6jnu - Revision history

OCA at 10:38, 27 March 2024

OCA — Wed, 27 Mar 2024 10:38:52 GMT

←Older revision		Revision as of 10:38, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='6jnu' size='340' side='right'caption='[[6jnu]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='6jnu' size='340' side='right'caption='[[6jnu]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jnu]] is a 4 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Bovin Bovin~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JNU OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6JNU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jnu]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JNU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6JNU FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene~~>, ~~<scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron crystallography, [[Resolution\|Resolution]] 3.001Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat"~~>CAT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&~~id=~~9913 BOVIN])</td~~><~~/tr>~~	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
-	~~<tr id~~='~~activity'><td class~~=~~"sblockLbl"><b>Activity~~:~~</b~~></td><~~td class~~=~~"sblockDat"><span class~~=~~'plainlinks~~'>~~[http://en.wikipedia.org/wiki/Catalase Catalase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6]~~ </~~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=6jnu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jnu OCA], [https://pdbe.org/6jnu PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6jnu RCSB], [https://www.ebi.ac.uk/pdbsum/6jnu PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6jnu ProSAT]</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=6jnu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jnu OCA], [~~http~~://pdbe.org/6jnu PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6jnu RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6jnu PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6jnu ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/CATA_BOVIN CATA_BOVIN]] Occurs in almost all aerobically respiring organisms and serves to protect cells from the toxic effects of hydrogen peroxide. Promotes growth of cells.	+	[https://www.uniprot.org/uniprot/CATA_BOVIN CATA_BOVIN] Occurs in almost all aerobically respiring organisms and serves to protect cells from the toxic effects of hydrogen peroxide. Promotes growth of cells.
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	A new cryo-EM system has been developed and investigated for use in protein electron 3D crystallography. The system provides parallel illumination of a coherent 300kV electron beam to a sample, filters out energy-loss electrons through the sample with an in-column energy filter, and allows rotational data collection on a fast camera. It also possesses motorized cryo-sample loading and automated liquid-nitrogen filling for cooling of multiple samples. To facilitate its use, we developed GUI programs for efficient operation and accurate structure analysis. Here we report on the performance of the system and first results for thin 3D crystals of the protein complexes, catalase and membrane protein complex ExbBD. Data quality is remarkably improved with this approach, which we name eEFD (electron energy-filtered diffraction of 3D crystals), compared with those collected at 200kV without energy filtration. Key advances include precise control of the microscope and recordings of lens fluctuations, which the programs process and respond to. We also discuss the merits of higher-energy electrons and filtration of energy-loss electrons in electron 3D crystallography.	+
-		+
-	A new cryo-EM system for electron 3D crystallography by eEFD.,Yonekura K, Ishikawa T, Maki-Yonekura S J Struct Biol. 2019 Mar 27. pii: S1047-8477(19)30063-2. doi:, 10.1016/j.jsb.2019.03.009. PMID:30928615<ref>PMID:30928615</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 6jnu" style="background-color:#fffaf0;"></div>~~	+

	==See Also==		==See Also==
	*[[Catalase 3D structures\|Catalase 3D structures]]		*[[Catalase 3D structures\|Catalase 3D structures]]
-	== References ==
-	<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Bovin]]~~	+	[[Category: Bos taurus]]
-	~~[[Category: Catalase~~]]	+
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Maki-Yonekura, S]]	+	[[Category: Maki-Yonekura S]]
-	[[Category: Yonekura, K]]	+	[[Category: Yonekura K]]
-	~~[[Category: Cryo arm]]~~	+
-	~~[[Category: Eefd]]~~	+
-	~~[[Category: Electron 3d crystallography]]~~	+
-	~~[[Category: Energy filter]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Parallem~~]]	+

OCA at 07:36, 23 May 2019

OCA — Thu, 23 May 2019 07:36:24 GMT

←Older revision		Revision as of 07:36, 23 May 2019
Line 3:		Line 3:
	<StructureSection load='6jnu' size='340' side='right'caption='[[6jnu]], [[Resolution\|resolution]] 3.00Å' scene=''>		<StructureSection load='6jnu' size='340' side='right'caption='[[6jnu]], [[Resolution\|resolution]] 3.00Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6jnu]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JNU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JNU FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6jnu]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JNU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JNU FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CAT ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9913 BOVIN])</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase Catalase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase Catalase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </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=6jnu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jnu OCA], [http://pdbe.org/6jnu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jnu RCSB], [http://www.ebi.ac.uk/pdbsum/6jnu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jnu ProSAT]</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=6jnu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jnu OCA], [http://pdbe.org/6jnu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jnu RCSB], [http://www.ebi.ac.uk/pdbsum/6jnu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jnu ProSAT]</span></td></tr>
Line 19:		Line 20:
	</div>		</div>
	<div class="pdbe-citations 6jnu" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 6jnu" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Catalase 3D structures\|Catalase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Bovin]]
	[[Category: Catalase]]		[[Category: Catalase]]
	[[Category: Large Structures]]		[[Category: Large Structures]]

OCA at 06:55, 24 April 2019

OCA — Wed, 24 Apr 2019 06:55:41 GMT

←Older revision		Revision as of 06:55, 24 April 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6jnu is ~~ON HOLD~~	+	==Catalase structure determined by eEFD (dataset 2)==
		+	<StructureSection load='6jnu' size='340' side='right'caption='[[6jnu]], [[Resolution\|resolution]] 3.00Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[6jnu]] is a 4 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6JNU OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6JNU FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=HEM:PROTOPORPHYRIN+IX+CONTAINING+FE'>HEM</scene>, <scene name='pdbligand=NDP:NADPH+DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE+PHOSPHATE'>NDP</scene></td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Catalase Catalase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.11.1.6 1.11.1.6] </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=6jnu FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6jnu OCA], [http://pdbe.org/6jnu PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6jnu RCSB], [http://www.ebi.ac.uk/pdbsum/6jnu PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6jnu ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CATA_BOVIN CATA_BOVIN]] Occurs in almost all aerobically respiring organisms and serves to protect cells from the toxic effects of hydrogen peroxide. Promotes growth of cells.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	A new cryo-EM system has been developed and investigated for use in protein electron 3D crystallography. The system provides parallel illumination of a coherent 300kV electron beam to a sample, filters out energy-loss electrons through the sample with an in-column energy filter, and allows rotational data collection on a fast camera. It also possesses motorized cryo-sample loading and automated liquid-nitrogen filling for cooling of multiple samples. To facilitate its use, we developed GUI programs for efficient operation and accurate structure analysis. Here we report on the performance of the system and first results for thin 3D crystals of the protein complexes, catalase and membrane protein complex ExbBD. Data quality is remarkably improved with this approach, which we name eEFD (electron energy-filtered diffraction of 3D crystals), compared with those collected at 200kV without energy filtration. Key advances include precise control of the microscope and recordings of lens fluctuations, which the programs process and respond to. We also discuss the merits of higher-energy electrons and filtration of energy-loss electrons in electron 3D crystallography.

-	~~Authors~~:	+	A new cryo-EM system for electron 3D crystallography by eEFD.,Yonekura K, Ishikawa T, Maki-Yonekura S J Struct Biol. 2019 Mar 27. pii: S1047-8477(19)30063-2. doi:, 10.1016/j.jsb.2019.03.009. PMID:30928615<ref>PMID:30928615</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased~~ Structures]]	+	</div>
		+	<div class="pdbe-citations 6jnu" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Catalase]]
		+	[[Category: Large Structures]]
		+	[[Category: Maki-Yonekura, S]]
		+	[[Category: Yonekura, K]]
		+	[[Category: Cryo arm]]
		+	[[Category: Eefd]]
		+	[[Category: Electron 3d crystallography]]
		+	[[Category: Energy filter]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Parallem]]

OCA: Protected "6jnu" [edit=sysop:move=sysop]

OCA — Wed, 27 Mar 2019 04:52:41 GMT

Protected "6jnu" [edit=sysop:move=sysop]

←Older revision

Revision as of 04:52, 27 March 2019

OCA: New page: '''Unreleased structure''' The entry 6jnu is ON HOLD Authors: Description: Category: Unreleased Structures

OCA — Wed, 27 Mar 2019 04:52:40 GMT

New page: '''Unreleased structure''' The entry 6jnu is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 6jnu is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]