1li1: Difference between revisions

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-[[Image:1li1.gif|left|200px]]
-<!--
-The line below this paragraph, containing "STRUCTURE_1li1", creates the "Structure Box" on the page.
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-{{STRUCTURE_1li1|  PDB=1li1  |  SCENE=  }}
-'''The 1.9-A crystal structure of the noncollagenous (NC1) domain of human placenta collagen IV shows stabilization via a novel type of covalent Met-Lys cross-link'''
+==The 1.9-A crystal structure of the noncollagenous (NC1) domain of human placenta collagen IV shows stabilization via a novel type of covalent Met-Lys cross-link==
+<StructureSection load='1li1' size='340' side='right'caption='[[1li1]], [[Resolution|resolution]] 1.90&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[1li1]] is a 6 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=1LI1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1LI1 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]] 1.9&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ACT:ACETATE+ION'>ACT</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=1li1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1li1 OCA], [https://pdbe.org/1li1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1li1 RCSB], [https://www.ebi.ac.uk/pdbsum/1li1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1li1 ProSAT]</span></td></tr>
+</table>
+== Disease ==
+[https://www.uniprot.org/uniprot/CO4A1_HUMAN CO4A1_HUMAN] Defects in COL4A1 are a cause of brain small vessel disease with hemorrhage (BSVDH) [MIM:[https://omim.org/entry/607595 607595]. Brain small vessel diseases underlie 20 to 30 percent of ischemic strokes and a larger proportion of intracerebral hemorrhages. Inheritance is autosomal dominant.<ref>PMID:16598045</ref> <ref>PMID:17696175</ref> <ref>PMID:17379824</ref> <ref>PMID:20385946</ref> <ref>PMID:19477666</ref>   Defects in COL4A1 are the cause of hereditary angiopathy with nephropathy aneurysms and muscle cramps (HANAC) [MIM:[https://omim.org/entry/611773 611773]. The clinical renal manifestations include hematuria and bilateral large cysts. Histologic analysis revealed complex basement membrane defects in kidney and skin. The systemic angiopathy appears to affect both small vessels and large arteries.<ref>PMID:18160688</ref> <ref>PMID:20818663</ref>   Defects in COL4A1 are a cause of familial porencephaly (POREN1) [MIM:[https://omim.org/entry/175780 175780]. Porencephaly is a term used for any cavitation or cerebrospinal fluid-filled cyst in the brain. Porencephaly type 1 is usually unilateral and results from focal destructive lesions such as fetal vascular occlusion or birth trauma. Type 2, or schizencephalic porencephaly, is usually symmetric and represents a primary defect or arrest in the development of the cerebral ventricles.<ref>PMID:15905400</ref> <ref>PMID:16107487</ref> <ref>PMID:19194877</ref>
+== Function ==
+[https://www.uniprot.org/uniprot/CO4A1_HUMAN CO4A1_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.<ref>PMID:10811134</ref> <ref>PMID:16481288</ref> <ref>PMID:16151532</ref> <ref>PMID:18775695</ref>   Arresten, comprising the C-terminal NC1 domain, inhibits angiogenesis and tumor formation. The C-terminal half is found to possess the anti-angiogenic activity. Specifically inhibits endothelial cell proliferation, migration and tube formation. Inhibits expression of hypoxia-inducible factor 1alpha and ERK1/2 and p38 MAPK activation. Ligand for alpha1/beta1 integrin.<ref>PMID:10811134</ref> <ref>PMID:16481288</ref> <ref>PMID:16151532</ref> <ref>PMID:18775695</ref>
+== Evolutionary Conservation ==
+[[Image:Consurf_key_small.gif|200px|right]]
+Check<jmol>
+  <jmolCheckbox>
+    <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/li/1li1_consurf.spt"</scriptWhenChecked>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
+    <text>to colour the structure by Evolutionary Conservation</text>
+  </jmolCheckbox>
+</jmol>, as determined by [http://consurfdb.tau.ac.il/ ConSurfDB]. You may read the [[Conservation%2C_Evolutionary|explanation]] of the method and the full data available from [http://bental.tau.ac.il/new_ConSurfDB/main_output.php?pdb_ID=1li1 ConSurf].
+<div style="clear:both"></div>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Triple-helical collagen IV protomers associate through their N- and C-termini forming a three-dimensional network, which provides basement membranes with an anchoring scaffold and mechanical strength. The noncollagenous (NC1) domain of the C-terminal junction between two adjacent collagen IV protomers from human placenta was crystallized and its 1.9-A structure was solved by multiple anomalous diffraction (MAD) phasing. This hexameric NC1 particle is composed of two trimeric caps, which interact through a large planar interface. Each cap is formed by two alpha 1 fragments and one alpha 2 fragment with a similar previously uncharacterized fold, segmentally arranged around an axial tunnel. Each monomer chain folds into two structurally very similar subdomains, which each contain a finger-like hairpin loop that inserts into a six-stranded beta-sheet of the neighboring subdomain of the same or the adjacent chain. Thus each trimer forms a quite regular, but nonclassical, sixfold propeller. The trimer-trimer interaction is further stabilized by a previously uncharacterized type of covalent cross-link between the side chains of a Met and a Lys residue of the alpha 1 and alpha 2 chains from opposite trimers, explaining previous findings of nonreducible cross-links in NC1. This structure provides insights into NC1-related diseases such as Goodpasture and Alport syndromes.
-==Overview==
+The 1.9-A crystal structure of the noncollagenous (NC1) domain of human placenta collagen IV shows stabilization via a novel type of covalent Met-Lys cross-link.,Than ME, Henrich S, Huber R, Ries A, Mann K, Kuhn K, Timpl R, Bourenkov GP, Bartunik HD, Bode W Proc Natl Acad Sci U S A. 2002 May 14;99(10):6607-12. PMID:12011424<ref>PMID:12011424</ref>
-Triple-helical collagen IV protomers associate through their N- and C-termini forming a three-dimensional network, which provides basement membranes with an anchoring scaffold and mechanical strength. The noncollagenous (NC1) domain of the C-terminal junction between two adjacent collagen IV protomers from human placenta was crystallized and its 1.9-A structure was solved by multiple anomalous diffraction (MAD) phasing. This hexameric NC1 particle is composed of two trimeric caps, which interact through a large planar interface. Each cap is formed by two alpha 1 fragments and one alpha 2 fragment with a similar previously uncharacterized fold, segmentally arranged around an axial tunnel. Each monomer chain folds into two structurally very similar subdomains, which each contain a finger-like hairpin loop that inserts into a six-stranded beta-sheet of the neighboring subdomain of the same or the adjacent chain. Thus each trimer forms a quite regular, but nonclassical, sixfold propeller. The trimer-trimer interaction is further stabilized by a previously uncharacterized type of covalent cross-link between the side chains of a Met and a Lys residue of the alpha 1 and alpha 2 chains from opposite trimers, explaining previous findings of nonreducible cross-links in NC1. This structure provides insights into NC1-related diseases such as Goodpasture and Alport syndromes.
-==About this Structure==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-LI1 is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1LI1 OCA].
+</div>
+<div class="pdbe-citations 1li1" style="background-color:#fffaf0;"></div>
-==Reference==
+==See Also==
-The 1.9-A crystal structure of the noncollagenous (NC1) domain of human placenta collagen IV shows stabilization via a novel type of covalent Met-Lys cross-link., Than ME, Henrich S, Huber R, Ries A, Mann K, Kuhn K, Timpl R, Bourenkov GP, Bartunik HD, Bode W, Proc Natl Acad Sci U S A. 2002 May 14;99(10):6607-12. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12011424 12011424]
+*[[Collagen 3D structures|Collagen 3D structures]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
 [[Category: Homo sapiens]]
-[[Category: Protein complex]]
+[[Category: Large Structures]]
-[[Category: Bartunik, H D.]]
+[[Category: Bartunik HD]]
-[[Category: Bode, W.]]
+[[Category: Bode W]]
-[[Category: Bourenkov, G P.]]
+[[Category: Bourenkov GP]]
-[[Category: Henrich, S.]]
+[[Category: Henrich S]]
-[[Category: Huber, R.]]
+[[Category: Huber R]]
-[[Category: Kuhn, K.]]
+[[Category: Kuhn K]]
-[[Category: Mann, K.]]
+[[Category: Mann K]]
-[[Category: Ries, A.]]
+[[Category: Ries A]]
-[[Category: Than, M E.]]
+[[Category: Than ME]]
-[[Category: Timpl, R.]]
+[[Category: Timpl R]]
-[[Category: Basement membrane]]
-[[Category: Collagen iv]]
-[[Category: Covalent cross-link]]
-[[Category: Nc1 domain]]
-[[Category: Protein-protein interaction]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May  2 23:56:25 2008''