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.


1m3d

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:31, 10 April 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1m3d.gif|left|200px]]
 
-
{{Structure
+
==Structure of Type IV Collagen NC1 Domains==
-
|PDB= 1m3d |SIZE=350|CAPTION= <scene name='initialview01'>1m3d</scene>, resolution 2.0&Aring;
+
<StructureSection load='1m3d' size='340' side='right'caption='[[1m3d]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
-
|SITE=
+
== Structural highlights ==
-
|LIGAND= <scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</scene>, <scene name='pdbligand=BR:BROMIDE+ION'>BR</scene> and <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>
+
<table><tr><td colspan='2'>[[1m3d]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M3D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1M3D FirstGlance]. <br>
-
|ACTIVITY=
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2&#8491;</td></tr>
-
|GENE=
+
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BR:BROMIDE+ION'>BR</scene>, <scene name='pdbligand=GOL:GLYCEROL'>GOL</scene>, <scene name='pdbligand=LU:LUTETIUM+(III)+ION'>LU</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=1m3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m3d OCA], [https://pdbe.org/1m3d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1m3d RCSB], [https://www.ebi.ac.uk/pdbsum/1m3d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1m3d ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/CO4A1_BOVIN CO4A1_BOVIN] 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.[UniProtKB:P02463] 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.[UniProtKB:P02462]
 +
== 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/m3/1m3d_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview01.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=1m3d ConSurf].
 +
<div style="clear:both"></div>
-
'''Structure of Type IV Collagen NC1 Domains'''
+
==See Also==
-
 
+
*[[Collagen 3D structures|Collagen 3D structures]]
-
 
+
__TOC__
-
==Overview==
+
</StructureSection>
-
Type IV collagen, which is present in all metazoan, exists as a family of six homologous alpha(IV) chains, alpha1-alpha6, in mammals. The six chains assemble into three different triple helical protomers and self-associate as three distinct networks. The network underlies all epithelia as a component of basement membranes, which play important roles in cell adhesion, growth, differentiation, tissue repair and molecular ultrafiltration. The specificity of both protomer and network assembly is governed by amino acid sequences of the C-terminal noncollagenous (NC1) domain of each chain. In this study, the structural basis for protomer and network assembly was investigated by determining the crystal structure of the ubiquitous [(alpha1)(2).alpha2](2) NC1 hexamer of bovine lens capsule basement membrane at 2.0 A resolution. The NC1 monomer folds into a novel tertiary structure. The (alpha1)(2).alpha2 trimer is organized through the unique three-dimensional domain swapping interactions. The differences in the primary sequences of the hypervariable region manifest in different secondary structures, which determine the chain specificity at the monomer-monomer interfaces. The trimer-trimer interface is stabilized by the extensive hydrophobic and hydrophilic interactions without a need for disulfide cross-linking.
+
-
 
+
-
==About this Structure==
+
-
1M3D is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1M3D OCA].
+
-
 
+
-
==Reference==
+
-
Crystal structure of NC1 domains. Structural basis for type IV collagen assembly in basement membranes., Sundaramoorthy M, Meiyappan M, Todd P, Hudson BG, J Biol Chem. 2002 Aug 23;277(34):31142-53. Epub 2002 Apr 22. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/11970952 11970952]
+
[[Category: Bos taurus]]
[[Category: Bos taurus]]
-
[[Category: Protein complex]]
+
[[Category: Large Structures]]
-
[[Category: Hudson, B G.]]
+
[[Category: Hudson BG]]
-
[[Category: Meiyappan, M.]]
+
[[Category: Meiyappan M]]
-
[[Category: Sundaramoorthy, M.]]
+
[[Category: Sundaramoorthy M]]
-
[[Category: Todd, P.]]
+
[[Category: Todd P]]
-
[[Category: BR]]
+
-
[[Category: GOL]]
+
-
[[Category: LU]]
+
-
[[Category: 3d domain swapping]]
+
-
[[Category: basement membrane]]
+
-
[[Category: br-mad]]
+
-
[[Category: nc1 domain]]
+
-
[[Category: network assembly]]
+
-
[[Category: type iv collagen]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Mar 20 12:38:24 2008''
+

Current revision

Structure of Type IV Collagen NC1 Domains

PDB ID 1m3d

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/1m3d"
Personal tools