2uur

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (01:25, 21 November 2024) (edit) (undo)
 
(6 intermediate revisions not shown.)
Line 1: Line 1:
-
{{STRUCTURE_2uur| PDB=2uur | SCENE= }}
 
-
===N-TERMINAL NC4 DOMAIN OF COLLAGEN IX===
 
-
{{ABSTRACT_PUBMED_17553797}}
 
-
==Disease==
+
==N-terminal NC4 domain of collagen IX==
-
[[http://www.uniprot.org/uniprot/CO9A1_HUMAN CO9A1_HUMAN]] Defects in COL9A1 are the cause of multiple epiphyseal dysplasia type 6 (EDM6) [MIM:[http://omim.org/entry/614135 614135]]. A generalized skeletal dysplasia associated with significant morbidity. Joint pain, joint deformity, waddling gait, and short stature are the main clinical signs and symptoms. Radiological examination of the skeleton shows delayed, irregular mineralization of the epiphyseal ossification centers and of the centers of the carpal and tarsal bones. Multiple epiphyseal dysplasia is broadly categorized into the more severe Fairbank and the milder Ribbing types. The Fairbank type is characterized by shortness of stature, short and stubby fingers, small epiphyses in several joints, including the knee, ankle, hand, and hip. The Ribbing type is confined predominantly to the hip joints and is characterized by hands that are normal and stature that is normal or near-normal.<ref>PMID:11565064</ref> Defects in COL9A1 are the cause of Stickler syndrome type 4 (STL4) [MIM:[http://omim.org/entry/614134 614134]]. An autosomal recessive form of Stickler syndrome, an inherited disorder that associates ocular signs with more or less complete forms of Pierre Robin sequence, bone disorders and sensorineural deafness. Ocular disorders may include juvenile cataract, myopia, strabismus, vitreoretinal or chorioretinal degeneration, retinal detachment, and chronic uveitis. Robin sequence includes an opening in the roof of the mouth (a cleft palate), a large tongue (macroglossia), and a small lower jaw (micrognathia). Bones are affected by slight platyspondylisis and large, often defective epiphyses. Juvenile joint laxity is followed by early signs of arthrosis. The degree of hearing loss varies among affected individuals and may become more severe over time. Syndrome expressivity is variable.<ref>PMID:16909383</ref>
+
<StructureSection load='2uur' size='340' side='right'caption='[[2uur]], [[Resolution|resolution]] 1.80&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[2uur]] 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=2UUR OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2UUR 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]] 1.8&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=EDO:1,2-ETHANEDIOL'>EDO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=2uur FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2uur OCA], [https://pdbe.org/2uur PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2uur RCSB], [https://www.ebi.ac.uk/pdbsum/2uur PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2uur ProSAT]</span></td></tr>
 +
</table>
 +
== 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/uu/2uur_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=2uur ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
Collagen IX, located on the surface of collagen fibrils, is crucial for cartilage integrity and stability. The N-terminal NC4 domain of the alpha1(IX) chain is probably important in this because it interacts with various macromolecules such as proteoglycans and cartilage oligomeric matrix protein. At least 17 distinct collagen polypeptides carry an NC4-like unit near their N terminus, but this report, describing the crystal structure of NC4 at 1.8-A resolution, represents the first atomic level structure for these domains. The structure is similar to previously characterized laminin-neurexin-sex hormone binding globulin (LNS) structures, dominated by an antiparallel beta-sheet sandwich. In addition, a zinc ion was found in a position similar to that of the metal binding site of other LNS domains. A partial backbone NMR assignment of NC4 was obtained and utilized in NMR titration studies to investigate the zinc binding in solution state and to quantitate the affinity of metal binding. The K(d) of 11.5 mM suggests a regulatory rather than a structural role for zinc in solution. NMR titration with a heparin tetrasaccharide revealed the presence of a secondary binding site for heparin on NC4, showing structural and functional conservation with thrombospondin-1, but a markedly reduced affinity for the ligand. Also the overall arrangement of the N and C termini of NC4 resembles most closely the N-terminal domain of thrombospondin-1, distinguishing the two from the majority of the published LNS structures.
-
==Function==
+
Crystal structure of the N-terminal NC4 domain of collagen IX, a zinc binding member of the laminin-neurexin-sex hormone binding globulin (LNS) domain family.,Leppanen VM, Tossavainen H, Permi P, Lehtio L, Ronnholm G, Goldman A, Kilpelainen I, Pihlajamaa T J Biol Chem. 2007 Aug 10;282(32):23219-30. Epub 2007 Jun 6. PMID:17553797<ref>PMID:17553797</ref>
-
[[http://www.uniprot.org/uniprot/CO9A1_HUMAN CO9A1_HUMAN]] Structural component of hyaline cartilage and vitreous of the eye.
+
-
==About this Structure==
+
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-
[[2uur]] is a 1 chain structure with sequence 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=2UUR OCA].
+
</div>
 +
<div class="pdbe-citations 2uur" style="background-color:#fffaf0;"></div>
==See Also==
==See Also==
-
*[[Collagen|Collagen]]
+
*[[Collagen 3D structures|Collagen 3D structures]]
-
 
+
== References ==
-
==Reference==
+
<references/>
-
<ref group="xtra">PMID:017553797</ref><references group="xtra"/><references/>
+
__TOC__
 +
</StructureSection>
[[Category: Homo sapiens]]
[[Category: Homo sapiens]]
-
[[Category: Goldman, A.]]
+
[[Category: Large Structures]]
-
[[Category: Kilpelainen, I.]]
+
[[Category: Goldman A]]
-
[[Category: Lehtio, L.]]
+
[[Category: Kilpelainen I]]
-
[[Category: Leppanen, V M.]]
+
[[Category: Lehtio L]]
-
[[Category: Permi, P.]]
+
[[Category: Leppanen V-M]]
-
[[Category: Pihlajamaa, T.]]
+
[[Category: Permi P]]
-
[[Category: Ronnholm, G.]]
+
[[Category: Pihlajamaa T]]
-
[[Category: Tossavainen, H.]]
+
[[Category: Ronnholm G]]
-
[[Category: Collagen]]
+
[[Category: Tossavainen H]]
-
[[Category: Collagen ix]]
+
-
[[Category: Extracellular matrix]]
+
-
[[Category: Glycoprotein]]
+
-
[[Category: Hydroxylation]]
+
-
[[Category: Nc4]]
+
-
[[Category: Structural protein]]
+

Current revision

N-terminal NC4 domain of collagen IX

PDB ID 2uur

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Personal tools