1mrf

From Proteopedia

(Difference between revisions)

Current revision

PREPARATION, CHARACTERIZATION AND CRYSTALLIZATION OF AN ANTIBODY FAB FRAGMENT THAT RECOGNIZES RNA. CRYSTAL STRUCTURES OF NATIVE FAB AND THREE FAB-MONONUCLEOTIDE COMPLEXES

Structural highlights

1mrf 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 2.4Å
Ligands:	, ,
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

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

Fab fragments from Jel 103, an antibody which specifically binds to single-stranded poly(rl), were prepared by papain digestion, separated into eight isoforms and characterized by mass spectrometry. One of the purified isoforms yielded crystals suitable for structural studies by X-ray diffraction and its crystal structure was determined to 2.4 A resolution. Soaking the crystals in solutions containing either of the mononucleotides inosine-5'-diphosphate, guanosine-5'-diphosphate or deoxyinosine-5'-monophosphate resulted in binding of the nucleotide in a single binding site. However, adenosine-5'-diphosphate does not bind to this antibody. The recognition of the base is achieved through hydrogen bonds to the C6 carbonyl oxygen and the imino NH group of the purine in a pattern similar to that of the base-base interactions in a double-stranded nucleic acid. Additional binding energy is provided by stacking of the base and the Tyr32L side-chain and by interaction of the alpha-phosphate with the antibody in an anionic binding site. Most of the side-chains interacting with the nucleotide come from the light chain. Surprisingly, this antibody shares the VL sequence with another nucleic acid-binding antibody, BV04-1. The latter binds to a single stranded DNA with a high preference for thymine bases. The structures of the unliganded and complexed Jel 103 Fab are compared to those of BV-04-1 Fab and while they show similarity in recognition of the base of the immunodominant nucleotide, their 5' phosphates occupy different positions, suggesting different orientation of the nucleic acid bound to these two antibodies. Differences in the conformations of the L1 loops between the two Fabs have been noted.

Preparation, characterization and crystallization of an antibody Fab fragment that recognizes RNA. Crystal structures of native Fab and three Fab-mononucleotide complexes.,Pokkuluri PR, Bouthillier F, Li Y, Kuderova A, Lee J, Cygler M J Mol Biol. 1994 Oct 21;243(2):283-97. PMID:7523684^[1]

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

References

↑ Pokkuluri PR, Bouthillier F, Li Y, Kuderova A, Lee J, Cygler M. Preparation, characterization and crystallization of an antibody Fab fragment that recognizes RNA. Crystal structures of native Fab and three Fab-mononucleotide complexes. J Mol Biol. 1994 Oct 21;243(2):283-97. PMID:7523684 doi:http://dx.doi.org/10.1006/jmbi.1994.1654

1 Structural highlights
2 Evolutionary Conservation
3 Publication Abstract from PubMed
4 See Also
5 References

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1mrf"

Categories: Large Structures | Mus musculus | Cygler M | Pokkuluri PR

@@ Line 1: / Line 1: @@
 ==PREPARATION, CHARACTERIZATION AND CRYSTALLIZATION OF AN ANTIBODY FAB FRAGMENT THAT RECOGNIZES RNA. CRYSTAL STRUCTURES OF NATIVE FAB AND THREE FAB-MONONUCLEOTIDE COMPLEXES==
-<StructureSection load='1mrf' size='340' side='right' caption='[[1mrf]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
+<StructureSection load='1mrf' size='340' side='right'caption='[[1mrf]], [[Resolution|resolution]] 2.40&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[1mrf]] is a 2 chain structure with sequence from [http://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=1MRF OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1MRF FirstGlance]. <br>
+<table><tr><td colspan='2'>[[1mrf]] 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=1MRF OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1MRF FirstGlance]. <br>
-</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</scene></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]] 2.4&#8491;</td></tr>
-<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1mrf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mrf OCA], [http://pdbe.org/1mrf PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=1mrf RCSB], [http://www.ebi.ac.uk/pdbsum/1mrf PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=1mrf ProSAT]</span></td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=DI:2-DEOXYINOSINE-5-MONOPHOSPHATE'>DI</scene>, <scene name='pdbligand=IMD:IMIDAZOLE'>IMD</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=1mrf FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1mrf OCA], [https://pdbe.org/1mrf PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1mrf RCSB], [https://www.ebi.ac.uk/pdbsum/1mrf PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1mrf ProSAT]</span></td></tr>
 </table>
 == Evolutionary Conservation ==
@@ Line 26: / Line 27: @@
 </div>
 <div class="pdbe-citations 1mrf" style="background-color:#fffaf0;"></div>
+==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: Lk3 transgenic mice]]
+[[Category: Large Structures]]
-[[Category: Cygler, M]]
+[[Category: Mus musculus]]
-[[Category: Pokkuluri, P R]]
+[[Category: Cygler M]]
-[[Category: Immunoglobulin]]
+[[Category: Pokkuluri PR]]

1mrf

From Proteopedia

Current revision

PREPARATION, CHARACTERIZATION AND CRYSTALLIZATION OF AN ANTIBODY FAB FRAGMENT THAT RECOGNIZES RNA. CRYSTAL STRUCTURES OF NATIVE FAB AND THREE FAB-MONONUCLEOTIDE COMPLEXES

Structural highlights

Evolutionary Conservation

Publication Abstract from PubMed

See Also

References

Contents

Proteopedia Page Contributors and Editors (what is this?)

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