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PDBsum entry 1flr
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Immunoglobulin PDB id
1flr

 

 

 

 

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Contents
Protein chains
219 a.a. *
216 a.a. *
Ligands
FLU
Waters ×292
* Residue conservation analysis
PDB id:
1flr
Name: Immunoglobulin
Title: 4-4-20 fab fragment
Structure: 4-4-20 (ig G2a=kappa=) fab fragment. Chain: l. 4-4-20 (ig G2a=kappa=) fab fragment. Chain: h
Source: Mus musculus. House mouse. Organism_taxid: 10090. Strain: balb/c. Variant: balb/cv. Cell_line: 4-4-20 murine-murine hybridoma. Organ: spleen. Cell: lymphocyte-plasma cell. Cell: lymphocyte-plasma cell
Biol. unit: Dimer (from PQS)
Resolution:
1.85Å     R-factor:   0.188    
Authors: M.Whitlow
Key ref: M.Whitlow et al. (1995). 1.85 A structure of anti-fluorescein 4-4-20 Fab. Protein Eng, 8, 749-761. PubMed id: 8637844
Date:
19-Jan-95     Release date:   15-Sep-95    
PROCHECK
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 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 219 a.a.
Protein chain
Pfam   ArchSchema ?
P01865  (GCAM_MOUSE) -  Immunoglobulin heavy constant gamma 2A from Mus musculus
Seq:
Struc: 		398 a.a.
216 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 

 
Protein Eng 8:749-761 (1995)
PubMed id: 8637844  
 
 
1.85 A structure of anti-fluorescein 4-4-20 Fab.
M.Whitlow, A.J.Howard, J.F.Wood, E.W.Voss, K.D.Hardman.
 
  ABSTRACT  
 
The crystal complex of fluorescein bound to the high-affinity anti-fluorescein 4-4-20 Fab (Ka = 10(10) M-1 at 2 degrees C) has been determined at 1.85 A. Isomorphous crystals of two isoelectric forms (pI = 7.5 and 7.9) of the anti-fluorescein 4-4-20 Fab, an IgG2A [Gibson et al. (1988) Proteins: Struct. Funct. Genet., 3, 155-160], have been grown. Both complexes crystallize with one molecule in the asymmetric unit in space group P1, with a = 42.75 A, b = 43.87 A, c = 58.17 A, alpha = 95.15 degrees, beta = 86.85 degrees and gamma = 98.01 degrees. The final structure has an R value of 0.188 at 1.85 A resolution. Interactions between bound fluorescein, the complementarity-determining regions (CDRs) of the Fab and the active-site mutants of the 4-4-20 single-chain Fv will be discussed. Differences were found between the structure reported here and the previously reported 2.7 A 4-4-20 Fab structure [Herron et al. (1989) Proteins: Struct. Funct. Genet., 5, 271-280]. Our structure determination was based on 26,328 unique reflections--four times the amount of data used in the previous report. Differences in the two structures could be explained by differences in interpreting the electron density maps at the various resolutions. The r.m.s. deviations between the variable and constant domains of the two structures were 0.77 and 1.54 A, respectively. Four regions of the light chain and four regions of the heavy chain had r.m.s. backbone deviations of > 4 A. The most significant of these was the conformation of the light chain CDR 1.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20847101 R.J.Pantazes, and C.D.Maranas (2010).
OptCDR: a general computational method for the design of antibody complementarity determining regions for targeted epitope binding.
  Protein Eng Des Sel, 23, 849-858.  
19415776 P.Xu, and A.S.Robinson (2009).
Decreased secretion and unfolded protein response up-regulation are correlated with intracellular retention for single-chain antibody variants produced in yeast.
  Biotechnol Bioeng, 104, 20-29.  
18309081 E.W.Debler, G.F.Kaufmann, M.M.Meijler, A.Heine, J.M.Mee, G.Pljevaljcic, A.J.Di Bilio, P.G.Schultz, D.P.Millar, K.D.Janda, I.A.Wilson, H.B.Gray, and R.A.Lerner (2008).
Deeply inverted electron-hole recombination in a luminescent antibody-stilbene complex.
  Science, 319, 1232-1235.
PDB codes: 3cfb 3cfc 3cfd 3cfe
17488816 I.F.Thorpe, and C.L.Brooks (2007).
Molecular evolution of affinity and flexibility in the immune system.
  Proc Natl Acad Sci U S A, 104, 8821-8826.  
17012279 I.Fukuda, K.Kojoh, N.Tabata, N.Doi, H.Takashima, E.Miyamoto-Sato, and H.Yanagawa (2006).
In vitro evolution of single-chain antibodies using mRNA display.
  Nucleic Acids Res, 34, e127.  
16906810 J.Tang, and S.H.Lin (2006).
Distance versus energy fluctuations and electron transfer in single protein molecules.
  Phys Rev E Stat Nonlin Soft Matter Phys, 73, 061108.  
16954202 J.Zimmermann, E.L.Oakman, I.F.Thorpe, X.Shi, P.Abbyad, C.L.Brooks, S.G.Boxer, and F.E.Romesberg (2006).
Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics.
  Proc Natl Acad Sci U S A, 103, 13722-13727.  
16434745 K.S.Midelfort, and K.D.Wittrup (2006).
Context-dependent mutations predominate in an engineered high-affinity single chain antibody fragment.
  Protein Sci, 15, 324-334.  
16090221 W.Min, G.Luo, B.J.Cherayil, S.C.Kou, and X.S.Xie (2005).
Observation of a power-law memory kernel for fluctuations within a single protein molecule.
  Phys Rev Lett, 94, 198302.  
15001706 R.Jimenez, G.Salazar, J.Yin, T.Joo, and F.E.Romesberg (2004).
Protein dynamics and the immunological evolution of molecular recognition.
  Proc Natl Acad Sci U S A, 101, 3803-3808.  
14962308 S.C.Song, M.Czerwinski, B.S.Wojczyk, and S.L.Spitalnik (2004).
Alteration of amino acid residues at the L-chain N-terminus and in complementarity-determining region 3 increases affinity of a recombinant F(ab) for the human N blood group antigen.
  Transfusion, 44, 173-186.  
12851924 F.E.Romesberg (2003).
Multidisciplinary experimental approaches to characterizing biomolecular dynamics.
  Chembiochem, 4, 563-571.  
12945055 I.P.Korndörfer, G.Beste, and A.Skerra (2003).
Crystallographic analysis of an "anticalin" with tailored specificity for fluorescein reveals high structural plasticity of the lipocalin loop region.
  Proteins, 53, 121-129.
PDB code: 1n0s
12518056 R.Jimenez, G.Salazar, K.K.Baldridge, and F.E.Romesberg (2003).
Flexibility and molecular recognition in the immune system.
  Proc Natl Acad Sci U S A, 100, 92-97.  
14581222 S.Mohan, N.Sinha, and S.J.Smith-Gill (2003).
Modeling the binding sites of anti-hen egg white lysozyme antibodies HyHEL-8 and HyHEL-26: an insight into the molecular basis of antibody cross-reactivity and specificity.
  Biophys J, 85, 3221-3236.  
11900559 M.Götz, S.Hess, G.Beste, A.Skerra, and M.E.Michel-Beyerle (2002).
Ultrafast electron transfer in the complex between fluorescein and a cognate engineered lipocalin protein, a so-called anticalin.
  Biochemistry, 41, 4156-4164.  
11058774 A.Skerra (2000).
Lipocalins as a scaffold.
  Biochim Biophys Acta, 1482, 337-350.  
10809958 D.S.Schabacker, K.S.Kirschbaum, and M.Segre (2000).
Exploring the feasibility of an anti-idiotypic cocaine vaccine: analysis of the specificity of anticocaine antibodies (Ab1) capable of inducing Ab2beta anti-idiotypic antibodies.
  Immunology, 100, 48-56.  
10984501 E.T.Boder, K.S.Midelfort, and K.D.Wittrup (2000).
Directed evolution of antibody fragments with monovalent femtomolar antigen-binding affinity.
  Proc Natl Acad Sci U S A, 97, 10701-10705.  
10963664 F.Schwesinger, R.Ros, T.Strunz, D.Anselmetti, H.J.Güntherodt, A.Honegger, L.Jermutus, L.Tiefenauer, and A.Pluckthun (2000).
Unbinding forces of single antibody-antigen complexes correlate with their thermal dissociation rates.
  Proc Natl Acad Sci U S A, 97, 9972-9977.  
11048945 G.A.Weiss, and H.B.Lowman (2000).
Anticalins versus antibodies: made-to-order binding proteins for small molecules.
  Chem Biol, 7, R177-R184.  
11056035 L.Choulier, V.Lafont, N.Hugo, and D.Altschuh (2000).
Covariance analysis of protein families: the case of the variable domains of antibodies.
  Proteins, 41, 475-484.  
10051566 G.Beste, F.S.Schmidt, T.Stibora, and A.Skerra (1999).
Small antibody-like proteins with prescribed ligand specificities derived from the lipocalin fold.
  Proc Natl Acad Sci U S A, 96, 1898-1903.  
10089402 S.Trakhanov, S.Parkin, R.Raffaï, R.Milne, Y.M.Newhouse, K.H.Weisgraber, and B.Rupp (1999).
Structure of a monoclonal 2E8 Fab antibody fragment specific for the low-density lipoprotein-receptor binding region of apolipoprotein E refined at 1.9 A.
  Acta Crystallogr D Biol Crystallogr, 55, 122-128.
PDB code: 12e8
9555730 H.Bothmann, and A.Plückthun (1998).
Selection for a periplasmic factor improving phage display and functional periplasmic expression.
  Nat Biotechnol, 16, 376-380.  
9613235 N.Klonis, A.H.Clayton, E.W.Voss, and W.H.Sawyer (1998).
Spectral properties of fluorescein in solvent-water mixtures: applications as a probe of hydrogen bonding environments in biological systems.
  Photochem Photobiol, 67, 500-510.  
9250664 D.Housset, G.Mazza, C.Grégoire, C.Piras, B.Malissen, and J.C.Fontecilla-Camps (1997).
The three-dimensional structure of a T-cell antigen receptor V alpha V beta heterodimer reveals a novel arrangement of the V beta domain.
  EMBO J, 16, 4205-4216.
PDB code: 1kb5
9305985 M.E.Mummert, and E.W.Voss (1997).
Effects of secondary forces on the ligand binding and conformational state of antifluorescein monoclonal antibody 9-40.
  Biochemistry, 36, 11918-11922.  
8679572 M.E.Mummert, and E.W.Voss (1996).
Transition-state theory and secondary forces in antigen--antibody complexes.
  Biochemistry, 35, 8187-8192.  
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 codes are shown on the right.

 

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