1m3d

From Proteopedia

(Difference between revisions)

Current revision

Structure of Type IV Collagen NC1 Domains

Structural highlights

1m3d is a 12 chain structure with sequence from Bos taurus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	X-ray diffraction, Resolution 2Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

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

Check, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

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.

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:11970952^[1]

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

References

↑ Sundaramoorthy M, Meiyappan M, Todd P, Hudson BG. Crystal structure of NC1 domains. Structural basis for type IV collagen assembly in basement membranes. J Biol Chem. 2002 Aug 23;277(34):31142-53. Epub 2002 Apr 22. PMID:11970952 doi:10.1074/jbc.M201740200

1 Structural highlights
2 Function
3 Evolutionary Conservation
4 Publication Abstract from PubMed
5 See Also
6 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1m3d"

@@ Line 3: / Line 3: @@
 <StructureSection load='1m3d' size='340' side='right'caption='[[1m3d]], [[Resolution|resolution]] 2.00&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1m3d]] is a 12 chain structure with sequence from [http://en.wikipedia.org/wiki/Bovin Bovin]. 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 [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1M3D FirstGlance]. <br>
+<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>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><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>
+</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>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1m3d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1m3d OCA], [http://pdbe.org/1m3d PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1m3d RCSB], [http://www.ebi.ac.uk/pdbsum/1m3d PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1m3d ProSAT]</span></td></tr>
+<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]]
@@ Line 12: / Line 15: @@
   <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>
+    <scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
     <text>to colour the structure by Evolutionary Conservation</text>
   </jmolCheckbox>
@@ Line 33: / Line 36: @@
 __TOC__
 </StructureSection>
-[[Category: Bovin]]
+[[Category: Bos taurus]]
 [[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: 3d domain swapping]]
-[[Category: Basement membrane]]
-[[Category: Br-mad]]
-[[Category: Nc1 domain]]
-[[Category: Network assembly]]
-[[Category: Structural protein]]
-[[Category: Type iv collagen]]

1m3d

From Proteopedia

Current revision

Structure of Type IV Collagen NC1 Domains

Structural highlights

Function

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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