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New page: left|200px<br /> <applet load="1dbb" size="450" color="white" frame="true" align="right" spinBox="true" caption="1dbb, resolution 2.7Å" /> '''THREE-DIMENSIONAL ST...
 
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[[Image:1dbb.gif|left|200px]]<br />
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'''THREE-DIMENSIONAL STRUCTURE OF AN ANTI-STEROID FAB' AND PROGESTERONE-FAB' COMPLEX'''<br />


==Overview==
==THREE-DIMENSIONAL STRUCTURE OF AN ANTI-STEROID FAB' AND PROGESTERONE-FAB' COMPLEX==
The monoclonal anti-progesterone antibody DB3 binds progesterone with, nanomolar affinity (Ka approximately 10(9) M-1), suggesting high, specificity. However, DB3 also cross-reacts with similar affinity with a, subgroup of structurally distinct, progesterone-like steroids. Crystals of, the unliganded Fab' and various steroid-Fab' complexes are isomorphous and, belong to the hexagonal space group, P6(4)22, with unit cell dimensions of, a = b = 135 A, c = 124 A. Structures of free and progesterone-bound Fab', have been determined by X-ray crystallography at 2.7 A resolution using, molecular replacement techniques. Progesterone is bound in a hydrophobic, pocket formed mainly by the interaction of three complementarity, determining regions L1, H2 and H3. The orientation of the ligand in the, binding site was aided by both crystallographic and biochemical analyses, of substituted steroids. The indole side-chain of TrpH100 of the DB3 has, two different conformations, inter-converting "open" and "closed" forms of, the antibody combining site. The TrpH100 indole thus appears to be acting, as an antibody-derived surrogate ligand for its own hydrophobic binding, pocket. These structures provide the first atomic view of how a steroid, interacts with a protein and offer a structural explanation for the, restriction of the anti-progesterone response to the VGAM3.8 family of VH, genes.
<StructureSection load='1dbb' size='340' side='right'caption='[[1dbb]], [[Resolution|resolution]] 2.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1dbb]] 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=1DBB OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1DBB FirstGlance]. <br>
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.7&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=STR:PROGESTERONE'>STR</scene></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=1dbb FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1dbb OCA], [https://pdbe.org/1dbb PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1dbb RCSB], [https://www.ebi.ac.uk/pdbsum/1dbb PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1dbb ProSAT]</span></td></tr>
</table>
== Function ==
[https://www.uniprot.org/uniprot/IGHG1_MOUSE IGHG1_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/db/1dbb_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=1dbb ConSurf].
<div style="clear:both"></div>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The monoclonal anti-progesterone antibody DB3 binds progesterone with nanomolar affinity (Ka approximately 10(9) M-1), suggesting high specificity. However, DB3 also cross-reacts with similar affinity with a subgroup of structurally distinct, progesterone-like steroids. Crystals of the unliganded Fab' and various steroid-Fab' complexes are isomorphous and belong to the hexagonal space group, P6(4)22, with unit cell dimensions of a = b = 135 A, c = 124 A. Structures of free and progesterone-bound Fab' have been determined by X-ray crystallography at 2.7 A resolution using molecular replacement techniques. Progesterone is bound in a hydrophobic pocket formed mainly by the interaction of three complementarity determining regions L1, H2 and H3. The orientation of the ligand in the binding site was aided by both crystallographic and biochemical analyses of substituted steroids. The indole side-chain of TrpH100 of the DB3 has two different conformations, inter-converting "open" and "closed" forms of the antibody combining site. The TrpH100 indole thus appears to be acting as an antibody-derived surrogate ligand for its own hydrophobic binding pocket. These structures provide the first atomic view of how a steroid interacts with a protein and offer a structural explanation for the restriction of the anti-progesterone response to the VGAM3.8 family of VH genes.


==About this Structure==
Three-dimensional structure of an anti-steroid Fab' and progesterone-Fab' complex.,Arevalo JH, Stura EA, Taussig MJ, Wilson IA J Mol Biol. 1993 May 5;231(1):103-18. PMID:8496956<ref>PMID:8496956</ref>
1DBB is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with STR as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1DBB OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Three-dimensional structure of an anti-steroid Fab' and progesterone-Fab' complex., Arevalo JH, Stura EA, Taussig MJ, Wilson IA, J Mol Biol. 1993 May 5;231(1):103-18. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8496956 8496956]
</div>
[[Category: Protein complex]]
<div class="pdbe-citations 1dbb" style="background-color:#fffaf0;"></div>
[[Category: Arevalo, J.H.]]
[[Category: Wilson, I.A.]]
[[Category: STR]]
[[Category: immunoglobulin]]


''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 18 09:28:13 2007''
==See Also==
*[[Antibody 3D structures|Antibody 3D structures]]
*[[3D structures of non-human antibody|3D structures of non-human antibody]]
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Mus musculus]]
[[Category: Arevalo JH]]
[[Category: Wilson IA]]

Latest revision as of 09:31, 30 October 2024

THREE-DIMENSIONAL STRUCTURE OF AN ANTI-STEROID FAB' AND PROGESTERONE-FAB' COMPLEXTHREE-DIMENSIONAL STRUCTURE OF AN ANTI-STEROID FAB' AND PROGESTERONE-FAB' COMPLEX

Structural highlights

1dbb 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:X-ray diffraction, Resolution 2.7Å
Ligands:
Resources:FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

IGHG1_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

The monoclonal anti-progesterone antibody DB3 binds progesterone with nanomolar affinity (Ka approximately 10(9) M-1), suggesting high specificity. However, DB3 also cross-reacts with similar affinity with a subgroup of structurally distinct, progesterone-like steroids. Crystals of the unliganded Fab' and various steroid-Fab' complexes are isomorphous and belong to the hexagonal space group, P6(4)22, with unit cell dimensions of a = b = 135 A, c = 124 A. Structures of free and progesterone-bound Fab' have been determined by X-ray crystallography at 2.7 A resolution using molecular replacement techniques. Progesterone is bound in a hydrophobic pocket formed mainly by the interaction of three complementarity determining regions L1, H2 and H3. The orientation of the ligand in the binding site was aided by both crystallographic and biochemical analyses of substituted steroids. The indole side-chain of TrpH100 of the DB3 has two different conformations, inter-converting "open" and "closed" forms of the antibody combining site. The TrpH100 indole thus appears to be acting as an antibody-derived surrogate ligand for its own hydrophobic binding pocket. These structures provide the first atomic view of how a steroid interacts with a protein and offer a structural explanation for the restriction of the anti-progesterone response to the VGAM3.8 family of VH genes.

Three-dimensional structure of an anti-steroid Fab' and progesterone-Fab' complex.,Arevalo JH, Stura EA, Taussig MJ, Wilson IA J Mol Biol. 1993 May 5;231(1):103-18. PMID:8496956[1]

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

See Also

References

  1. ↑ Arevalo JH, Stura EA, Taussig MJ, Wilson IA. Three-dimensional structure of an anti-steroid Fab' and progesterone-Fab' complex. J Mol Biol. 1993 May 5;231(1):103-18. PMID:8496956 doi:http://dx.doi.org/10.1006/jmbi.1993.1260

1dbb, resolution 2.70Å

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