1h8s

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[[Image:1h8s.gif|left|200px]]<br />
 
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<applet load="1h8s" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1h8s, resolution 2.4&Aring;" />
 
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'''THREE-DIMENSIONAL STRUCTURE OF ANTI-AMPICILLIN SINGLE CHAIN FV FRAGMENT COMPLEXED WITH THE HAPTEN.'''<br />
 
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==Overview==
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==Three-dimensional structure of anti-ampicillin single chain Fv fragment complexed with the hapten.==
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Single-chain Fv (scFv) antibody libraries were constructed from mice, immunized with an ampicillin-bovine serum albumin conjugate. Several, antibodies with specificity for intact ampicillin were selected by phage, display and characterized. The antibody scFv fragment aL2 binds to intact, ampicillin and shows no detectable cross-reactivity with hydrolyzed, ampicillin. We determined the X-ray structures of two crystal forms of, w.t. aL2, which differ mainly in the side-chain conformation of Trp H109, (according to a new consensus nomenclature Kabat residue number H95) in, the extremely short (three residues) CDR H3 and the presence or absence of, a well-resolved molecule of 2-methyl-pentane-2,4-diol in the bottom of the, binding pocket. Attempts to co-crystallize aL2 with its antigen or to, diffuse ampicillin into the wild-type aL2 crystals were unsuccessful, since crystal contacts obstruct the binding pocket. However, a mutant with, two point mutations near the N terminus (Gln H6 replaced by Glu and Ala, H10 (Kabat H9) replaced by Gly) crystallized in a form compatible with, antigen-binding. Although the mutations affect the conformation of, framework I, the conformations of the binding pocket of the uncomplexed, wild-type aL2 and of the mutant complex were almost identical. The, structure explains the specificity of the antibody for intact ampicillin, and the degree of cross-reactivity of aL2 with a wide variety of, ampicillin analogs. This antibody system will be very useful as a, diagnostic reagent for antibiotics use and abuse, as a model for the, effect of expression of antibiotic binding molecules in Escherichia coli, and for directed evolution towards high antibiotic resistance.
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<StructureSection load='1h8s' size='340' side='right'caption='[[1h8s]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1h8s]] 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=1H8S OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1H8S FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.4&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AIC:(2S,5R,6R)-6-{[(2R)-2-AMINO-2-PHENYLETHANOYL]AMINO}-3,3-DIMETHYL-7-OXO-4-THIA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC+ACID'>AIC</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1h8s FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1h8s OCA], [https://pdbe.org/1h8s PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1h8s RCSB], [https://www.ebi.ac.uk/pdbsum/1h8s PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1h8s ProSAT]</span></td></tr>
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</table>
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== Evolutionary Conservation ==
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[[Image:Consurf_key_small.gif|200px|right]]
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Check<jmol>
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<jmolCheckbox>
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<scriptWhenChecked>; select protein; define ~consurf_to_do selected; consurf_initial_scene = true; script "/wiki/ConSurf/h8/1h8s_consurf.spt"</scriptWhenChecked>
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<scriptWhenUnchecked>script /wiki/extensions/Proteopedia/spt/initialview03.spt</scriptWhenUnchecked>
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<text>to colour the structure by Evolutionary Conservation</text>
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</jmolCheckbox>
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</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=1h8s ConSurf].
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<div style="clear:both"></div>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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Single-chain Fv (scFv) antibody libraries were constructed from mice immunized with an ampicillin-bovine serum albumin conjugate. Several antibodies with specificity for intact ampicillin were selected by phage display and characterized. The antibody scFv fragment aL2 binds to intact ampicillin and shows no detectable cross-reactivity with hydrolyzed ampicillin. We determined the X-ray structures of two crystal forms of w.t. aL2, which differ mainly in the side-chain conformation of Trp H109 (according to a new consensus nomenclature Kabat residue number H95) in the extremely short (three residues) CDR H3 and the presence or absence of a well-resolved molecule of 2-methyl-pentane-2,4-diol in the bottom of the binding pocket. Attempts to co-crystallize aL2 with its antigen or to diffuse ampicillin into the wild-type aL2 crystals were unsuccessful, since crystal contacts obstruct the binding pocket. However, a mutant with two point mutations near the N terminus (Gln H6 replaced by Glu and Ala H10 (Kabat H9) replaced by Gly) crystallized in a form compatible with antigen-binding. Although the mutations affect the conformation of framework I, the conformations of the binding pocket of the uncomplexed wild-type aL2 and of the mutant complex were almost identical. The structure explains the specificity of the antibody for intact ampicillin and the degree of cross-reactivity of aL2 with a wide variety of ampicillin analogs. This antibody system will be very useful as a diagnostic reagent for antibiotics use and abuse, as a model for the effect of expression of antibiotic binding molecules in Escherichia coli, and for directed evolution towards high antibiotic resistance.
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==About this Structure==
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Selection, characterization and x-ray structure of anti-ampicillin single-chain Fv fragments from phage-displayed murine antibody libraries.,Burmester J, Spinelli S, Pugliese L, Krebber A, Honegger A, Jung S, Schimmele B, Cambillau C, Pluckthun A J Mol Biol. 2001 Jun 8;309(3):671-85. PMID:11397088<ref>PMID:11397088</ref>
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1H8S is a [http://en.wikipedia.org/wiki/Single_protein Single protein] structure of sequence from [http://en.wikipedia.org/wiki/Mouse_e_010090 Mouse e 010090] with SO4 and AIC as [http://en.wikipedia.org/wiki/ligands ligands]. Structure known Active Site: AIC. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1H8S OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Selection, characterization and x-ray structure of anti-ampicillin single-chain Fv fragments from phage-displayed murine antibody libraries., Burmester J, Spinelli S, Pugliese L, Krebber A, Honegger A, Jung S, Schimmele B, Cambillau C, Pluckthun A, J Mol Biol. 2001 Jun 8;309(3):671-85. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=11397088 11397088]
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</div>
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[[Category: Mouse e 010090]]
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<div class="pdbe-citations 1h8s" style="background-color:#fffaf0;"></div>
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[[Category: Single protein]]
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== References ==
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[[Category: Burmester, J.]]
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<references/>
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[[Category: Cambillau, C.]]
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__TOC__
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[[Category: Honegger, A.]]
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</StructureSection>
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[[Category: Jung, S.]]
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[[Category: Large Structures]]
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[[Category: Krebber, A.]]
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[[Category: Mus musculus]]
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[[Category: Pluckthun, A.]]
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[[Category: Burmester J]]
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[[Category: Pugliese, L.]]
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[[Category: Cambillau C]]
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[[Category: Schimmele, B.]]
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[[Category: Honegger A]]
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[[Category: Spinelli, S.]]
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[[Category: Jung S]]
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[[Category: AIC]]
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[[Category: Krebber A]]
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[[Category: SO4]]
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[[Category: Pluckthun A]]
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[[Category: anti-ampicillin antibodies]]
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[[Category: Pugliese L]]
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[[Category: Schimmele B]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Mon Nov 5 13:56:18 2007''
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[[Category: Spinelli S]]

Current revision

Three-dimensional structure of anti-ampicillin single chain Fv fragment complexed with the hapten.

PDB ID 1h8s

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