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.


1ncd

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
(New page: 200px<br /> <applet load="1ncd" size="450" color="white" frame="true" align="right" spinBox="true" caption="1ncd, resolution 2.9&Aring;" /> '''REFINED CRYSTAL STRU...)
Current revision (08:48, 10 April 2024) (edit) (undo)
 
(17 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1ncd.gif|left|200px]]<br />
 
-
<applet load="1ncd" size="450" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1ncd, resolution 2.9&Aring;" />
 
-
'''REFINED CRYSTAL STRUCTURE OF THE INFLUENZA VIRUS N9 NEURAMINIDASE-NC41 FAB COMPLEX'''<br />
 
-
==Overview==
+
==REFINED CRYSTAL STRUCTURE OF THE INFLUENZA VIRUS N9 NEURAMINIDASE-NC41 FAB COMPLEX==
-
The crystal structure of the complex between neuraminidase from influenza, virus (subtype N9 and isolated from an avian source) and the, antigen-binding fragment (Fab) of monoclonal antibody NC41 has been, refined by both least-squares and simulated annealing methods to an, R-factor of 0.191 using 31,846 diffraction data in the resolution range, 8.0 to 2.5 A. The resulting model has a root-mean-square deviation from, ideal bond-length of 0.016 A. One fourth of the tetrameric complex, comprises the crystallographic model, which has 6577 non-hydrogen atoms, and consists of 389 protein residues and eight carbohydrate residues in, the neuraminidase, 214 residues in the Fab light chain, and 221 residues, in the heavy chain. One putative Ca ion buried in the neuraminidase, and, 73 water molecules, are also included. A remarkable shape complementarity, exists between the interacting surfaces of the antigen and the antibody, although the packing density of atoms at the interface is somewhat looser, than in the interior of a protein. Similarly, there is a high degree of, chemical complementarity between the antigen and antibody, mediated by one, buried salt-link, two solvated salt-links and 12 hydrogen bonds. The, antibody-binding site on neuraminidase is discontinuous and comprises five, chain segments and 19 residues in contact, whilst 33 neuraminidase, residues in eight segments have 899 A2 of surface area buried by the, interaction (to a 1.7 A probe), including two hexose units. Seventeen, residues in NC41 Fab lying in five of the six complementarity determining, regions (CDRs) make contact with the neuraminidase and 36 antibody, residues in seven segments have 916 A2 of buried surface area. The, interface is more extensive than those of the three lysozyme-Fab complexes, whose crystal structures have been determined, as judged by buried surface, area and numbers of contact residues. There are only small differences, (less than 1.5 A) between the complexed and uncomplexed neuraminidase, structures and, at this resolution and accuracy, those differences are not, unequivocal. The main-chain conformations of five of the CDRs follow the, predicted canonical structures. The interface between the variable domains, of the light and heavy chains is not as extensive as in other Fabs, due to, less CDR-CDR interaction in NC41. The first CDR on the NC41 Fab light, chain is positioned so that it could sterically hinder the approach of, small as well as large substrates to the neuraminidase active-site pocket, suggesting a possible mechanism for the observed inhibition of enzyme, activity by the antibody.(ABSTRACT TRUNCATED AT 400 WORDS)
+
<StructureSection load='1ncd' size='340' side='right'caption='[[1ncd]], [[Resolution|resolution]] 2.90&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1ncd]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Influenza_A_virus_(A/whale/Maine/1/84(H13N9)) Influenza A virus (A/whale/Maine/1/84(H13N9))] and [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1NCD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1NCD 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]] 2.9&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=CA:CALCIUM+ION'>CA</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NAG:N-ACETYL-D-GLUCOSAMINE'>NAG</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=1ncd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ncd OCA], [https://pdbe.org/1ncd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ncd RCSB], [https://www.ebi.ac.uk/pdbsum/1ncd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ncd ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/NRAM_I84A1 NRAM_I84A1] Catalyzes the removal of terminal sialic acid residues from viral and cellular glycoconjugates. Cleaves off the terminal sialic acids on the glycosylated HA during virus budding to facilitate virus release. Additionally helps virus spread through the circulation by further removing sialic acids from the cell surface. These cleavages prevent self-aggregation and ensure the efficient spread of the progeny virus from cell to cell. Otherwise, infection would be limited to one round of replication. Described as a receptor-destroying enzyme because it cleaves a terminal sialic acid from the cellular receptors. May facilitate viral invasion of the upper airways by cleaving the sialic acid moities on the mucin of the airway epithelial cells. Likely to plays a role in the budding process through its association with lipid rafts during intracellular transport. May additionally display a raft-association independent effect on budding. Plays a role in the determination of host range restriction on replication and virulence. Sialidase activity in late endosome/lysosome traffic seems to enhance virus replication.
 +
== 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/nc/1ncd_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=1ncd ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1NCD is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/Influenza_a_virus_(strain_a/whale/maine/1/84) Influenza a virus (strain a/whale/maine/1/84)] and [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus] with NAG and CA as [http://en.wikipedia.org/wiki/ligands ligands]. Active as [http://en.wikipedia.org/wiki/Exo-alpha-sialidase Exo-alpha-sialidase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.2.1.18 3.2.1.18] Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1NCD OCA].
+
*[[Antibody 3D structures|Antibody 3D structures]]
-
 
+
*[[Neuraminidase 3D structures|Neuraminidase 3D structures]]
-
==Reference==
+
*[[3D structures of non-human antibody|3D structures of non-human antibody]]
-
Refined crystal structure of the influenza virus N9 neuraminidase-NC41 Fab complex., Tulip WR, Varghese JN, Laver WG, Webster RG, Colman PM, J Mol Biol. 1992 Sep 5;227(1):122-48. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1381757 1381757]
+
__TOC__
-
[[Category: Exo-alpha-sialidase]]
+
</StructureSection>
-
[[Category: Influenza a virus (strain a/whale/maine/1/84)]]
+
[[Category: Large Structures]]
[[Category: Mus musculus]]
[[Category: Mus musculus]]
-
[[Category: Protein complex]]
+
[[Category: Colman PM]]
-
[[Category: Colman, P.M.]]
+
[[Category: Tulip WR]]
-
[[Category: Tulip, W.R.]]
+
[[Category: Varghese JN]]
-
[[Category: Varghese, J.N.]]
+
-
[[Category: CA]]
+
-
[[Category: NAG]]
+
-
[[Category: hydrolase(o-glycosyl)]]
+
-
 
+
-
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 18 09:38:03 2007''
+

Current revision

REFINED CRYSTAL STRUCTURE OF THE INFLUENZA VIRUS N9 NEURAMINIDASE-NC41 FAB COMPLEX

PDB ID 1ncd

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/1ncd"
Personal tools