1p4b

From Proteopedia

(Difference between revisions)

Current revision

Three-Dimensional Structure Of a Single Chain Fv Fragment Complexed With The peptide GCN4(7P-14P).

Structural highlights

1p4b is a 3 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:	X-ray diffraction, Resolution 2.35Å
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LV1A_MOUSE

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

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.

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^[1]

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

References

↑ Zahnd C, Spinelli S, Luginbuhl B, Amstutz P, Cambillau C, Pluckthun A. Directed in vitro evolution and crystallographic analysis of a peptide-binding single chain antibody fragment (scFv) with low picomolar affinity. J Biol Chem. 2004 Apr 30;279(18):18870-7. Epub 2004 Jan 30. PMID:14754898 doi:10.1074/jbc.M309169200

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/1p4b"

@@ Line 3: / Line 3: @@
 <StructureSection load='1p4b' size='340' side='right'caption='[[1p4b]], [[Resolution|resolution]] 2.35&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1p4b]] is a 3 chain structure with sequence from [https://en.wikipedia.org/wiki/Lk3_transgenic_mice Lk3 transgenic mice]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1P4B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P4B FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1p4b]] is a 3 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=1P4B OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1P4B FirstGlance]. <br>
-</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=1p4b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4b OCA], [https://pdbe.org/1p4b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p4b RCSB], [https://www.ebi.ac.uk/pdbsum/1p4b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p4b ProSAT]</span></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]] 2.35&#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=1p4b FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1p4b OCA], [https://pdbe.org/1p4b PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1p4b RCSB], [https://www.ebi.ac.uk/pdbsum/1p4b PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1p4b ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/LV1A_MOUSE LV1A_MOUSE]
 == Evolutionary Conservation ==
 [[Image:Consurf_key_small.gif|200px|right]]
@@ Line 35: / Line 38: @@
 </StructureSection>
 [[Category: Large Structures]]
-[[Category: Lk3 transgenic mice]]
+[[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: Antigen peptide binder]]
-[[Category: Fv antibody]]
-[[Category: Immune system]]
-[[Category: Picomolar binder]]
-[[Category: Scfv]]

1p4b

From Proteopedia

Current revision

Three-Dimensional Structure Of a Single Chain Fv Fragment Complexed With The peptide GCN4(7P-14P).

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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