OCA at 21:19, 28 June 2023

OCA — Wed, 28 Jun 2023 21:19:11 GMT

←Older revision		Revision as of 21:19, 28 June 2023
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 8fwa is ~~ON HOLD until Paper~~ Publication	+	==Phycocyanin structure from a modular droplet injector for serial femtosecond crystallography==
		+	<StructureSection load='8fwa' size='340' side='right'caption='[[8fwa]], [[Resolution\|resolution]] 2.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[8fwa]] is a 2 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=8FWA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8FWA 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]] 2Å</td></tr>
		+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CYC:PHYCOCYANOBILIN'>CYC</scene>, <scene name='pdbligand=MEN:N-METHYL+ASPARAGINE'>MEN</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</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=8fwa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8fwa OCA], [https://pdbe.org/8fwa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8fwa RCSB], [https://www.ebi.ac.uk/pdbsum/8fwa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8fwa ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[https://www.uniprot.org/uniprot/PHCA_THEVB PHCA_THEVB] Light-harvesting photosynthetic bile pigment-protein from the phycobiliprotein complex (phycobilisome, PBS). Phycocyanin is the major phycobiliprotein in the PBS rod.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Droplet injection strategies are a promising tool to reduce the large amount of sample consumed in serial femtosecond crystallography (SFX) measurements at X-ray free electron lasers (XFELs) with continuous injection approaches. Here, we demonstrate a new modular microfluidic droplet injector (MDI) design that was successfully applied to deliver microcrystals of the human NAD(P)H:quinone oxidoreductase 1 (NQO1) and phycocyanin. We investigated droplet generation conditions through electrical stimulation for both protein samples and implemented hardware and software components for optimized crystal injection at the Macromolecular Femtosecond Crystallography (MFX) instrument at the Stanford Linac Coherent Light Source (LCLS). Under optimized droplet injection conditions, we demonstrate that up to 4-fold sample consumption savings can be achieved with the droplet injector. In addition, we collected a full data set with droplet injection for NQO1 protein crystals with a resolution up to 2.7 A, leading to the first room-temperature structure of NQO1 at an XFEL. NQO1 is a flavoenzyme associated with cancer, Alzheimer's and Parkinson's disease, making it an attractive target for drug discovery. Our results reveal for the first time that residues Tyr128 and Phe232, which play key roles in the function of the protein, show an unexpected conformational heterogeneity at room temperature within the crystals. These results suggest that different substates exist in the conformational ensemble of NQO1 with functional and mechanistic implications for the enzyme's negative cooperativity through a conformational selection mechanism. Our study thus demonstrates that microfluidic droplet injection constitutes a robust sample-conserving injection method for SFX studies on protein crystals that are difficult to obtain in amounts necessary for continuous injection, including the large sample quantities required for time-resolved mix-and-inject studies.

-	~~Authors: Botha, S~~., Doppler, D~~.L.~~, Sonker, M., Egatz-Gomez, A., Grieco, A., Zaare, S., Jernigan, R., Meza-Aguilar~~, J.D.~~, Rabbani~~, M.T.~~, Manna, A., Alvarez~~, R.~~, Karpos, K., Cruz Villarreal, J., Nelson, G., ~~Ketawala~~, G.K., Pey~~, A.L.~~, Ruiz-Fresneda~~, M.A.~~, Pacheco-Garcia, ~~J.L.~~, Nazari, R., Sierra, R., Hunter~~, M.S.~~, Batyuk, A., Kupitz~~, C.J.~~, Sublett~~, R.E.~~, Lisova, S., Mariani, V., Boutet, S., Fromme, R., Grant, ~~T.D.~~, Fromme, P., Kirian~~, R.A.~~, Martin-Garcia~~, J.M.~~, Ros, A.	+	Modular droplet injector for sample conservation providing new structural insight for the conformational heterogeneity in the disease-associated NQO1 enzyme.,Doppler D, Sonker M, Egatz-Gomez A, Grieco A, Zaare S, Jernigan R, Meza-Aguilar JD, Rabbani MT, Manna A, Alvarez RC, Karpos K, Cruz Villarreal J, Nelson G, Yang JH, Carrion J, Morin K, Ketawala GK, Pey AL, Ruiz-Fresneda MA, Pacheco-Garcia JL, Hermoso JA, Nazari R, Sierra R, Hunter MS, Batyuk A, Kupitz CJ, Sublett RE, Lisova S, Mariani V, Boutet S, Fromme R, Grant TD, Botha S, Fromme P, Kirian RA, Martin-Garcia JM, Ros A Lab Chip. 2023 Jun 28;23(13):3016-3033. doi: 10.1039/d3lc00176h. PMID:37294576<ref>PMID:37294576</ref>

-	~~Description: Phycocyanin structure from~~ a ~~modular droplet injector for serial femtosecond crystallography~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
-	[[Category: ~~Sierra, R~~]]	+	<div class="pdbe-citations 8fwa" style="background-color:#fffaf0;"></div>
-	[[Category: ~~Sublett,~~ R.E]]	+	== References ==
-	[[Category: ~~Alvarez, R~~]]	+	<references/>
-	[[Category: ~~Grieco, A~~]]	+	__TOC__
-	[[Category: ~~Hunter, M.~~S]]	+	</StructureSection>
-	[[Category: ~~Botha, S~~]]	+	[[Category: Large Structures]]
-	[[Category: ~~Fromme, P~~]]	+	[[Category: Thermosynechococcus vestitus BP-1]]
-	[[Category: ~~Ketawala, G.K~~]]	+	[[Category: Alvarez R]]
-	[[Category: ~~Ros, A~~]]	+	[[Category: Batyuk A]]
-	[[Category: ~~Sonker, M~~]]	+	[[Category: Botha S]]
-	[[Category: ~~Doppler, D.L~~]]	+	[[Category: Boutet S]]
-	[[Category: ~~Martin-Garcia, J.M~~]]	+	[[Category: Cruz Villarreal J]]
-	[[Category: ~~Grant, T.D~~]]	+	[[Category: Doppler DL]]
-	[[Category: ~~Fromme,~~ R]]	+	[[Category: Egatz-Gomez A]]
-	[[Category: ~~Manna, A~~]]	+	[[Category: Fromme P]]
-	[[Category: ~~Kirian, R.A~~]]	+	[[Category: Fromme R]]
-	[[Category: ~~Jernigan, R~~]]	+	[[Category: Grant TD]]
-	[[Category: ~~Zaare, S~~]]	+	[[Category: Grieco A]]
-	[[Category: ~~Boutet,~~ S]]	+	[[Category: Hunter MS]]
-	[[Category: ~~Karpos, K~~]]	+	[[Category: Jernigan R]]
-	[[Category: ~~Ruiz-Fresneda, M.A~~]]	+	[[Category: Karpos K]]
-	[[Category: ~~Nelson, G~~]]	+	[[Category: Ketawala GK]]
-	[[Category: ~~Pey, A.L~~]]	+	[[Category: Kirian RA]]
-	[[Category: ~~Cruz Villarreal, J~~]]	+	[[Category: Kupitz CJ]]
-	[[Category: ~~Nazari, R~~]]	+	[[Category: Lisova S]]
-	[[Category: Pacheco-Garcia~~, J.L~~]]	+	[[Category: Manna A]]
-	[[Category: ~~Meza-Aguilar, J.D~~]]	+	[[Category: Mariani V]]
-	[[Category: ~~Kupitz, C.J~~]]	+	[[Category: Martin-Garcia JM]]
-	[[Category: ~~Egatz-Gomez,~~ A]]	+	[[Category: Meza-Aguilar JD]]
-	[[Category: ~~Rabbani, M.T~~]]	+	[[Category: Nazari R]]
-	[[Category: ~~Lisova, S~~]]	+	[[Category: Nelson G]]
-	[[Category: ~~Mariani, V~~]]	+	[[Category: Pacheco-Garcia JL]]
-	[[Category: ~~Batyuk, A~~]]	+	[[Category: Pey AL]]
		+	[[Category: Rabbani MT]]
		+	[[Category: Ros A]]
		+	[[Category: Ruiz-Fresneda MA]]
		+	[[Category: Sierra R]]
		+	[[Category: Sonker M]]
		+	[[Category: Sublett RE]]
		+	[[Category: Zaare S]]

OCA at 04:25, 2 March 2023

OCA — Thu, 02 Mar 2023 04:25:26 GMT

←Older revision		Revision as of 04:25, 2 March 2023
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 8fwa is ON HOLD	+	The entry 8fwa is ON HOLD until Paper Publication

	Authors: Botha, S., Doppler, D.L., Sonker, M., Egatz-Gomez, A., Grieco, A., Zaare, S., Jernigan, R., Meza-Aguilar, J.D., Rabbani, M.T., Manna, A., Alvarez, R., Karpos, K., Cruz Villarreal, J., Nelson, G., Ketawala, G.K., Pey, A.L., Ruiz-Fresneda, M.A., Pacheco-Garcia, J.L., Nazari, R., Sierra, R., Hunter, M.S., Batyuk, A., Kupitz, C.J., Sublett, R.E., Lisova, S., Mariani, V., Boutet, S., Fromme, R., Grant, T.D., Fromme, P., Kirian, R.A., Martin-Garcia, J.M., Ros, A.		Authors: Botha, S., Doppler, D.L., Sonker, M., Egatz-Gomez, A., Grieco, A., Zaare, S., Jernigan, R., Meza-Aguilar, J.D., Rabbani, M.T., Manna, A., Alvarez, R., Karpos, K., Cruz Villarreal, J., Nelson, G., Ketawala, G.K., Pey, A.L., Ruiz-Fresneda, M.A., Pacheco-Garcia, J.L., Nazari, R., Sierra, R., Hunter, M.S., Batyuk, A., Kupitz, C.J., Sublett, R.E., Lisova, S., Mariani, V., Boutet, S., Fromme, R., Grant, T.D., Fromme, P., Kirian, R.A., Martin-Garcia, J.M., Ros, A.

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

OCA — Wed, 01 Feb 2023 09:24:57 GMT

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

←Older revision

Revision as of 09:24, 1 February 2023

OCA: New page: '''Unreleased structure''' The entry 8fwa is ON HOLD Authors: Botha, S., Doppler, D.L., Sonker, M., Egatz-Gomez, A., Grieco, A., Zaare, S., Jernigan, R., Meza-Aguilar, J.D., Rabbani, M....

OCA — Wed, 01 Feb 2023 09:24:56 GMT

New page: '''Unreleased structure''' The entry 8fwa is ON HOLD Authors: Botha, S., Doppler, D.L., Sonker, M., Egatz-Gomez, A., Grieco, A., Zaare, S., Jernigan, R., Meza-Aguilar, J.D., Rabbani, M....

New page

'''Unreleased structure'''

The entry 8fwa is ON HOLD

Authors: Botha, S., Doppler, D.L., Sonker, M., Egatz-Gomez, A., Grieco, A., Zaare, S., Jernigan, R., Meza-Aguilar, J.D., Rabbani, M.T., Manna, A., Alvarez, R., Karpos, K., Cruz Villarreal, J., Nelson, G., Ketawala, G.K., Pey, A.L., Ruiz-Fresneda, M.A., Pacheco-Garcia, J.L., Nazari, R., Sierra, R., Hunter, M.S., Batyuk, A., Kupitz, C.J., Sublett, R.E., Lisova, S., Mariani, V., Boutet, S., Fromme, R., Grant, T.D., Fromme, P., Kirian, R.A., Martin-Garcia, J.M., Ros, A.

Description: Phycocyanin structure from a modular droplet injector for serial femtosecond crystallography
[[Category: Unreleased Structures]]
[[Category: Sierra, R]]
[[Category: Sublett, R.E]]
[[Category: Alvarez, R]]
[[Category: Grieco, A]]
[[Category: Hunter, M.S]]
[[Category: Botha, S]]
[[Category: Fromme, P]]
[[Category: Ketawala, G.K]]
[[Category: Ros, A]]
[[Category: Sonker, M]]
[[Category: Doppler, D.L]]
[[Category: Martin-Garcia, J.M]]
[[Category: Grant, T.D]]
[[Category: Fromme, R]]
[[Category: Manna, A]]
[[Category: Kirian, R.A]]
[[Category: Jernigan, R]]
[[Category: Zaare, S]]
[[Category: Boutet, S]]
[[Category: Karpos, K]]
[[Category: Ruiz-Fresneda, M.A]]
[[Category: Nelson, G]]
[[Category: Pey, A.L]]
[[Category: Cruz Villarreal, J]]
[[Category: Nazari, R]]
[[Category: Pacheco-Garcia, J.L]]
[[Category: Meza-Aguilar, J.D]]
[[Category: Kupitz, C.J]]
[[Category: Egatz-Gomez, A]]
[[Category: Rabbani, M.T]]
[[Category: Lisova, S]]
[[Category: Mariani, V]]
[[Category: Batyuk, A]]

8fwa - Revision history

OCA at 21:19, 28 June 2023

OCA at 04:25, 2 March 2023

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

OCA: New page: '''Unreleased structure''' The entry 8fwa is ON HOLD Authors: Botha, S., Doppler, D.L., Sonker, M., Egatz-Gomez, A., Grieco, A., Zaare, S., Jernigan, R., Meza-Aguilar, J.D., Rabbani, M....