PDBsum entry 1a5f

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Immunoglobulin PDB id
Protein chains
220 a.a. *
212 a.a. *
Waters ×10
* Residue conservation analysis
PDB id:
Name: Immunoglobulin
Title: Fab fragment of a monoclonal anti-e-selectin antibody
Structure: Monoclonal anti-e-selectin 7a9 antibody (light chain). Chain: l. Fragment: fab fragment. Monoclonal anti-e-selectin 7a9 antibody (heavy chain). Chain: h. Fragment: fab fragment
Source: Mus musculus. House mouse. Organism_taxid: 10090. Cell_line: sp-20 fusion mouse-mouse hybridoma. Cell_line: sp-20 fusion mouse-mouse hybridoma
Biol. unit: Dimer (from PQS)
2.80Å     R-factor:   0.195    
Authors: A.Rodriguez-Romero,O.Almog,M.Tordova,Z.Randhawa
Key ref:
A.Rodríguez-Romero et al. (1998). Primary and tertiary structures of the Fab fragment of a monoclonal anti-E-selectin 7A9 antibody that inhibits neutrophil attachment to endothelial cells. J Biol Chem, 273, 11770-11775. PubMed id: 9565600 DOI: 10.1074/jbc.273.19.11770
16-Feb-98     Release date:   20-Apr-99    
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Protein chain
No UniProt id for this chain
Struc: 220 a.a.
Protein chain
No UniProt id for this chain
Struc: 212 a.a.
Key:    Secondary structure  CATH domain


DOI no: 10.1074/jbc.273.19.11770 J Biol Chem 273:11770-11775 (1998)
PubMed id: 9565600  
Primary and tertiary structures of the Fab fragment of a monoclonal anti-E-selectin 7A9 antibody that inhibits neutrophil attachment to endothelial cells.
A.Rodríguez-Romero, O.Almog, M.Tordova, Z.Randhawa, G.L.Gilliland.
The murine monoclonal IgG1 antibody 7A9 binds specifically to the endothelial leukocyte adhesion molecule-1 (E-selectin), inhibiting the attachment of neutrophils to endothelial cells. The primary and three-dimensional structures of the Fab fragment of 7A9 are reported. The amino acid sequence was determined by automated Edman degradation analysis of proteolytic fragments of both the heavy and light chains of the Fab. The sequences of the two chains are consistent with that of the IgG1 class with an associated kappa light chain with two intrachain disulfide bridges in each of the heavy and light chains. The tertiary structure of the antibody fragment was determined by x-ray crystallographic methods at 2.8 A resolution. The F(ab')2 molecule, treated with dithiothreitol, crystallizes in the space group P2(1) 2(1) 2(1) with unit cell parameters a = 44.5 A, b = 83.8 A, and c = 132.5 A with one Fab molecule in the asymmetric unit. The structure was solved by the molecular replacement method and subsequently refined using simulated annealing followed by conventional least squares optimization of the coordinates. The resulting model has reasonable stereochemistry with an R factor of 0.195. The 7A9 Fab structure has an elbow bend of 162 degrees and is remarkably similar to that of the monoclonal anti-intercellular adhesion molecule-1 (ICAM-1) antibody Fab fragment. The 7A9 antigen combining site presents a groove resembling the structure of the anti-ICAM-1 antibody, and other antibodies raised against surface receptors and peptides. Residues from the six complementary determining regions (CDRs) and framework residues form the floor and walls of the groove that is approximately 22 A wide and 8 A deep and that is lined with many aromatic residues. The groove is large enough to accommodate the loop between beta-strands beta4 and beta5 of the lectin domain of E-selectin that has been implicated in neutrophil adhesion (1).
  Selected figure(s)  
Figure 5.
Fig. 5. A superposition of the CA chains of the Fv fragments of anti-E-selectin (7A9) (V[L] in blue and V[H] in magenta), anti-ICAM-1 (R6.5) (green), and anti-human rhinovirus (8F5) (yellow). The drawing was made using the RIBBONS program (38).
Figure 6.
Fig. 6. A comparison of the surface contour of R6.5 and 7A9 CDRs. Concave features are shown in green; convex features are shown in gray. The drawings were made using the GRASP program (22).
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1998, 273, 11770-11775) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
15148373 Y.Yu, K.S.Moulton, M.K.Khan, S.Vineberg, E.Boye, V.M.Davis, P.E.O'Donnell, J.Bischoff, and D.S.Milstone (2004).
E-selectin is required for the antiangiogenic activity of endostatin.
  Proc Natl Acad Sci U S A, 101, 8005-8010.  
11055388 T.Takai, T.Yuuki, N.Iwamoto-Yasue, K.Okumura, and C.Ra (2000).
Epitope analysis and primary structures of variable regions of anti-human FcepsilonRI monoclonal antibodies, and expression of the chimeric antibodies fused with human constant regions.
  Biosci Biotechnol Biochem, 64, 1856-1867.  
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