This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


6laf

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (10:45, 27 March 2024) (edit) (undo)
 
(One intermediate revision not shown.)
Line 1: Line 1:
-
==Crystal structure of core domain of a Pili-like protein==
+
==Crystal structure of the core domain of Amuc_1100 from Akkermansia muciniphila==
<StructureSection load='6laf' size='340' side='right'caption='[[6laf]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
<StructureSection load='6laf' size='340' side='right'caption='[[6laf]], [[Resolution|resolution]] 3.00&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>[[6laf]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Akkm8 Akkm8]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LAF OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=6LAF FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[6laf]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Akkermansia_muciniphila_ATCC_BAA-835 Akkermansia muciniphila ATCC BAA-835]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6LAF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6LAF FirstGlance]. <br>
-
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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]] 3.001&#8491;</td></tr>
-
<tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[6lad|6lad]]</td></tr>
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
-
<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">Amuc_1100 ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=349741 AKKM8])</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=6laf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6laf OCA], [https://pdbe.org/6laf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6laf RCSB], [https://www.ebi.ac.uk/pdbsum/6laf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6laf 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=6laf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6laf OCA], [http://pdbe.org/6laf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=6laf RCSB], [http://www.ebi.ac.uk/pdbsum/6laf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=6laf ProSAT]</span></td></tr>
+
</table>
</table>
-
<div style="background-color:#fffaf0;">
+
== Function ==
-
== Publication Abstract from PubMed ==
+
[https://www.uniprot.org/uniprot/B2UR41_AKKM8 B2UR41_AKKM8]
-
Akkermansia muciniphila is a beneficial microorganism colonized in the human gut that can reverse many intestinal metabolic-related diseases. Amuc_1100 is an outer-membrane protein of A. muciniphila. Oral administration of Amuc_1100 can reduce fat mass development, insulin resistance, and dyslipidemia in mice and activated the toll-like receptor 2 (TLR2) to regulate the immune response of the host, but the molecular mechanism remains unclear. Here we report the crystal structure of the extramembranous domain of Amuc_1100, which consists of a four-stranded antiparallel beta-sheet and four alpha-helices. Two C-terminal helices and the four-stranded antiparallel beta-sheet formed two "alphabetabeta" motifs and constituted the core domain, which shared a similar fold with type IV pili and type II Secretion system protein. Although the full-length of the extramembranous domain of Amuc_1100 existed as a monomer in solution, they formed trimer in the crystal. Elimination of the N-terminal coiled-coil helix alpha1 led to dimerization of Amuc_1100 both in solution and in crystal, indicating that the oligomeric state of Amuc_1100 was variable and could be influenced by alpha1. In addition, we identified that Amuc_1100 could directly bind human TLR2 (hTRL2) in vitro, suggesting that Amuc_1100 may serve as a new ligand for hTLR2. Dimerization of Amuc_1100 improved its hTLR2-binding affinity, suggesting that the alpha1-truncated Amuc_1100 could be a beneficial candidate for the development of A. muciniphila related drugs.
+
-
 
+
-
The variable oligomeric state of Amuc_1100 from Akkermansia muciniphila.,Wang J, Xiang R, Wang R, Zhang B, Gong W, Zhang J, Zhang M, Wang M J Struct Biol. 2020 Jul 28:107593. doi: 10.1016/j.jsb.2020.107593. PMID:32736072<ref>PMID:32736072</ref>
+
-
 
+
-
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
+
-
</div>
+
-
<div class="pdbe-citations 6laf" style="background-color:#fffaf0;"></div>
+
-
== References ==
+
-
<references/>
+
__TOC__
__TOC__
</StructureSection>
</StructureSection>
-
[[Category: Akkm8]]
+
[[Category: Akkermansia muciniphila ATCC BAA-835]]
[[Category: Large Structures]]
[[Category: Large Structures]]
-
[[Category: Wang, J]]
+
[[Category: Wang J]]
-
[[Category: Wang, M]]
+
[[Category: Wang M]]
-
[[Category: Xiang, R]]
+
[[Category: Xiang R]]
-
[[Category: Zhang, M]]
+
[[Category: Zhang M]]
-
[[Category: Akkermansia muciniphila]]
+
-
[[Category: Amuc_1100]]
+
-
[[Category: Membrane protein]]
+
-
[[Category: Outer-membrane protein]]
+
-
[[Category: Toll-like receptor 2]]
+
-
[[Category: Type ii secretion system]]
+

Current revision

Crystal structure of the core domain of Amuc_1100 from Akkermansia muciniphila

PDB ID 6laf

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/6laf"
Personal tools