1p4i

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:23, 9 October 2024) (edit) (undo)
 
(9 intermediate revisions not shown.)
Line 1: Line 1:
-
{{Seed}}
 
-
[[Image:1p4i.png|left|200px]]
 
-
<!--
+
==Crystal Structure of scFv against peptide GCN4==
-
The line below this paragraph, containing "STRUCTURE_1p4i", creates the "Structure Box" on the page.
+
<StructureSection load='1p4i' size='340' side='right'caption='[[1p4i]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
-
You may change the PDB parameter (which sets the PDB file loaded into the applet)
+
== Structural highlights ==
-
or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
+
<table><tr><td colspan='2'>[[1p4i]] 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=1P4I OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P4I FirstGlance]. <br>
-
or leave the SCENE parameter empty for the default display.
+
</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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1p4i FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4i OCA], [https://pdbe.org/1p4i PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p4i RCSB], [https://www.ebi.ac.uk/pdbsum/1p4i PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p4i ProSAT]</span></td></tr>
-
{{STRUCTURE_1p4i| PDB=1p4i | SCENE= }}
+
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/LV1A_MOUSE LV1A_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/p4/1p4i_consurf.spt"</scriptWhenChecked>
 +
<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.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=1p4i ConSurf].
 +
<div style="clear:both"></div>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
We generated a single chain Fv fragment of an antibody (scFv) with a binding affinity of about 5 pm to a short peptide by applying rigorous directed evolution. Starting from a high affinity peptide binder, originally obtained by ribosome display from a murine library, we generated libraries of mutants with error-prone PCR and DNA shuffling and applied off-rate selection by using ribosome display. Crystallographic analysis of the scFv in its antigen-bound and free state showed that only few mutations, which do not make direct contact to the antigen, lead to a 500-fold affinity improvement over its potential germ line precursor. These results suggest that the affinity optimization of very high affinity binders is achieved by modulating existing interactions via subtle changes in the framework rather than by introducing new contacts. Off-rate selection in combination with ribosome display can evolve binders to the low picomolar affinity range even for peptide targets.
-
===Crystal Structure of scFv against peptide GCN4===
+
Directed in vitro evolution and crystallographic analysis of a peptide-binding single chain antibody fragment (scFv) with low picomolar affinity.,Zahnd C, Spinelli S, Luginbuhl B, Amstutz P, Cambillau C, Pluckthun A J Biol Chem. 2004 Apr 30;279(18):18870-7. Epub 2004 Jan 30. PMID:14754898<ref>PMID:14754898</ref>
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 1p4i" style="background-color:#fffaf0;"></div>
-
<!--
+
==See Also==
-
The line below this paragraph, {{ABSTRACT_PUBMED_14754898}}, adds the Publication Abstract to the page
+
*[[Antibody 3D structures|Antibody 3D structures]]
-
(as it appears on PubMed at http://www.pubmed.gov), where 14754898 is the PubMed ID number.
+
*[[Monoclonal Antibodies 3D structures|Monoclonal Antibodies 3D structures]]
-
-->
+
*[[3D structures of non-human antibody|3D structures of non-human antibody]]
-
{{ABSTRACT_PUBMED_14754898}}
+
== References ==
-
 
+
<references/>
-
==About this Structure==
+
__TOC__
-
1P4I is a 2 chains structure of sequences 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=1P4I OCA].
+
</StructureSection>
-
 
+
[[Category: Large Structures]]
-
==Reference==
+
-
<ref group="xtra">PMID:14754898</ref><references group="xtra"/>
+
[[Category: Mus musculus]]
[[Category: Mus musculus]]
-
[[Category: Amstutz, P.]]
+
[[Category: Amstutz P]]
-
[[Category: Cambillau, C.]]
+
[[Category: Cambillau C]]
-
[[Category: Jermutus, L.]]
+
[[Category: Jermutus L]]
-
[[Category: Luginbuhl, B.]]
+
[[Category: Luginbuhl B]]
-
[[Category: Pluckthun, A.]]
+
[[Category: Pluckthun A]]
-
[[Category: Spinelli, S.]]
+
[[Category: Spinelli S]]
-
[[Category: Zahnd, C.]]
+
[[Category: Zahnd C]]
-
[[Category: Peptide binder]]
+
-
[[Category: Picomolar binder]]
+
-
[[Category: Scfv]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Feb 18 06:42:39 2009''
+

Current revision

Crystal Structure of scFv against peptide GCN4

PDB ID 1p4i

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/1p4i"
Personal tools