1cbv

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[[Image:1cbv.gif|left|200px]]
 
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==AN AUTOANTIBODY TO SINGLE-STRANDED DNA: COMPARISON OF THE THREE-DIMENSIONAL STRUCTURES OF THE UNLIGANDED FAB AND A DEOXYNUCLEOTIDE-FAB COMPLEX==
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The line below this paragraph, containing "STRUCTURE_1cbv", creates the "Structure Box" on the page.
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<StructureSection load='1cbv' size='340' side='right'caption='[[1cbv]], [[Resolution|resolution]] 2.66&Aring;' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[1cbv]] 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=1CBV OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1CBV FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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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]] 2.66&#8491;</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=1cbv FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1cbv OCA], [https://pdbe.org/1cbv PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1cbv RCSB], [https://www.ebi.ac.uk/pdbsum/1cbv PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1cbv ProSAT]</span></td></tr>
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{{STRUCTURE_1cbv| PDB=1cbv | SCENE= }}
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</table>
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== Function ==
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[https://www.uniprot.org/uniprot/A2NHM3_MOUSE A2NHM3_MOUSE]
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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/cb/1cbv_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=1cbv 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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Crystal structures of the Fabs from an autoantibody (BV04-01) with specificity for single-stranded DNA have been determined in the presence and absence of a trinucleotide of deoxythymidylic acid, d(pT)3. Formation of the ligand-protein complex was accompanied by small adjustments in the orientations of the variable (VL and VH) domains. In addition, there were local conformational changes in the first hypervariable loop of the light chain and the third hypervariable loop of the heavy chain, which together with the domain shifts led to an improvement in the complementarity of nucleotide and Fab. The sugar-phosphate chain adopted an extended and "open" conformation, with the base, sugar, and phosphate components available for interactions with the protein. Nucleotide 1 (5'-end) was associated exclusively with the heavy chain, nucleotide 2 was shared by both heavy and light chains, and nucleotide 3 was bound by the light chain. The orientation of phosphate 1 was stabilized by hydrogen bonds with serine H52a and asparagine H53. Phosphate 2 formed an ion pair with arginine H52, but no other charge-charge interactions were observed. Insertion of the side chain of histidine L27d between nucleotides 2 and 3 resulted in a bend in the sugar-phosphate chain. The most dominant contacts with the protein involved the central thymine base, which was immobilized by cooperative stacking and hydrogen bonding interactions. This base was intercalated between a tryptophan ring (no. H100a) from the heavy chain and a tyrosine ring (no. L32) from the light chain. The resulting orientation of thymine was favorable for the simultaneous formation of two hydrogen bonds with the backbone carbonyl oxygen and the side chain hydroxyl group of serine L91 (the thymine atoms were the hydrogen on nitrogen 3 and keto oxygen 4).
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'''AN AUTOANTIBODY TO SINGLE-STRANDED DNA: COMPARISON OF THE THREE-DIMENSIONAL STRUCTURES OF THE UNLIGANDED FAB AND A DEOXYNUCLEOTIDE-FAB COMPLEX'''
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An autoantibody to single-stranded DNA: comparison of the three-dimensional structures of the unliganded Fab and a deoxynucleotide-Fab complex.,Herron JN, He XM, Ballard DW, Blier PR, Pace PE, Bothwell AL, Voss EW Jr, Edmundson AB Proteins. 1991;11(3):159-75. PMID:1749770<ref>PMID:1749770</ref>
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==Overview==
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Crystal structures of the Fabs from an autoantibody (BV04-01) with specificity for single-stranded DNA have been determined in the presence and absence of a trinucleotide of deoxythymidylic acid, d(pT)3. Formation of the ligand-protein complex was accompanied by small adjustments in the orientations of the variable (VL and VH) domains. In addition, there were local conformational changes in the first hypervariable loop of the light chain and the third hypervariable loop of the heavy chain, which together with the domain shifts led to an improvement in the complementarity of nucleotide and Fab. The sugar-phosphate chain adopted an extended and "open" conformation, with the base, sugar, and phosphate components available for interactions with the protein. Nucleotide 1 (5'-end) was associated exclusively with the heavy chain, nucleotide 2 was shared by both heavy and light chains, and nucleotide 3 was bound by the light chain. The orientation of phosphate 1 was stabilized by hydrogen bonds with serine H52a and asparagine H53. Phosphate 2 formed an ion pair with arginine H52, but no other charge-charge interactions were observed. Insertion of the side chain of histidine L27d between nucleotides 2 and 3 resulted in a bend in the sugar-phosphate chain. The most dominant contacts with the protein involved the central thymine base, which was immobilized by cooperative stacking and hydrogen bonding interactions. This base was intercalated between a tryptophan ring (no. H100a) from the heavy chain and a tyrosine ring (no. L32) from the light chain. The resulting orientation of thymine was favorable for the simultaneous formation of two hydrogen bonds with the backbone carbonyl oxygen and the side chain hydroxyl group of serine L91 (the thymine atoms were the hydrogen on nitrogen 3 and keto oxygen 4).
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==About this Structure==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1CBV OCA].
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</div>
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<div class="pdbe-citations 1cbv" style="background-color:#fffaf0;"></div>
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==Reference==
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==See Also==
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An autoantibody to single-stranded DNA: comparison of the three-dimensional structures of the unliganded Fab and a deoxynucleotide-Fab complex., Herron JN, He XM, Ballard DW, Blier PR, Pace PE, Bothwell AL, Voss EW Jr, Edmundson AB, Proteins. 1991;11(3):159-75. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/1749770 1749770]
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*[[Antibody 3D structures|Antibody 3D structures]]
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[[Category: Ballard, D W.]]
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*[[3D structures of non-human antibody|3D structures of non-human antibody]]
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[[Category: Blier, P R.]]
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== References ==
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[[Category: Bothwell, A L.M.]]
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<references/>
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[[Category: Edmundson, A B.]]
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__TOC__
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[[Category: He, X M.]]
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</StructureSection>
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[[Category: Herron, J N.]]
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[[Category: Large Structures]]
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[[Category: Junior, E W.Voss.]]
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[[Category: Mus musculus]]
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[[Category: Pace, P E.]]
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[[Category: Ballard DW]]
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[[Category: Protein-dna complex]]
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[[Category: Blier PR]]
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[[Category: Single strand]]
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[[Category: Bothwell ALM]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 12:33:43 2008''
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[[Category: Edmundson AB]]
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[[Category: He XM]]
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[[Category: Herron JN]]
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[[Category: Pace PE]]
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[[Category: Voss Junior EW]]

Current revision

AN AUTOANTIBODY TO SINGLE-STRANDED DNA: COMPARISON OF THE THREE-DIMENSIONAL STRUCTURES OF THE UNLIGANDED FAB AND A DEOXYNUCLEOTIDE-FAB COMPLEX

PDB ID 1cbv

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