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PDBsum entry 1mrf
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protein ligands metals Protein-protein interface(s) links
Immunoglobulin PDB id
1mrf

 

 

 

 

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Contents
Protein chains
216 a.a. *
205 a.a. *
Ligands
IMD
_DI
Metals
_ZN
Waters ×82
* Residue conservation analysis
PDB id:
1mrf
Name: Immunoglobulin
Title: Preparation, characterization and crystallization of an antibody fab fragment that recognizes RNA. Crystal structures of native fab and three fab-mononucleotide complexes
Structure: Igg2b-kappa jel103 fab (light chain). Chain: l. Engineered: yes. Igg2b-kappa jel103 fab (heavy chain). Chain: h. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Organism_taxid: 10090
Biol. unit: Dimer (from PQS)
Resolution:
2.40Å     R-factor:   0.184    
Authors: P.R.Pokkuluri,M.Cygler
Key ref: P.R.Pokkuluri et al. (1994). 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, 243, 283-297. PubMed id: 7523684
Date:
13-Jun-94     Release date:   14-Feb-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 216 a.a.
Protein chain
No UniProt id for this chain
Struc: 205 a.a.
Key:    Secondary structure  CATH domain

 

 
J Mol Biol 243:283-297 (1994)
PubMed id: 7523684  
 
 
Preparation, characterization and crystallization of an antibody Fab fragment that recognizes RNA. Crystal structures of native Fab and three Fab-mononucleotide complexes.
P.R.Pokkuluri, F.Bouthillier, Y.Li, A.Kuderova, J.Lee, M.Cygler.
 
  ABSTRACT  
 
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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19699528 S.Chang, L.Yang, Y.M.Moon, Y.G.Cho, S.Y.Min, T.J.Kim, Y.J.Kim, W.Patrick, H.Y.Kim, and C.Mohan (2009).
Anti-nuclear antibody reactivity in lupus may be partly hard-wired into the primary B-cell repertoire.
  Mol Immunol, 46, 3420-3426.  
19556006 Z.Liang, S.Chang, M.S.Youn, and C.Mohan (2009).
Molecular hallmarks of anti-chromatin antibodies associated with the lupus susceptibility locus, Sle1.
  Mol Immunol, 46, 2671-2681.  
18162543 J.D.Ye, V.Tereshko, J.K.Frederiksen, A.Koide, F.A.Fellouse, S.S.Sidhu, S.Koide, A.A.Kossiakoff, and J.A.Piccirilli (2008).
Synthetic antibodies for specific recognition and crystallization of structured RNA.
  Proc Natl Acad Sci U S A, 105, 82-87.
PDB code: 2r8s
17252586 M.J.Bobeck, and G.D.Glick (2007).
Role of conformational dynamics in sequence-specific autoantibody*ssDNA recognition.
  Biopolymers, 85, 481-489.  
17712773 P.Scheerer, A.Kramer, L.Otte, M.Seifert, H.Wessner, C.Scholz, N.Krauss, J.Schneider-Mergener, and W.Höhne (2007).
Structure of an anti-cholera toxin antibody Fab in complex with an epitope-derived D-peptide: a case of polyspecific recognition.
  J Mol Recognit, 20, 263-274.
PDB code: 1zea
16251186 M.J.Clément, A.Fortuné, A.Phalipon, V.Marcel-Peyre, C.Simenel, A.Imberty, M.Delepierre, and L.A.Mulard (2006).
Toward a better understanding of the basis of the molecular mimicry of polysaccharide antigens by peptides: the example of Shigella flexneri 5a.
  J Biol Chem, 281, 2317-2332.  
15788533 E.W.Debler, S.Ito, F.P.Seebeck, A.Heine, D.Hilvert, and I.A.Wilson (2005).
Structural origins of efficient proton abstraction from carbon by a catalytic antibody.
  Proc Natl Acad Sci U S A, 102, 4984-4989.
PDB codes: 1y0l 1y18
14757744 Z.Liang, C.Xie, C.Chen, D.Kreska, K.Hsu, L.Li, X.J.Zhou, and C.Mohan (2004).
Pathogenic profiles and molecular signatures of antinuclear autoantibodies rescued from NZM2410 lupus mice.
  J Exp Med, 199, 381-398.  
11976502 R.Kuroki, M.Hirose, Y.Kato, M.D.Feese, T.Tamada, H.Shigematsu, H.Watarai, Y.Maeda, T.Tahara, T.Kato, and H.Miyazaki (2002).
Crystallization of the functional domain of human thrombopoietin using an antigen-binding fragment derived from neutralizing monoclonal antibody.
  Acta Crystallogr D Biol Crystallogr, 58, 856-858.  
10648787 T.Torizawa, N.Yamamoto, T.Suzuki, K.Nobuoka, Y.Komatsu, H.Morioka, O.Nikaido, E.Ohtsuka, K.Kato, and I.Shimada (2000).
DNA binding mode of the Fab fragment of a monoclonal antibody specific for cyclobutane pyrimidine dimer.
  Nucleic Acids Res, 28, 944-951.  
10411130 H.F.Becker, Y.Corda, M.B.Mathews, J.L.Fourrey, and H.Grosjean (1999).
Inosine and N1-methylinosine within a synthetic oligomer mimicking the anticodon loop of human tRNA(Ala) are major epitopes for anti-PL-12 myositis autoantibodies.
  RNA, 5, 865-875.  
10024024 N.Kessler, D.Perl-Treves, L.Addadi, and M.Eisenstein (1999).
Structural and chemical complementarity between antibodies and the crystal surfaces they recognize.
  Proteins, 34, 383-394.  
9786848 K.Lim, S.M.Owens, L.Arnold, J.C.Sacchettini, and D.S.Linthicum (1998).
Crystal structure of monoclonal 6B5 Fab complexed with phencyclidine.
  J Biol Chem, 273, 28576-28582.
PDB code: 2pcp
9208940 B.Gigant, J.B.Charbonnier, B.Golinelli-Pimpaneau, R.R.Zemel, Z.Eshhar, B.S.Green, and M.Knossow (1997).
Mechanism of inactivation of a catalytic antibody by p-nitrophenyl esters.
  Eur J Biochem, 246, 471-476.  
8650212 K.Rajagopalan, G.Pavlinkova, S.Levy, P.R.Pokkuluri, M.Schiffer, B.E.Haley, and H.Kohler (1996).
Novel unconventional binding site in the variable region of immunoglobulins.
  Proc Natl Acad Sci U S A, 93, 6019-6024.  
7621866 M.Herrmann, T.H.Winkler, H.Fehr, and J.R.Kalden (1995).
Preferential recognition of specific DNA motifs by anti-double-stranded DNA autoantibodies.
  Eur J Immunol, 25, 1897-1904.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.

 

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