category: Kern, J.]]
+[[Category: Kern, J]]
-[[Category: Koglin, J E.]]
+[[Category: Koglin, J E]]
-[[Category: Koroidov, S.]]
+[[Category: Koroidov, S]]
-[[Category: Laksmono, H.]]
+[[Category: Laksmono, H]]
-[[Category: Lampe, A.]]
+[[Category: Lampe, A]]
-[[Category: Lassalle-Kaiser, B.]]
+[[Category: Lassalle-Kaiser, B]]
-[[Category: Latimer, M J.]]
+[[Category: Latimer, M J]]
-[[Category: Messerschmidt, M.]]
+[[Category: Messerschmidt, M]]
-[[Category: Messinger, J.]]
+[[Category: Messinger, J]]
-[[Category: Miahnahri, A.]]
+[[Category: Miahnahri, A]]
-[[Category: Milathianaki, D.]]
+[[Category: Milathianaki, D]]
-[[Category: Sauter, N K.]]
+[[Category: Sauter, N K]]
-[[Category: Schafer, D W.]]
+[[Category: Schafer, D W]]
-[[Category: Seibert, M M.]]
+[[Category: Seibert, M M]]
-[[Category: Sellberg, J.]]
+[[Category: Sellberg, J]]
-[[Category: Sierra, R G.]]
+[[Category: Sierra, R G]]
-[[Category: Sokaras, D.]]
+[[Category: Sokaras, D]]
-[[Category: Tran, R.]]
+[[Category: Tran, R]]
-[[Category: Weng, T C.]]
+[[Category: Weng, T C]]
-[[Category: White, W E.]]
+[[Category: White, W E]]
-[[Category: Williams, G J.]]
+[[Category: Williams, G J]]
-[[Category: Yachandra, V K.]]
+[[Category: Yachandra, V K]]
-[[Category: Yano, J.]]
+[[Category: Yano, J]]
-[[Category: Zouni, A.]]
+[[Category: Zouni, A]]
-[[Category: Zwart, P H.]]
+[[Category: Zwart, P H]]
 [[Category: Electron transport]]
 [[Category: Iron]]

4ixq: Difference between revisions

Revision as of 07:28, 25 December 2014

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

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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4ixq: Difference between revisions

Revision as of 07:28, 25 December 2014

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

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

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