5zxa - Revision history

OCA at 10:29, 27 March 2024

OCA — Wed, 27 Mar 2024 10:29:28 GMT

←Older revision		Revision as of 10:29, 27 March 2024
Line 3:		Line 3:
	<StructureSection load='5zxa' size='340' side='right'caption='[[5zxa]], [[Resolution\|resolution]] 1.77Å' scene=''>		<StructureSection load='5zxa' size='340' side='right'caption='[[5zxa]], [[Resolution\|resolution]] 1.77Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zxa]] is a 1 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/~~Myctu Myctu~~]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZXA OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5ZXA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zxa]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Mycobacterium_tuberculosis_H37Rv Mycobacterium tuberculosis H37Rv]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZXA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5ZXA FirstGlance]. <br>
-	</td></tr><tr id='~~ligand~~'><td class="sblockLbl"><b>[[~~Ligand~~\|~~Ligands~~:]]</b></td><td class="sblockDat"~~><scene name~~=~~'pdbligand=GOL:GLYCEROL'>GOL</scene~~>, ~~<scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</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]] 1.77Å</td></tr>
-	<tr id='~~gene~~'><td class="sblockLbl"><b>[[~~Gene~~\|~~Gene~~:]]</b></td><td class="sblockDat">~~1860c ([http~~:/~~/www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode~~=~~Info&srchmode~~=~~5&id=83332 MYCTU]~~)</td></tr>	+	<tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</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=5zxa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zxa OCA], [~~http~~://pdbe.org/5zxa PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5zxa RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5zxa PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5zxa 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=5zxa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zxa OCA], [https://pdbe.org/5zxa PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5zxa RCSB], [https://www.ebi.ac.uk/pdbsum/5zxa PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5zxa ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/APA_MYCTU APA_MYCTU]] A potent antigen in animals immunized with live bacteria, it induces a strong delayed-type hypersensitivity (DTH) in immunized animals (PubMed:10531201). Elicits a mostly Th1 type of T-cell response in healthy humans; induces IFN-gamma production from CD4(+) and CD8(+) cells (PubMed:12654810). Functions as an adhesin, binds to mouse macrophages via mannose residues (PubMed:10531201, PubMed:25359607). Might interact via host CD209 (PubMed:16092920).<ref>PMID:10531201</ref> <ref>PMID:12654810</ref> <ref>PMID:16092920</ref> <ref>PMID:25359607</ref>	+	[https://www.uniprot.org/uniprot/APA_MYCTU APA_MYCTU] A potent antigen in animals immunized with live bacteria, it induces a strong delayed-type hypersensitivity (DTH) in immunized animals (PubMed:10531201). Elicits a mostly Th1 type of T-cell response in healthy humans; induces IFN-gamma production from CD4(+) and CD8(+) cells (PubMed:12654810). Functions as an adhesin, binds to mouse macrophages via mannose residues (PubMed:10531201, PubMed:25359607). Might interact via host CD209 (PubMed:16092920).<ref>PMID:10531201</ref> <ref>PMID:12654810</ref> <ref>PMID:16092920</ref> <ref>PMID:25359607</ref>
-	~~<div style="background-color:#fffaf0;">~~	+
-	~~== Publication Abstract from PubMed ==~~	+
-	BACKGROUND: Alanine and proline-rich protein (Apa) is a secreted antigen of Mycobacterium spp. which involves in stimulating immune responses and adhering to host cells by binding to fibronectin (Fn). Here, we report the crystal structure of Apa from Mycobacterium tuberculosis (Mtb) and its Fn-binding characteristics. METHODS: The crystal structure of Mtb Apa was determined at resolutions of 1.54A. The dissociation constants (KD) of Apa and individual modules of Fn were determined by surface plasmon resonance and enzyme-linked immunosorbent assay. Site-directed mutagenesis was performed to investigate the putative Fn-binding motif of Apa. RESULTS: Mtb Apa folds into a large seven-stranded anti-parallel beta-sheet which is flanked by three alpha-helices. The binding affinity of Mtb Apa to individual Fn modules was assessed and the results indicated that the Mtb Apa binds to FnIII-4 and FnIII-5 of Fn CBD segment. Notably, structure analysis suggested that the previously proposed Fn-binding motif (258)RWFV(261) is buried within the protein and may not be accessible to the binding counterpart. CONCLUSIONS: The structural and Fn-binding characteristics we reported here provide molecular insights into the multifunctional protein Mtb Apa. FnIII-4 and FnIII-5 of CBD are the only two modules contributing to Apa-Fn interaction. GENERAL SIGNIFICANCE: This is the first study to report the structure and Fn-binding characteristics of mycobacterial Apa. Since Apa plays a central role in stimulating immune responses and host cells adhesion, these results are of great importance in understanding the pathogenesis of mycobacterium. This information shall provide a guidance for the development of anti-mycobacteria regimen.	+
-		+
-	Functional and structural investigations of fibronectin-binding protein Apa from Mycobacterium tuberculosis.,Kuo CJ, Gao J, Huang JW, Ko TP, Zhai C, Ma L, Liu W, Dai L, Chang YF, Chen TH, Hu Y, Yu X, Guo RT, Chen CC Biochim Biophys Acta Gen Subj. 2019 Sep;1863(9):1351-1359. doi:, 10.1016/j.bbagen.2019.06.003. Epub 2019 Jun 5. PMID:31175911<ref>PMID:31175911</ref>	+
-		+
-	~~From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>~~	+
-	~~</div>~~	+
-	~~<div class="pdbe-citations 5zxa" style="background-color:#fffaf0;"></div~~>	+
	== References ==		== References ==
	<references/>		<references/>
Line 24:		Line 15:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: ~~Myctu~~]]	+	[[Category: Mycobacterium tuberculosis H37Rv]]
-	[[Category: Chen~~, C C~~]]	+	[[Category: Chen CC]]
-	[[Category: Gao, J]]	+	[[Category: Gao J]]
-	[[Category: Guo~~, R T~~]]	+	[[Category: Guo RT]]
-	[[Category: Liu~~, W D]]~~	+	[[Category: Liu WD]]
-	~~[[Category: Cyclolavandulyl diphosphate synthase]]~~	+
-	~~[[Category: Inhibitor]]~~	+
-	~~[[Category: Protein binding]]~~	+
-	~~[[Category: Substrate binding~~]]	+

OCA at 17:37, 11 December 2019

OCA — Wed, 11 Dec 2019 17:37:24 GMT

←Older revision		Revision as of 17:37, 11 December 2019
Line 1:		Line 1:

-	==Crystal structure of a protein mutant from Mycobacterium==	+	==Crystal structure of fibronectin-binding protein Apa mutant from Mycobacterium tuberculosis==
	<StructureSection load='5zxa' size='340' side='right'caption='[[5zxa]], [[Resolution\|resolution]] 1.77Å' scene=''>		<StructureSection load='5zxa' size='340' side='right'caption='[[5zxa]], [[Resolution\|resolution]] 1.77Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5zxa]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZXA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZXA FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5zxa]] is a 1 chain structure with sequence from [http://en.wikipedia.org/wiki/Myctu Myctu]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZXA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZXA FirstGlance]. <br>
	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></td></tr>		</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</scene></td></tr>
		+	<tr id='gene'><td class="sblockLbl"><b>[[Gene\|Gene:]]</b></td><td class="sblockDat">1860c ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=83332 MYCTU])</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=5zxa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zxa OCA], [http://pdbe.org/5zxa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zxa RCSB], [http://www.ebi.ac.uk/pdbsum/5zxa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zxa 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=5zxa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zxa OCA], [http://pdbe.org/5zxa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zxa RCSB], [http://www.ebi.ac.uk/pdbsum/5zxa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zxa ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==
	[[http://www.uniprot.org/uniprot/APA_MYCTU APA_MYCTU]] A potent antigen in animals immunized with live bacteria, it induces a strong delayed-type hypersensitivity (DTH) in immunized animals (PubMed:10531201). Elicits a mostly Th1 type of T-cell response in healthy humans; induces IFN-gamma production from CD4(+) and CD8(+) cells (PubMed:12654810). Functions as an adhesin, binds to mouse macrophages via mannose residues (PubMed:10531201, PubMed:25359607). Might interact via host CD209 (PubMed:16092920).<ref>PMID:10531201</ref> <ref>PMID:12654810</ref> <ref>PMID:16092920</ref> <ref>PMID:25359607</ref>		[[http://www.uniprot.org/uniprot/APA_MYCTU APA_MYCTU]] A potent antigen in animals immunized with live bacteria, it induces a strong delayed-type hypersensitivity (DTH) in immunized animals (PubMed:10531201). Elicits a mostly Th1 type of T-cell response in healthy humans; induces IFN-gamma production from CD4(+) and CD8(+) cells (PubMed:12654810). Functions as an adhesin, binds to mouse macrophages via mannose residues (PubMed:10531201, PubMed:25359607). Might interact via host CD209 (PubMed:16092920).<ref>PMID:10531201</ref> <ref>PMID:12654810</ref> <ref>PMID:16092920</ref> <ref>PMID:25359607</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	BACKGROUND: Alanine and proline-rich protein (Apa) is a secreted antigen of Mycobacterium spp. which involves in stimulating immune responses and adhering to host cells by binding to fibronectin (Fn). Here, we report the crystal structure of Apa from Mycobacterium tuberculosis (Mtb) and its Fn-binding characteristics. METHODS: The crystal structure of Mtb Apa was determined at resolutions of 1.54A. The dissociation constants (KD) of Apa and individual modules of Fn were determined by surface plasmon resonance and enzyme-linked immunosorbent assay. Site-directed mutagenesis was performed to investigate the putative Fn-binding motif of Apa. RESULTS: Mtb Apa folds into a large seven-stranded anti-parallel beta-sheet which is flanked by three alpha-helices. The binding affinity of Mtb Apa to individual Fn modules was assessed and the results indicated that the Mtb Apa binds to FnIII-4 and FnIII-5 of Fn CBD segment. Notably, structure analysis suggested that the previously proposed Fn-binding motif (258)RWFV(261) is buried within the protein and may not be accessible to the binding counterpart. CONCLUSIONS: The structural and Fn-binding characteristics we reported here provide molecular insights into the multifunctional protein Mtb Apa. FnIII-4 and FnIII-5 of CBD are the only two modules contributing to Apa-Fn interaction. GENERAL SIGNIFICANCE: This is the first study to report the structure and Fn-binding characteristics of mycobacterial Apa. Since Apa plays a central role in stimulating immune responses and host cells adhesion, these results are of great importance in understanding the pathogenesis of mycobacterium. This information shall provide a guidance for the development of anti-mycobacteria regimen.
		+
		+	Functional and structural investigations of fibronectin-binding protein Apa from Mycobacterium tuberculosis.,Kuo CJ, Gao J, Huang JW, Ko TP, Zhai C, Ma L, Liu W, Dai L, Chang YF, Chen TH, Hu Y, Yu X, Guo RT, Chen CC Biochim Biophys Acta Gen Subj. 2019 Sep;1863(9):1351-1359. doi:, 10.1016/j.bbagen.2019.06.003. Epub 2019 Jun 5. PMID:31175911<ref>PMID:31175911</ref>
		+
		+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
		+	</div>
		+	<div class="pdbe-citations 5zxa" style="background-color:#fffaf0;"></div>
	== References ==		== References ==
	<references/>		<references/>
Line 14:		Line 24:
	</StructureSection>		</StructureSection>
	[[Category: Large Structures]]		[[Category: Large Structures]]
		+	[[Category: Myctu]]
	[[Category: Chen, C C]]		[[Category: Chen, C C]]
	[[Category: Gao, J]]		[[Category: Gao, J]]

OCA at 06:02, 29 May 2019

OCA — Wed, 29 May 2019 06:02:34 GMT

←Older revision		Revision as of 06:02, 29 May 2019
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5zxa is ~~ON HOLD until May 18 2020~~	+	==Crystal structure of a protein mutant from Mycobacterium==
-		+	<StructureSection load='5zxa' size='340' side='right'caption='[[5zxa]], [[Resolution\|resolution]] 1.77Å' scene=''>
-	~~Authors~~: ~~Gao~~, J., ~~Liu~~, W.D., ~~Chen, C~~.C., ~~Guo, R~~.T.	+	== Structural highlights ==
-		+	<table><tr><td colspan='2'>[[5zxa]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5ZXA OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ZXA FirstGlance]. <br>
-	~~Description: Crystal structure of a protein mutant from Mycobacterium~~	+	</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand\|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=HG:MERCURY+(II)+ION'>HG</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=5zxa FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5zxa OCA], [http://pdbe.org/5zxa PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5zxa RCSB], [http://www.ebi.ac.uk/pdbsum/5zxa PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5zxa ProSAT]</span></td></tr>
-	~~[[Category~~: ~~Liu~~, W.~~D]]~~	+	</table>
-	[[Category: ~~Chen, C.C~~]]	+	== Function ==
-	[[Category: ~~Guo~~, ~~R.T~~]]	+	[[http://www.uniprot.org/uniprot/APA_MYCTU APA_MYCTU]] A potent antigen in animals immunized with live bacteria, it induces a strong delayed-type hypersensitivity (DTH) in immunized animals (PubMed:10531201). Elicits a mostly Th1 type of T-cell response in healthy humans; induces IFN-gamma production from CD4(+) and CD8(+) cells (PubMed:12654810). Functions as an adhesin, binds to mouse macrophages via mannose residues (PubMed:10531201, PubMed:25359607). Might interact via host CD209 (PubMed:16092920).<ref>PMID:10531201</ref> <ref>PMID:12654810</ref> <ref>PMID:16092920</ref> <ref>PMID:25359607</ref>
		+	== References ==
		+	<references/>
		+	__TOC__
		+	</StructureSection>
		+	[[Category: Large Structures]]
		+	[[Category: Chen, C C]]
	[[Category: Gao, J]]		[[Category: Gao, J]]
		+	[[Category: Guo, R T]]
		+	[[Category: Liu, W D]]
		+	[[Category: Cyclolavandulyl diphosphate synthase]]
		+	[[Category: Inhibitor]]
		+	[[Category: Protein binding]]
		+	[[Category: Substrate binding]]

OCA at 05:46, 20 March 2019

OCA — Wed, 20 Mar 2019 05:46:02 GMT

←Older revision		Revision as of 05:46, 20 March 2019
Line 1:		Line 1:
	'''Unreleased structure'''		'''Unreleased structure'''

-	The entry 5zxa is ON HOLD	+	The entry 5zxa is ON HOLD until May 18 2020

	Authors: Gao, J., Liu, W.D., Chen, C.C., Guo, R.T.		Authors: Gao, J., Liu, W.D., Chen, C.C., Guo, R.T.
Line 7:		Line 7:
	Description: Crystal structure of a protein mutant from Mycobacterium		Description: Crystal structure of a protein mutant from Mycobacterium
	[[Category: Unreleased Structures]]		[[Category: Unreleased Structures]]
-	[[Category: Chen, C.C]]
	[[Category: Liu, W.D]]		[[Category: Liu, W.D]]
		+	[[Category: Chen, C.C]]
	[[Category: Guo, R.T]]		[[Category: Guo, R.T]]
	[[Category: Gao, J]]		[[Category: Gao, J]]

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

OCA — Wed, 23 May 2018 05:55:08 GMT

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

←Older revision

Revision as of 05:55, 23 May 2018

OCA: New page: '''Unreleased structure''' The entry 5zxa is ON HOLD Authors: Gao, J., Liu, W.D., Chen, C.C., Guo, R.T. Description: Crystal structure of a protein mutant from Mycobacterium [[Category...

OCA — Wed, 23 May 2018 05:55:07 GMT

New page: '''Unreleased structure''' The entry 5zxa is ON HOLD Authors: Gao, J., Liu, W.D., Chen, C.C., Guo, R.T. Description: Crystal structure of a protein mutant from Mycobacterium [[Category...

New page

'''Unreleased structure'''

The entry 5zxa is ON HOLD

Authors: Gao, J., Liu, W.D., Chen, C.C., Guo, R.T.

Description: Crystal structure of a protein mutant from Mycobacterium
[[Category: Unreleased Structures]]
[[Category: Chen, C.C]]
[[Category: Liu, W.D]]
[[Category: Guo, R.T]]
[[Category: Gao, J]]