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.


1bbd

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (15:31, 13 March 2024) (edit) (undo)
 
(18 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1bbd.gif|left|200px]]<br /><applet load="1bbd" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1bbd, resolution 2.8&Aring;" />
 
-
'''THREE DIMENSIONAL STRUCTURE OF THE FAB FRAGMENT OF A NEUTRALIZING ANTIBODY TO HUMAN RHINOVIRUS SEROTYPE 2'''<br />
 
-
==Overview==
+
==THREE DIMENSIONAL STRUCTURE OF THE FAB FRAGMENT OF A NEUTRALIZING ANTIBODY TO HUMAN RHINOVIRUS SEROTYPE 2==
-
The crystal structure of the antigen-binding fragment of a monoclonal antibody (8F5) that neutralizes human rhinovirus serotype 2 has been determined by X-ray diffraction studies. Antibody 8F5, obtained by immunization with native HRV2 virions, cross-reacts with peptides of the viral capsid protein VP2, which contribute to the neutralizing immunogenic site B in this serotype. The structure was solved by the molecular replacement method and has been refined to an R-factor of 18.9% at 2.8 A resolution. The elbow angle, relating the variable and constant modules of the molecule is 127 degrees, representing the smallest elbow angle observed so far in an Fab fragment. Furthermore, the charged residues of the epitope can be well accommodated in the antigen-binding site. This is the first crystal structure reported for an antibody directed against an icosahedral virus.
+
<StructureSection load='1bbd' size='340' side='right'caption='[[1bbd]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 +
== Structural highlights ==
 +
<table><tr><td colspan='2'>[[1bbd]] is a 2 chain structure with sequence from [https://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BBD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1BBD 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]] 2.8&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=1bbd FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1bbd OCA], [https://pdbe.org/1bbd PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1bbd RCSB], [https://www.ebi.ac.uk/pdbsum/1bbd PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1bbd ProSAT]</span></td></tr>
 +
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/Q52L64_MOUSE Q52L64_MOUSE]
 +
== 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/bb/1bbd_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=1bbd ConSurf].
 +
<div style="clear:both"></div>
-
==About this Structure==
+
==See Also==
-
1BBD is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=SO4:'>SO4</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1BBD OCA].
+
*[[Antibody 3D structures|Antibody 3D structures]]
-
 
+
*[[Sandbox 20009|Sandbox 20009]]
-
==Reference==
+
*[[3D structures of non-human antibody|3D structures of non-human antibody]]
-
Three-dimensional structure of the Fab fragment of a neutralizing antibody to human rhinovirus serotype 2., Tormo J, Stadler E, Skern T, Auer H, Kanzler O, Betzel C, Blaas D, Fita I, Protein Sci. 1992 Sep;1(9):1154-61. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=1338980 1338980]
+
__TOC__
-
[[Category: Protein complex]]
+
</StructureSection>
-
[[Category: Blaas, D.]]
+
[[Category: Large Structures]]
-
[[Category: Fita, I.]]
+
[[Category: Mus musculus]]
-
[[Category: Tormo, J.]]
+
[[Category: Blaas D]]
-
[[Category: SO4]]
+
[[Category: Fita I]]
-
[[Category: immunoglobulin]]
+
[[Category: Tormo J]]
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 11:53:30 2008''
+

Current revision

THREE DIMENSIONAL STRUCTURE OF THE FAB FRAGMENT OF A NEUTRALIZING ANTIBODY TO HUMAN RHINOVIRUS SEROTYPE 2

PDB ID 1bbd

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/1bbd"
Personal tools