5um1 - Revision history

OCA at 10:07, 16 August 2023

2023-08-16T10:07:47Z

←Older revision		Revision as of 10:07, 16 August 2023
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	<StructureSection load='5um1' size='340' side='right'caption='[[5um1]], [[Resolution\|resolution]] 1.45Å' scene=''>		<StructureSection load='5um1' size='340' side='right'caption='[[5um1]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5um1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UM1 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5UM1 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5um1]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Influenza_A_virus_(A/Hickox/1940(H1N1)) Influenza A virus (A/Hickox/1940(H1N1))]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UM1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UM1 FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=CA:CALCIUM+ION'>CA</scene~~>, ~~<scene name='pdbligand=CL:CHLORIDE+ION'>CL</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]] 1.451Å</td></tr>
-	<tr id='~~NonStdRes~~'><td class="sblockLbl"><b>[[~~Non-Standard_Residue~~\|~~NonStd Res~~:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=~~NH2~~:~~AMINO~~+~~GROUP~~'>~~NH2~~</scene><~~/td~~></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
-	<~~tr id~~='~~related'><td class~~=~~"sblockLbl"><b>[[Related_structure\|Related~~:~~]]</b~~></td>~~<td class="sblockDat">[[5joo\|5joo]], [[5ttc\|5ttc]]~~</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=5um1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5um1 OCA], [https://pdbe.org/5um1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5um1 RCSB], [https://www.ebi.ac.uk/pdbsum/5um1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5um1 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=5um1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5um1 OCA], [~~http~~://pdbe.org/5um1 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5um1 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5um1 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5um1 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/M2_I40A0 M2_I40A0]] Forms a proton-selective ion channel that is necessary for the efficient release of the viral genome during virus entry. After attaching to the cell surface, the virion enters the cell by endocytosis. Acidification of the endosome triggers M2 ion channel activity. The influx of protons into virion interior is believed to disrupt interactions between the viral ribonucleoprotein (RNP), matrix protein 1 (M1), and lipid bilayers, thereby freeing the viral genome from interaction with viral proteins and enabling RNA segments to migrate to the host cell nucleus, where influenza virus RNA transcription and replication occur. Also plays a role in viral proteins secretory pathway. Elevates the intravesicular pH of normally acidic compartments, such as trans-Golgi network, preventing newly formed hemagglutinin from premature switching to the fusion-active conformation.	+	[https://www.uniprot.org/uniprot/M2_I40A0 M2_I40A0] Forms a proton-selective ion channel that is necessary for the efficient release of the viral genome during virus entry. After attaching to the cell surface, the virion enters the cell by endocytosis. Acidification of the endosome triggers M2 ion channel activity. The influx of protons into virion interior is believed to disrupt interactions between the viral ribonucleoprotein (RNP), matrix protein 1 (M1), and lipid bilayers, thereby freeing the viral genome from interaction with viral proteins and enabling RNA segments to migrate to the host cell nucleus, where influenza virus RNA transcription and replication occur. Also plays a role in viral proteins secretory pathway. Elevates the intravesicular pH of normally acidic compartments, such as trans-Golgi network, preventing newly formed hemagglutinin from premature switching to the fusion-active conformation.
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
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	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: DeGrado~~, W F~~]]	+	[[Category: DeGrado WF]]
-	[[Category: Fraser~~, J S~~]]	+	[[Category: Fraser JS]]
-	[[Category: Thomaston~~, J L~~]]	+	[[Category: Thomaston JL]]
-	[[Category: Woldeyes~~, R A]]~~	+	[[Category: Woldeyes RA]]
-	~~[[Category: Influenza]]~~	+
-	~~[[Category: Proton channel]]~~	+
-	~~[[Category: Proton transport]]~~	+
-	~~[[Category: Room temperature]]~~	+
-	~~[[Category: Xfel~~]]	+

OCA at 09:18, 1 January 2020

2020-01-01T09:18:49Z

←Older revision		Revision as of 09:18, 1 January 2020
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	==XFEL structure of influenza A M2 wild type TM domain at intermediate pH in the lipidic cubic phase at room temperature==		==XFEL structure of influenza A M2 wild type TM domain at intermediate pH in the lipidic cubic phase at room temperature==
-	<StructureSection load='5um1' size='340' side='right' caption='[[5um1]], [[Resolution\|resolution]] 1.45Å' scene=''>	+	<StructureSection load='5um1' size='340' side='right'caption='[[5um1]], [[Resolution\|resolution]] 1.45Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5um1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UM1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UM1 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5um1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UM1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UM1 FirstGlance]. <br>
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	</div>		</div>
	<div class="pdbe-citations 5um1" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5um1" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Ion channels 3D structures\|Ion channels 3D structures]]
		+	*[[M2 protein\|M2 protein]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Large Structures]]
	[[Category: DeGrado, W F]]		[[Category: DeGrado, W F]]
	[[Category: Fraser, J S]]		[[Category: Fraser, J S]]

OCA at 03:53, 6 September 2017

2017-09-06T03:53:30Z

←Older revision		Revision as of 03:53, 6 September 2017
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-	'''Unreleased structure'''

-	~~The entry~~ 5um1 is ~~ON HOLD until Paper~~ Publication	+	==XFEL structure of influenza A M2 wild type TM domain at intermediate pH in the lipidic cubic phase at room temperature==
		+	<StructureSection load='5um1' size='340' side='right' caption='[[5um1]], [[Resolution\|resolution]] 1.45Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5um1]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UM1 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5UM1 FirstGlance]. <br>
		+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene></td></tr>
		+	<tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue\|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=ACE:ACETYL+GROUP'>ACE</scene>, <scene name='pdbligand=NH2:AMINO+GROUP'>NH2</scene></td></tr>
		+	<tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5joo\|5joo]], [[5ttc\|5ttc]]</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=5um1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5um1 OCA], [http://pdbe.org/5um1 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5um1 RCSB], [http://www.ebi.ac.uk/pdbsum/5um1 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5um1 ProSAT]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/M2_I40A0 M2_I40A0]] Forms a proton-selective ion channel that is necessary for the efficient release of the viral genome during virus entry. After attaching to the cell surface, the virion enters the cell by endocytosis. Acidification of the endosome triggers M2 ion channel activity. The influx of protons into virion interior is believed to disrupt interactions between the viral ribonucleoprotein (RNP), matrix protein 1 (M1), and lipid bilayers, thereby freeing the viral genome from interaction with viral proteins and enabling RNA segments to migrate to the host cell nucleus, where influenza virus RNA transcription and replication occur. Also plays a role in viral proteins secretory pathway. Elevates the intravesicular pH of normally acidic compartments, such as trans-Golgi network, preventing newly formed hemagglutinin from premature switching to the fusion-active conformation.
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	The M2 proton channel of influenza A is a drug target that is essential for the reproduction of the flu virus. It is also a model system for the study of selective, unidirectional proton transport across a membrane. Ordered water molecules arranged in "wires" inside the channel pore have been proposed to play a role in both the conduction of protons to the four gating His37 residues and the stabilization of multiple positive charges within the channel. To visualize the solvent in the pore of the channel at room temperature while minimizing the effects of radiation damage, data were collected to a resolution of 1.4 A using an X-ray free-electron laser (XFEL) at three different pH conditions: pH 5.5, pH 6.5, and pH 8.0. Data were collected on the Inwardopen state, which is an intermediate that accumulates at high protonation of the His37 tetrad. At pH 5.5, a continuous hydrogen-bonded network of water molecules spans the vertical length of the channel, consistent with a Grotthuss mechanism model for proton transport to the His37 tetrad. This ordered solvent at pH 5.5 could act to stabilize the positive charges that build up on the gating His37 tetrad during the proton conduction cycle. The number of ordered pore waters decreases at pH 6.5 and 8.0, where the Inwardopen state is less stable. These studies provide a graphical view of the response of water to a change in charge within a restricted channel environment.

-	~~Authors~~:	+	XFEL structures of the influenza M2 proton channel: Room temperature water networks and insights into proton conduction.,Thomaston JL, Woldeyes RA, Nakane T, Yamashita A, Tanaka T, Koiwai K, Brewster AS, Barad BA, Chen Y, Lemmin T, Uervirojnangkoorn M, Arima T, Kobayashi J, Masuda T, Suzuki M, Sugahara M, Sauter NK, Tanaka R, Nureki O, Tono K, Joti Y, Nango E, Iwata S, Yumoto F, Fraser JS, DeGrado WF Proc Natl Acad Sci U S A. 2017 Aug 23. pii: 201705624. doi:, 10.1073/pnas.1705624114. PMID:28835537<ref>PMID:28835537</ref>

-	~~Description~~:	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	[[Category: ~~Unreleased Structures~~]]	+	</div>
		+	<div class="pdbe-citations 5um1" style="background-color:#fffaf0;"></div>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: DeGrado, W F]]
		+	[[Category: Fraser, J S]]
		+	[[Category: Thomaston, J L]]
		+	[[Category: Woldeyes, R A]]
		+	[[Category: Influenza]]
		+	[[Category: Proton channel]]
		+	[[Category: Proton transport]]
		+	[[Category: Room temperature]]
		+	[[Category: Xfel]]

OCA at 11:12, 5 April 2017

2017-04-05T11:12:04Z

←Older revision		Revision as of 11:12, 5 April 2017
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	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5um1 is ON HOLD	+	The entry 5um1 is ON HOLD until Paper Publication

	Authors:		Authors:

OCA: Protected "5um1" [edit=sysop:move=sysop]

2017-02-01T16:49:15Z

Protected "5um1" [edit=sysop:move=sysop]

←Older revision

Revision as of 16:49, 1 February 2017

OCA: New page: '''Unreleased structure''' The entry 5um1 is ON HOLD Authors: Description: Category: Unreleased Structures

2017-02-01T16:49:14Z

New page: '''Unreleased structure''' The entry 5um1 is ON HOLD Authors: Description: Category: Unreleased Structures

New page

'''Unreleased structure'''

The entry 5um1 is ON HOLD

Authors:

Description:
[[Category: Unreleased Structures]]