6pfy

From Proteopedia

(Difference between revisions)

Revision as of 07:28, 11 October 2023

Membrane Protein Megahertz Crystallography at the European XFEL, Photosystem I at synchrotron to 2.9 A

Structural highlights

6pfy is a 30 chain structure with sequence from Thermosynechococcus vestitus BP-1. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2.9Å
Ligands:	, , , , , , ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

PSAA_THEVB 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.^[1] ^[2] ^[3] ^[4]

Publication Abstract from PubMed

The world's first superconducting megahertz repetition rate hard X-ray free-electron laser (XFEL), the European XFEL, began operation in 2017, featuring a unique pulse train structure with 886 ns between pulses. With its rapid pulse rate, the European XFEL may alleviate some of the increasing demand for XFEL beamtime, particularly for membrane protein serial femtosecond crystallography (SFX), leveraging orders-of-magnitude faster data collection. Here, we report the first membrane protein megahertz SFX experiment, where we determined a 2.9 A-resolution SFX structure of the large membrane protein complex, Photosystem I, a > 1 MDa complex containing 36 protein subunits and 381 cofactors. We address challenges to megahertz SFX for membrane protein complexes, including growth of large quantities of crystals and the large molecular and unit cell size that influence data collection and analysis. The results imply that megahertz crystallography could have an important impact on structure determination of large protein complexes with XFELs.

Membrane protein megahertz crystallography at the European XFEL.,Gisriel C, Coe J, Letrun R, Yefanov OM, Luna-Chavez C, Stander NE, Lisova S, Mariani V, Kuhn M, Aplin S, Grant TD, Dorner K, Sato T, Echelmeier A, Cruz Villarreal J, Hunter MS, Wiedorn MO, Knoska J, Mazalova V, Roy-Chowdhury S, Yang JH, Jones A, Bean R, Bielecki J, Kim Y, Mills G, Weinhausen B, Meza JD, Al-Qudami N, Bajt S, Brehm G, Botha S, Boukhelef D, Brockhauser S, Bruce BD, Coleman MA, Danilevski C, Discianno E, Dobson Z, Fangohr H, Martin-Garcia JM, Gevorkov Y, Hauf S, Hosseinizadeh A, Januschek F, Ketawala GK, Kupitz C, Maia L, Manetti M, Messerschmidt M, Michelat T, Mondal J, Ourmazd A, Previtali G, Sarrou I, Schon S, Schwander P, Shelby ML, Silenzi A, Sztuk-Dambietz J, Szuba J, Turcato M, White TA, Wrona K, Xu C, Abdellatif MH, Zook JD, Spence JCH, Chapman HN, Barty A, Kirian RA, Frank M, Ros A, Schmidt M, Fromme R, Mancuso AP, Fromme P, Zatsepin NA Nat Commun. 2019 Nov 4;10(1):5021. doi: 10.1038/s41467-019-12955-3. PMID:31685819^[5]

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

References

↑ Klukas O, Schubert WD, Jordan P, Krauss N, Fromme P, Witt HT, Saenger W. Photosystem I, an improved model of the stromal subunits PsaC, PsaD, and PsaE. J Biol Chem. 1999 Mar 12;274(11):7351-60. PMID:10066799
↑ Klukas O, Schubert WD, Jordan P, Krau N, Fromme P, Witt HT, Saenger W. Localization of two phylloquinones, QK and QK', in an improved electron density map of photosystem I at 4-A resolution. J Biol Chem. 1999 Mar 12;274(11):7361-7. PMID:10066800
↑ Jordan P, Fromme P, Witt HT, Klukas O, Saenger W, Krauss N. Three-dimensional structure of cyanobacterial photosystem I at 2.5 A resolution. Nature. 2001 Jun 21;411(6840):909-17. PMID:11418848 doi:10.1038/35082000
↑ Krauss N, Schubert WD, Klukas O, Fromme P, Witt HT, Saenger W. Photosystem I at 4 A resolution represents the first structural model of a joint photosynthetic reaction centre and core antenna system. Nat Struct Biol. 1996 Nov;3(11):965-73. PMID:8901876
↑ Gisriel C, Coe J, Letrun R, Yefanov OM, Luna-Chavez C, Stander NE, Lisova S, Mariani V, Kuhn M, Aplin S, Grant TD, Dorner K, Sato T, Echelmeier A, Cruz Villarreal J, Hunter MS, Wiedorn MO, Knoska J, Mazalova V, Roy-Chowdhury S, Yang JH, Jones A, Bean R, Bielecki J, Kim Y, Mills G, Weinhausen B, Meza JD, Al-Qudami N, Bajt S, Brehm G, Botha S, Boukhelef D, Brockhauser S, Bruce BD, Coleman MA, Danilevski C, Discianno E, Dobson Z, Fangohr H, Martin-Garcia JM, Gevorkov Y, Hauf S, Hosseinizadeh A, Januschek F, Ketawala GK, Kupitz C, Maia L, Manetti M, Messerschmidt M, Michelat T, Mondal J, Ourmazd A, Previtali G, Sarrou I, Schon S, Schwander P, Shelby ML, Silenzi A, Sztuk-Dambietz J, Szuba J, Turcato M, White TA, Wrona K, Xu C, Abdellatif MH, Zook JD, Spence JCH, Chapman HN, Barty A, Kirian RA, Frank M, Ros A, Schmidt M, Fromme R, Mancuso AP, Fromme P, Zatsepin NA. Membrane protein megahertz crystallography at the European XFEL. Nat Commun. 2019 Nov 4;10(1):5021. doi: 10.1038/s41467-019-12955-3. PMID:31685819 doi:http://dx.doi.org/10.1038/s41467-019-12955-3

1 Structural highlights
2 Function
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6pfy"

Categories: Large Structures | Thermosynechococcus vestitus BP-1 | Fromme R

@@ Line 3: / Line 3: @@
 <StructureSection load='6pfy' size='340' side='right'caption='[[6pfy]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6pfy]] is a 36 chain structure with sequence from [http://en.wikipedia.org/wiki/Thermosynechococcus_elongatus_(strain_bp-1) Thermosynechococcus elongatus (strain bp-1)]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PFY OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PFY FirstGlance]. <br>
+<table><tr><td colspan='2'>[[6pfy]] is a 30 chain structure with sequence from [https://en.wikipedia.org/wiki/Thermosynechococcus_vestitus_BP-1 Thermosynechococcus vestitus BP-1]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PFY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PFY 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=LHG:1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE'>LHG</scene>, <scene name='pdbligand=LMG:1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE'>LMG</scene>, <scene name='pdbligand=PQN:PHYLLOQUINONE'>PQN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></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]] 2.9&#8491;</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='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=LHG:1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE'>LHG</scene>, <scene name='pdbligand=LMG:1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE'>LMG</scene>, <scene name='pdbligand=PQN:PHYLLOQUINONE'>PQN</scene>, <scene name='pdbligand=SF4:IRON/SULFUR+CLUSTER'>SF4</scene></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=6pfy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pfy OCA], [http://pdbe.org/6pfy PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6pfy RCSB], [http://www.ebi.ac.uk/pdbsum/6pfy PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6pfy 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=6pfy FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6pfy OCA], [https://pdbe.org/6pfy PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6pfy RCSB], [https://www.ebi.ac.uk/pdbsum/6pfy PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6pfy ProSAT]</span></td></tr>
 </table>
 == Function ==
-[[http://www.uniprot.org/uniprot/PSAF_THEEB PSAF_THEEB]] Probably participates in efficiency of electron transfer from plastocyanin to P700 (or cytochrome c553 in algae and cyanobacteria). This plastocyanin-docking protein contributes to the specific association of plastocyanin to PSI (By similarity). [[http://www.uniprot.org/uniprot/PSAC_THEEB PSAC_THEEB]] 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. [[http://www.uniprot.org/uniprot/PSAI_THEEB PSAI_THEEB]] May help in the organization of the PsaL subunit. [[http://www.uniprot.org/uniprot/PSAB_THEEB PSAB_THEEB]] 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. [[http://www.uniprot.org/uniprot/PSAJ_THEEB PSAJ_THEEB]] May help in the organization of the PsaE and PsaF subunits. [[http://www.uniprot.org/uniprot/PSAA_THEEB PSAA_THEEB]] 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. [[http://www.uniprot.org/uniprot/PSAD_THEEB PSAD_THEEB]] PsaD can form complexes with ferredoxin and ferredoxin-oxidoreductase in photosystem I (PS I) reaction center. [[http://www.uniprot.org/uniprot/PSAE_THEEB PSAE_THEEB]] Stabilizes the interaction between PsaC and the PSI core, assists the docking of the ferredoxin to PSI and interacts with ferredoxin-NADP oxidoreductase.
+[https://www.uniprot.org/uniprot/PSAA_THEVB PSAA_THEVB] 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.<ref>PMID:10066799</ref> <ref>PMID:10066800</ref> <ref>PMID:11418848</ref> <ref>PMID:8901876</ref>
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 21: / Line 21: @@
 ==See Also==
-*[[Photosystem I|Photosystem I]]
+*[[Photosystem I 3D structures|Photosystem I 3D structures]]
 == References ==
 <references/>
@@ Line 27: / Line 27: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Photosystem I]]
+[[Category: Thermosynechococcus vestitus BP-1]]
-[[Category: Fromme, R]]
+[[Category: Fromme R]]
-[[Category: Light harvesting]]
-[[Category: Photosynthesis]]
-[[Category: Photosystem i]]

6pfy

From Proteopedia

Revision as of 07:28, 11 October 2023

Membrane Protein Megahertz Crystallography at the European XFEL, Photosystem I at synchrotron to 2.9 A

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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