3iy3

From Proteopedia

(Difference between revisions)

Current revision

Variable domains of the computer generated model (WAM) of Fab 8 fitted into the cryoEM reconstruction of the virus-Fab 8 complex

3iy3, resolution 11.10Å

Structural highlights

3iy3 is a 2 chain structure with sequence from Mus musculus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 11.1Å
Experimental data:	Check to display Experimental Data
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Evolutionary Conservation

Checkto colour the structure by Evolutionary Conservation, as determined by ConSurfDB. You may read the explanation of the method and the full data available from ConSurf.

Publication Abstract from PubMed

The structures of canine parvovirus (CPV) and feline parvovirus (FPV) complexed with antibody fragments from eight different neutralizing monoclonal antibodies were determined by cryo-electron microscopy (cryoEM) reconstruction to resolutions varying from 8.5 to 18 A. The crystal structure of one of the Fab molecules and the sequence of the variable domain for each of the Fab molecules have been determined. The structures of Fab fragments not determined crystallographically were predicted by homology modeling according to the amino acid sequence. Fitting of the Fab and virus structures into the cryoEM densities identified the footprints of each antibody on the viral surface. As anticipated from earlier analyses, the Fab binding sites are directed to two epitopes, A and B. The A site is on an exposed part of the surface near an icosahedral threefold axis, whereas the B site is about equidistant from the surrounding five-, three-, and twofold axes. One antibody directed to the A site binds CPV but not FPV. Two of the antibodies directed to the B site neutralize the virus as Fab fragments. The differences in antibody properties have been linked to the amino acids within the antibody footprints, the position of the binding site relative to the icosahedral symmetry elements, and the orientation of the Fab structure relative to the surface of the virus. Most of the exposed surface area was antigenic, although each of the antibodies had a common area of overlap that coincided with the positions of the previously mapped escape mutations.

Structural comparison of different antibodies interacting with parvovirus capsids.,Hafenstein S, Bowman VD, Sun T, Nelson CD, Palermo LM, Chipman PR, Battisti AJ, Parrish CR, Rossmann MG J Virol. 2009 Jun;83(11):5556-66. Epub 2009 Mar 25. PMID:19321620^[1]

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

References

↑ Hafenstein S, Bowman VD, Sun T, Nelson CD, Palermo LM, Chipman PR, Battisti AJ, Parrish CR, Rossmann MG. Structural comparison of different antibodies interacting with parvovirus capsids. J Virol. 2009 Jun;83(11):5556-66. Epub 2009 Mar 25. PMID:19321620 doi:10.1128/JVI.02532-08

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

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/3iy3"

@@ Line 3: / Line 3: @@
 <SX load='3iy3' size='340' side='right' viewer='molstar' caption='[[3iy3]], [[Resolution|resolution]] 11.10&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[3iy3]] is a 2 chain structure with sequence from [http://en.wikipedia.org/wiki/Mus_musculus Mus musculus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3IY3 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=3IY3 FirstGlance]. <br>
+<table><tr><td colspan='2'>[[3iy3]] 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=3IY3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3IY3 FirstGlance]. <br>
-</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=3iy3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iy3 OCA], [http://pdbe.org/3iy3 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=3iy3 RCSB], [http://www.ebi.ac.uk/pdbsum/3iy3 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=3iy3 ProSAT]</span></td></tr>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 11.1&#8491;</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=3iy3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3iy3 OCA], [https://pdbe.org/3iy3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3iy3 RCSB], [https://www.ebi.ac.uk/pdbsum/3iy3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3iy3 ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 11: / Line 12: @@
   <jmolCheckbox>
     <scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/iy/3iy3_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 28: / Line 29: @@
 ==See Also==
 *[[Antibody 3D structures|Antibody 3D structures]]
+*[[Sandbox 20009|Sandbox 20009]]
+*[[3D structures of non-human antibody|3D structures of non-human antibody]]
 == References ==
 <references/>
@@ Line 34: / Line 37: @@
 [[Category: Large Structures]]
 [[Category: Mus musculus]]
-[[Category: Battisti, A J]]
+[[Category: Battisti AJ]]
-[[Category: Bowman, V D]]
+[[Category: Bowman VD]]
-[[Category: Chipman, P R]]
+[[Category: Chipman PR]]
-[[Category: Hafenstein, S]]
+[[Category: Hafenstein S]]
-[[Category: Nelson, C D]]
+[[Category: Nelson CD]]
-[[Category: Palermo, L M]]
+[[Category: Palermo LM]]
-[[Category: Parrish, C R]]
+[[Category: Parrish CR]]
-[[Category: Rossmann, M G]]
+[[Category: Rossmann MG]]
-[[Category: Sun, T]]
+[[Category: Sun T]]
-[[Category: Canine]]
-[[Category: Cryoem]]
-[[Category: Fab footprint]]
-[[Category: Feline]]
-[[Category: Immune system]]
-[[Category: Neutralizing antibody]]
-[[Category: Parvovirus]]

3iy3

From Proteopedia

Current revision

Variable domains of the computer generated model (WAM) of Fab 8 fitted into the cryoEM reconstruction of the virus-Fab 8 complex

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

Views

Personal tools

Navigation

Search

Toolbox