6wku: Difference between revisions

Latest revision as of 08:26, 17 October 2024

Twelve Chloride Ions Drive Assembly of Human alpha345 Collagen IV NC1 domain

Structural highlights

Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 1.76Å
Ligands:	1PE, CL, EDO, P6G, PE8, PEG, PG4, PGE
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Publication Abstract from PubMed

Our recent work identified a genetic variant of the alpha345 hexamer of the collagen IV scaffold that is present in patients with glomerular basement membrane diseases, Goodpasture's disease (GP) and Alport syndrome (AS), and phenocopies AS in knock-in mice (see Companion Paper I). To understand the context of this "Zurich" variant, an 8-amino acid appendage, we developed a construct of the wild-type alpha345 hexamer using single-chain NC1 trimer technology, which allowed us to solve a crystal structure of this key connection module. The alpha345 hexamer structure revealed a ring of twelve chloride ions at the trimer-trimer interface, analogous to the collagen alpha121 hexamer, and the location of the 170 AS variants. The hexamer surface is marked by multiple pores and crevices that are potentially accessible to small molecules. Loop-crevice-loop (LCL) features constitute bioactive sites, where pathogenic pathways converge that are linked to Alport and GP diseases, and, potentially, diabetic nephropathy. In Companion Paper III, we demonstrate that these sites exhibit conformational plasticity, a dynamic property underlying assembly of bioactive sites and hexamer dysfunction. The alpha345 hexamer structure is a platform to decipher how variants cause AS, and how hypoepitopes can be triggered causing GP. Furthermore, the bioactive sites, along with the pores and crevices on the hexamer surface, are prospective targets for therapeutic interventions.

Collagen IV(alpha345) dysfunction in glomerular basement membrane diseases. II. Crystal structure of the alpha345 hexamer.,Boudko SP, Bauer R, Chetyrkin SV, Ivanov S, Smith J, Voziyan PA, Hudson BG J Biol Chem. 2021 Mar 25:100591. doi: 10.1016/j.jbc.2021.100591. PMID:33775698^[1]

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

References

↑ Boudko SP, Bauer R, Chetyrkin SV, Ivanov S, Smith J, Voziyan PA, Hudson BG. Collagen IV(alpha345) dysfunction in glomerular basement membrane diseases. II. Crystal structure of the alpha345 hexamer. J Biol Chem. 2021 Mar 25:100591. doi: 10.1016/j.jbc.2021.100591. PMID:33775698 doi:https://dx.doi.org/10.1016/j.jbc.2021.100591

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OCA

[1] Boudko SP, Bauer R, Chetyrkin SV, Ivanov S, Smith J, Voziyan PA, Hudson BG. Collagen IV(alpha345) dysfunction in glomerular basement membrane diseases. II. Crystal structure of the alpha345 hexamer. J Biol Chem. 2021 Mar 25:100591. doi: 10.1016/j.jbc.2021.100591. PMID:33775698 doi:https://dx.doi.org/10.1016/j.jbc.2021.100591

[1]

@@ Line 3: / Line 3: @@
 <StructureSection load='6wku' size='340' side='right'caption='[[6wku]], [[Resolution|resolution]] 1.76&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[6wku]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WKU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WKU FirstGlance]. <br>
+<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=6WKU OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=6WKU FirstGlance]. <br>
 </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.76&#8491;</td></tr>
 <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=1PE:PENTAETHYLENE+GLYCOL'>1PE</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=P6G:HEXAETHYLENE+GLYCOL'>P6G</scene>, <scene name='pdbligand=PE8:3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL'>PE8</scene>, <scene name='pdbligand=PEG:DI(HYDROXYETHYL)ETHER'>PEG</scene>, <scene name='pdbligand=PG4:TETRAETHYLENE+GLYCOL'>PG4</scene>, <scene name='pdbligand=PGE:TRIETHYLENE+GLYCOL'>PGE</scene></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=6wku FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=6wku OCA], [https://pdbe.org/6wku PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=6wku RCSB], [https://www.ebi.ac.uk/pdbsum/6wku PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=6wku ProSAT]</span></td></tr>
 </table>
-== Disease ==
-[https://www.uniprot.org/uniprot/CO4A5_HUMAN CO4A5_HUMAN] X-linked diffuse leiomyomatosis - Alport syndrome;X-linked Alport syndrome. The disease is caused by mutations affecting the gene represented in this entry.  Deletions covering the N-terminal regions of COL4A5 and COL4A6, which are localized in a head-to-head manner, are found in the chromosome Xq22.3 centromeric deletion syndrome. This results in a phenotype with features of diffuse leiomyomatosis and Alport syndrome (DL-ATS).[https://www.uniprot.org/uniprot/CO4A4_HUMAN CO4A4_HUMAN] Benign familial hematuria;Autosomal dominant Alport syndrome;Autosomal recessive Alport syndrome. The disease is caused by mutations affecting the gene represented in this entry.  The disease is caused by mutations affecting the gene represented in this entry.[https://www.uniprot.org/uniprot/CO4A3_HUMAN CO4A3_HUMAN] Benign familial hematuria;Autosomal dominant Alport syndrome;Autosomal recessive Alport syndrome. Autoantibodies against the NC1 domain of alpha 3(IV) are found in Goodpasture syndrome, an autoimmune disease of lung and kidney.  The disease is caused by mutations affecting the gene represented in this entry.  The disease is caused by mutations affecting the gene represented in this entry.  The disease is caused by mutations affecting the gene represented in this entry.
-== Function ==
-[https://www.uniprot.org/uniprot/CO4A5_HUMAN CO4A5_HUMAN] Type IV collagen is the major structural component of glomerular basement membranes (GBM), forming a 'chicken-wire' meshwork together with laminins, proteoglycans and entactin/nidogen.[https://www.uniprot.org/uniprot/CO4A4_HUMAN CO4A4_HUMAN] Type IV collagen is the major structural component of glomerular basement membranes (GBM), forming a 'chicken-wire' meshwork together with laminins, proteoglycans and entactin/nidogen.[https://www.uniprot.org/uniprot/CO4A3_HUMAN CO4A3_HUMAN] Type IV collagen is the major structural component of glomerular basement membranes (GBM), forming a 'chicken-wire' meshwork together with laminins, proteoglycans and entactin/nidogen.  Tumstatin, a cleavage fragment corresponding to the collagen alpha 3(IV) NC1 domain, possesses both anti-angiogenic and anti-tumor cell activity; these two anti-tumor properties may be regulated via RGD-independent ITGB3-mediated mechanisms.
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 28: / Line 24: @@
 __TOC__
 </StructureSection>
-[[Category: Homo sapiens]]
 [[Category: Large Structures]]
 [[Category: Boudko SP]]
 [[Category: Hudson BG]]

6wku: Difference between revisions

Latest revision as of 08:26, 17 October 2024

Twelve Chloride Ions Drive Assembly of Human alpha345 Collagen IV NC1 domain

Structural highlights

Publication Abstract from PubMed

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