PDBsum entry 1b2w

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protein Protein-protein interface(s) links
Immune system PDB id
Protein chains
214 a.a. *
220 a.a. *
* Residue conservation analysis
PDB id:
Name: Immune system
Title: Comparison of the three-dimensional structures of a humanize chimeric fab of an anti-gamma-interferon antibody
Structure: Protein (antibody (light chain)). Chain: l. Fragment: v domain and c domain. Synonym: immunoglobulin. Engineered: yes. Protein (antibody (heavy chain)). Chain: h. Fragment: v domain and c domain. Synonym: immunoglobulin.
Source: Mus musculus, homo sapiens. Organism_taxid: 10090, 9606. Organism_taxid: 10090, 9606
Biol. unit: Dimer (from PQS)
2.90Å     R-factor:   0.188     R-free:   0.330
Authors: Z.Fan,L.Shan,B.Z.Goldsteen,L.W.Guddat,A.Thakur,N.F.Landolfi, M.Vasquez,C.Queen,P.A.Ramsland,A.B.Edmundson
Key ref: Z.C.Fan et al. (1999). Comparison of the three-dimensional structures of a humanized and a chimeric Fab of an anti-gamma-interferon antibody. J Mol Recognit, 12, 19-32. PubMed id: 10398393
01-Dec-98     Release date:   06-May-99    
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Protein chain
No UniProt id for this chain
Struc: 214 a.a.
Protein chain
No UniProt id for this chain
Struc: 220 a.a.
Key:    Secondary structure  CATH domain


J Mol Recognit 12:19-32 (1999)
PubMed id: 10398393  
Comparison of the three-dimensional structures of a humanized and a chimeric Fab of an anti-gamma-interferon antibody.
Z.C.Fan, L.Shan, B.Z.Goldsteen, L.W.Guddat, A.Thakur, N.F.Landolfi, M.S.Co, M.Vasquez, C.Queen, P.A.Ramsland, A.B.Edmundson.
The objective of this work is to compare the three-dimensional structures of "humanized" and mouse-human chimeric forms of a murine monoclonal antibody elicited against human gamma-interferon. It is also to provide structural explanations for the small differences in the affinities and biological interactions of the two molecules for this antigen. Antigen-binding fragments (Fabs) were produced by papain hydrolysis of the antibodies and crystallized with polyethylene glycol (PEG) 8,000 by nearly identical microseeding procedures. Their structures were solved by X-ray analyses at 2.9 A resolution, using molecular replacement methods and crystallographic refinement. Comparison of these structures revealed marked similarities in the light (L) chains and near identities of the constant (C) domains of the heavy (H) chains. However, the variable (V) domains of the heavy chains exhibited substantial differences in the conformations of all three complementarity-determining regions (CDRs), and in their first framework segments (FR1). In FR1 of the humanized VH, the substitution of serine for proline in position 7 allowed the N-terminal segment (designated strand 4-1) to be closely juxtaposed to an adjacent strand (4-2) and form hydrogen bonds typical of an antiparallel beta-pleated sheet. The tightening of the humanized structure was relayed in such a way as to decrease the space available for the last portion of HFR1 and the first part of HCDR1. This compression led to the formation of an alpha-helix involving residues 25-32. With fewer steric constraints, the corresponding segment in the chimeric Fab lengthened by at least 1 A to a random coil which terminated in a single turn of 310 helix. In the humanized Fab, HCDR1, which is sandwiched between HCDR2 and HCDR3, significantly influenced the structures of both regions. HCDR2 was forced into a bent and twisted orientation different from that in the chimeric Fab, both at the crown of the loop (around proline H52a) and at its base. As in HCDR1, the last few residues of HCDR2 in the humanized Fab were compressed into a space-saving alpha-helix, contrasting with a more extended 310 helix in the chimeric form. HCDR3 in the humanized Fab was also adjusted in shape and topography. The observed similarities in the functional binding activities of the two molecules can be rationalized by limited induced fit adjustments in their structures on antigen binding. While not perfect replicas, the two structures are testimonials to the progress in making high affinity monoclonal antibodies safe for human use.

Literature references that cite this PDB file's key reference

  PubMed id Reference
15152083 E.Carredano, H.Baumann, A.Grönberg, N.Norrman, G.Glad, J.Zou, O.Ersoy, E.Steensma, and A.Axén (2004).
A novel and conserved pocket of human kappa-Fab fragments: design, synthesis, and verification of directed affinity ligands.
  Protein Sci, 13, 1476-1488.  
15388922 P.C.Bourne, S.S.Terzyan, G.Cloud, N.F.Landolfi, M.Vásquez, and A.B.Edmundson (2004).
Three-dimensional structures of a humanized anti-IFN-gamma Fab (HuZAF) in two crystal forms.
  Acta Crystallogr D Biol Crystallogr, 60, 1761-1769.
PDB codes: 1t04 1t3f
12874380 C.Breithaupt, A.Schubart, H.Zander, A.Skerra, R.Huber, C.Linington, and U.Jacob (2003).
Structural insights into the antigenicity of myelin oligodendrocyte glycoprotein.
  Proc Natl Acad Sci U S A, 100, 9446-9451.
PDB codes: 1pko 1pkq
12447901 P.A.Ramsland, and W.Farrugia (2002).
Crystal structures of human antibodies: a detailed and unfinished tapestry of immunoglobulin gene products.
  J Mol Recognit, 15, 248-259.  
11369849 H.Zhao, M.H.Chen, Z.M.Shen, P.C.Kahn, and P.N.Lipke (2001).
Environmentally induced reversible conformational switching in the yeast cell adhesion protein alpha-agglutinin.
  Protein Sci, 10, 1113-1123.  
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.  
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.