6ppo - Revision history

OCA at 09:26, 20 March 2024

2024-03-20T09:26:57Z

←Older revision		Revision as of 09:26, 20 March 2024
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	<StructureSection load='6ppo' size='340' side='right'caption='[[6ppo]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='6ppo' size='340' side='right'caption='[[6ppo]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ppo]] is a 5 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Human Human~~] and [~~http~~://en.wikipedia.org/wiki/~~Rhinovirus_c~~ Rhinovirus c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PPO OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=6PPO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ppo]] is a 5 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens] and [https://en.wikipedia.org/wiki/Rhinovirus_C Rhinovirus C]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PPO OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6PPO FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat" id="~~ligandDat~~">~~<scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>~~</td></tr>	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 3.2Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~CDHR3, CDH28 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=9606 HUMAN])~~</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=6ppo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ppo OCA], [~~http~~://pdbe.org/6ppo PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=6ppo RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/6ppo PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=6ppo 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=6ppo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ppo OCA], [https://pdbe.org/6ppo PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6ppo RCSB], [https://www.ebi.ac.uk/pdbsum/6ppo PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6ppo ProSAT]</span></td></tr>
	</table>		</table>
-	== Disease ==
-	[[http://www.uniprot.org/uniprot/CDHR3_HUMAN CDHR3_HUMAN]] Asthma susceptibility may be associated with variations affecting the gene represented in this entry in early childhood asthma with severe exacerbations occurring between 2 and 6 years of age.<ref>PMID:24241537</ref>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/~~CDHR3_HUMAN CDHR3_HUMAN~~]] Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types. (Microbial infection) Acts as a receptor for rhinovirus C.<ref>PMID:25848009</ref>	+	[https://www.uniprot.org/uniprot/E5D8F2_9ENTO E5D8F2_9ENTO]
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	Infection by Rhinovirus-C (RV-C), a species of Picornaviridae Enterovirus, is strongly associated with childhood asthma exacerbations. Cellular binding and entry by all RV-C, which trigger these episodes, is mediated by the first extracellular domain (EC1) of cadherin-related protein 3 (CDHR3), a surface cadherin-like protein expressed primarily on the apical surfaces of ciliated airway epithelial cells. Although recombinant EC1 is a potent inhibitor of viral infection, there is no molecular description of this protein or its binding site on RV-C. Here we present cryo-electron microscopy (EM) data resolving the EC1 and EC1+2 domains of human CDHR3 complexed with viral isolate C15a. Structure-suggested residues contributing to required interfaces on both EC1 and C15a were probed and identified by mutagenesis studies with four different RV-C genotypes. In contrast to most other rhinoviruses, which bind intercellular adhesion molecule 1 receptors via a capsid protein VP1-specific fivefold canyon feature, the CDHR3 EC1 contacts C15a, and presumably all RV-Cs, in a unique cohesive footprint near the threefold vertex, encompassing residues primarily from viral protein VP3, but also from VP1 and VP2. The EC1+2 footprint on C15a is similar to that of EC1 alone but shows that steric hindrance imposed by EC2 would likely prevent multiprotein binding by the native receptor at any singular threefold vertex. Definition of the molecular interface between the RV-Cs and their receptors provides new avenues that can be explored for potential antiviral therapies.	+

-	Cryo-EM structure of rhinovirus C15a bound to its cadherin-related protein 3 receptor.,Sun Y, Watters K, Hill MG, Fang Q, Liu Y, Kuhn RJ, Klose T, Rossmann MG, Palmenberg AC Proc Natl Acad Sci U S A. 2020 Mar 24;117(12):6784-6791. doi:, 10.1073/pnas.1921640117. Epub 2020 Mar 9. PMID:32152109<ref>PMID:32152109</ref>	+	==See Also==
-		+	*[[Human rhinovirus\|Human rhinovirus]]
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class~~=~~"pdbe-citations 6ppo" style~~=~~"background-color:#fffaf0;"></div>~~	+
-	~~== References~~ ==	+
-	~~<references/>~~	+
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
-	[[Category: ~~Human~~]]	+	[[Category: Homo sapiens]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Rhinovirus c]]	+	[[Category: Rhinovirus C]]
-	[[Category: Klose, T]]	+	[[Category: Klose T]]
-	[[Category: Palmenberg~~, A C~~]]	+	[[Category: Palmenberg AC]]
-	[[Category: Sun, Y]]	+	[[Category: Sun Y]]
-	[[Category: Watters, K]]	+	[[Category: Watters K]]
-	~~[[Category: Cadherin]]~~	+
-	~~[[Category: Receptor]]~~	+
-	~~[[Category: Virus-cell adhesion complex~~]]	+

OCA at 07:15, 15 April 2020

2020-04-15T07:15:19Z

←Older revision		Revision as of 07:15, 15 April 2020
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	<StructureSection load='6ppo' size='340' side='right'caption='[[6ppo]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='6ppo' size='340' side='right'caption='[[6ppo]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ppo]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Rhinovirus_c Rhinovirus c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PPO OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=6PPO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ppo]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Rhinovirus_c Rhinovirus c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PPO OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6PPO 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></td></tr>	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CDHR3, CDH28 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</td></tr>		<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CDHR3, CDH28 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6ppo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ppo OCA], [http://pdbe.org/6ppo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ppo RCSB], [http://www.ebi.ac.uk/pdbsum/6ppo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ppo ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=6ppo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ppo OCA], [http://pdbe.org/6ppo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ppo RCSB], [http://www.ebi.ac.uk/pdbsum/6ppo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ppo ProSAT]</span></td></tr>
	</table>		</table>
	== Disease ==		== Disease ==

OCA at 10:37, 27 March 2020

2020-03-27T10:37:24Z

←Older revision		Revision as of 10:37, 27 March 2020
Line 3:		Line 3:
	<StructureSection load='6ppo' size='340' side='right'caption='[[6ppo]], [[Resolution\|resolution]] 3.20Å' scene=''>		<StructureSection load='6ppo' size='340' side='right'caption='[[6ppo]], [[Resolution\|resolution]] 3.20Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[6ppo]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Rhinovirus_c Rhinovirus c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PPO FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[6ppo]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/Human Human] and [http://en.wikipedia.org/wiki/Rhinovirus_c Rhinovirus c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PPO 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></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">CDHR3, CDH28 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9606 HUMAN])</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=6ppo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ppo OCA], [http://pdbe.org/6ppo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ppo RCSB], [http://www.ebi.ac.uk/pdbsum/6ppo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ppo 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=6ppo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ppo OCA], [http://pdbe.org/6ppo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ppo RCSB], [http://www.ebi.ac.uk/pdbsum/6ppo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ppo ProSAT]</span></td></tr>
	</table>		</table>
Line 11:		Line 12:
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/CDHR3_HUMAN CDHR3_HUMAN]] Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types. (Microbial infection) Acts as a receptor for rhinovirus C.<ref>PMID:25848009</ref>		[[http://www.uniprot.org/uniprot/CDHR3_HUMAN CDHR3_HUMAN]] Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types. (Microbial infection) Acts as a receptor for rhinovirus C.<ref>PMID:25848009</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Infection by Rhinovirus-C (RV-C), a species of Picornaviridae Enterovirus, is strongly associated with childhood asthma exacerbations. Cellular binding and entry by all RV-C, which trigger these episodes, is mediated by the first extracellular domain (EC1) of cadherin-related protein 3 (CDHR3), a surface cadherin-like protein expressed primarily on the apical surfaces of ciliated airway epithelial cells. Although recombinant EC1 is a potent inhibitor of viral infection, there is no molecular description of this protein or its binding site on RV-C. Here we present cryo-electron microscopy (EM) data resolving the EC1 and EC1+2 domains of human CDHR3 complexed with viral isolate C15a. Structure-suggested residues contributing to required interfaces on both EC1 and C15a were probed and identified by mutagenesis studies with four different RV-C genotypes. In contrast to most other rhinoviruses, which bind intercellular adhesion molecule 1 receptors via a capsid protein VP1-specific fivefold canyon feature, the CDHR3 EC1 contacts C15a, and presumably all RV-Cs, in a unique cohesive footprint near the threefold vertex, encompassing residues primarily from viral protein VP3, but also from VP1 and VP2. The EC1+2 footprint on C15a is similar to that of EC1 alone but shows that steric hindrance imposed by EC2 would likely prevent multiprotein binding by the native receptor at any singular threefold vertex. Definition of the molecular interface between the RV-Cs and their receptors provides new avenues that can be explored for potential antiviral therapies.
		+
		+	Cryo-EM structure of rhinovirus C15a bound to its cadherin-related protein 3 receptor.,Sun Y, Watters K, Hill MG, Fang Q, Liu Y, Kuhn RJ, Klose T, Rossmann MG, Palmenberg AC Proc Natl Acad Sci U S A. 2020 Mar 24;117(12):6784-6791. doi:, 10.1073/pnas.1921640117. Epub 2020 Mar 9. PMID:32152109<ref>PMID:32152109</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 6ppo" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
	</StructureSection>		</StructureSection>
		+	[[Category: Human]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
	[[Category: Rhinovirus c]]		[[Category: Rhinovirus c]]

OCA at 07:25, 11 March 2020

2020-03-11T07:25:00Z

←Older revision		Revision as of 07:25, 11 March 2020
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 6ppo is ~~ON HOLD~~	+	==Rhinovirus C15 complexed with domain I of receptor CDHR3==
-		+	<StructureSection load='6ppo' size='340' side='right'caption='[[6ppo]], [[Resolution\|resolution]] 3.20Å' scene=''>
-	~~Authors~~: ~~Sun~~, Y., ~~Watters~~, K., ~~Klose, T~~., ~~Palmenberg, A~~.C.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[6ppo]] is a 5 chain structure with sequence from [http://en.wikipedia.org/wiki/ ] and [http://en.wikipedia.org/wiki/Rhinovirus_c Rhinovirus c]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6PPO OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=6PPO FirstGlance]. <br>
-	~~Description~~: ~~Rhinovirus C15 complexed~~ with ~~domain I~~ of receptor ~~CDHR3~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=CA:CALCIUM+ION'>CA</scene></td></tr>
-	[[Category: ~~Unreleased~~ Structures]]	+	<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=6ppo FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6ppo OCA], [http://pdbe.org/6ppo PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6ppo RCSB], [http://www.ebi.ac.uk/pdbsum/6ppo PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6ppo ProSAT]</span></td></tr>
-	[[Category: ~~Watters, K~~]]	+	</table>
		+	== Disease ==
		+	[[http://www.uniprot.org/uniprot/CDHR3_HUMAN CDHR3_HUMAN]] Asthma susceptibility may be associated with variations affecting the gene represented in this entry in early childhood asthma with severe exacerbations occurring between 2 and 6 years of age.<ref>PMID:24241537</ref>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/CDHR3_HUMAN CDHR3_HUMAN]] Cadherins are calcium-dependent cell adhesion proteins. They preferentially interact with themselves in a homophilic manner in connecting cells; cadherins may thus contribute to the sorting of heterogeneous cell types. (Microbial infection) Acts as a receptor for rhinovirus C.<ref>PMID:25848009</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Rhinovirus c]]
	[[Category: Klose, T]]		[[Category: Klose, T]]
-	[[Category: Palmenberg, A.C]]	+	[[Category: Palmenberg, A C]]
	[[Category: Sun, Y]]		[[Category: Sun, Y]]
		+	[[Category: Watters, K]]
		+	[[Category: Cadherin]]
		+	[[Category: Receptor]]
		+	[[Category: Virus-cell adhesion complex]]

OCA at 05:13, 19 February 2020

2020-02-19T05:13:45Z

←Older revision		Revision as of 05:13, 19 February 2020
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ppo is ON HOLD ~~until Paper Publication~~	+	The entry 6ppo is ON HOLD

	Authors: Sun, Y., Watters, K., Klose, T., Palmenberg, A.C.		Authors: Sun, Y., Watters, K., Klose, T., Palmenberg, A.C.

OCA at 04:28, 24 July 2019

2019-07-24T04:28:19Z

←Older revision		Revision as of 04:28, 24 July 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 6ppo is ON HOLD	+	The entry 6ppo is ON HOLD until Paper Publication

	Authors: Sun, Y., Watters, K., Klose, T., Palmenberg, A.C.		Authors: Sun, Y., Watters, K., Klose, T., Palmenberg, A.C.

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

2019-07-17T09:04:32Z

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

←Older revision

Revision as of 09:04, 17 July 2019

OCA: New page: '''Unreleased structure''' The entry 6ppo is ON HOLD Authors: Sun, Y., Watters, K., Klose, T., Palmenberg, A.C. Description: Rhinovirus C15 complexed with domain I of receptor CDHR3 [[...

2019-07-17T09:04:30Z

New page: '''Unreleased structure''' The entry 6ppo is ON HOLD Authors: Sun, Y., Watters, K., Klose, T., Palmenberg, A.C. Description: Rhinovirus C15 complexed with domain I of receptor CDHR3 [[...

New page

'''Unreleased structure'''

The entry 6ppo is ON HOLD

Authors: Sun, Y., Watters, K., Klose, T., Palmenberg, A.C.

Description: Rhinovirus C15 complexed with domain I of receptor CDHR3
[[Category: Unreleased Structures]]
[[Category: Watters, K]]
[[Category: Klose, T]]
[[Category: Palmenberg, A.C]]
[[Category: Sun, Y]]