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PDBsum entry 2imm
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Immunoglobulin PDB id
2imm

 

 

 

 

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Contents
Protein chain
114 a.a. *
Ligands
SO4
ACT
Waters ×121
* Residue conservation analysis
PDB id:
2imm
Name: Immunoglobulin
Title: Refined crystal structure of a recombinant immunoglobulin domain and a complementarity-determining region 1-grafted mutant
Structure: Iga-kappa mcpc603 fv (light chain). Chain: a. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.149    
Authors: B.Steipe,R.Huber
Key ref: B.Steipe et al. (1992). Refined crystal structure of a recombinant immunoglobulin domain and a complementarity-determining region 1-grafted mutant. J Mol Biol, 225, 739-753. PubMed id: 1602480
Date:
01-Mar-93     Release date:   15-Jul-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 114 a.a.
Key:    Secondary structure  CATH domain

 

 
J Mol Biol 225:739-753 (1992)
PubMed id: 1602480  
 
 
Refined crystal structure of a recombinant immunoglobulin domain and a complementarity-determining region 1-grafted mutant.
B.Steipe, A.Plückthun, R.Huber.
 
  ABSTRACT  
 
We report the solution of the crystal structure of a mutant of the immunoglobulin VL domain of the antibody McPC603, in which the complementarity-determining region 1 segment is replaced with that of a different antibody. The wild-type and mutant crystal structures have been refined to a crystallographic R-factor of 14.9% at a nominal resolution of 1.97 A. A detailed description of the structures is given. Crystal packing results in a dimeric association of domains, in a fashion closely resembling that of an Fv fragment. The comparison of this VL domain with the same domain in the Fab fragment of McPC603 shows that the structure of an immunoglobulin VL domain is largely independent of its mode of association, even in places where the inter-subunit contacts are not conserved between VL and VH. In all three complementarity-determining regions we observe conformations that would not have been predicted by the canonical structure hypothesis. Significant differences between the VL domain dimer and the Fab fragment in the third complementarity-determining region show that knowledge of the structure of the dimerization partner and its exact mode of association may be needed to predict the precise conformation of antigen-binding loops.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19606431 C.N.Falco, K.M.Dykstra, B.P.Yates, and P.B.Berget (2009).
scFv-based fluorogen activating proteins and variable domain inhibitors as fluorescent biosensor platforms.
  Biotechnol J, 4, 1328-1336.  
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
12657787 L.O.Essen, A.Harrenga, C.Ostermeier, and H.Michel (2003).
1.3 A X-ray structure of an antibody Fv fragment used for induced membrane-protein crystallization.
  Acta Crystallogr D Biol Crystallogr, 59, 677-687.
PDB code: 1mqk
12070321 P.R.Pokkuluri, M.Gu, X.Cai, R.Raffen, F.J.Stevens, and M.Schiffer (2002).
Factors contributing to decreased protein stability when aspartic acid residues are in beta-sheet regions.
  Protein Sci, 11, 1687-1694.
PDB codes: 1eeu 1efq
11751325 P.R.Pokkuluri, R.Raffen, L.Dieckman, C.Boogaard, F.J.Stevens, and M.Schiffer (2002).
Increasing protein stability by polar surface residues: domain-wide consequences of interactions within a loop.
  Biophys J, 82, 391-398.
PDB code: 1eeq
  10752617 M.Jäger, and A.Plückthun (2000).
Direct evidence by H/D exchange and ESI-MS for transient unproductive domain interaction in the refolding of an antibody scFv fragment.
  Protein Sci, 9, 552-563.  
  11045631 P.R.Pokkuluri, X.Cai, G.Johnson, F.J.Stevens, and M.Schiffer (2000).
Change in dimerization mode by removal of a single unsatisfied polar residue located at the interface.
  Protein Sci, 9, 1852-1855.
PDB codes: 1qac 5lve
9739086 P.R.Pokkuluri, D.B.Huang, R.Raffen, X.Cai, G.Johnson, P.W.Stevens, F.J.Stevens, and M.Schiffer (1998).
A domain flip as a result of a single amino-acid substitution.
  Structure, 6, 1067-1073.
PDB codes: 2lve 3lve 4lve
  9007995 E.C.Ohage, W.Graml, M.M.Walter, S.Steinbacher, and B.Steipe (1997).
Beta-turn propensities as paradigms for the analysis of structural motifs to engineer protein stability.
  Protein Sci, 6, 233-241.  
9275175 X.Y.Pei, P.Holliger, A.G.Murzin, and R.L.Williams (1997).
The 2.0-A resolution crystal structure of a trimeric antibody fragment with noncognate VH-VL domain pairs shows a rearrangement of VH CDR3.
  Proc Natl Acad Sci U S A, 94, 9637-9642.
PDB code: 1nqb
9370345 Y.E.Bruggeman, A.Honegger, H.Kreuwel, A.J.Visser, C.Laane, A.Schots, and R.Hilhorst (1997).
Regulation of the flavin redox potential by flavin-binding antibodies.
  Eur J Biochem, 249, 393-400.  
8879196 D.Plaksin, S.Chacko, P.McPhie, A.Bax, E.A.Padlan, and D.H.Margulies (1996).
A T cell receptor V alpha domain expressed in bacteria: does it dimerize in solution?
  J Exp Med, 184, 1251-1258.  
8784347 S.Spinelli, L.Frenken, D.Bourgeois, L.de Ron, W.Bos, T.Verrips, C.Anguille, C.Cambillau, and M.Tegoni (1996).
The crystal structure of a llama heavy chain variable domain.
  Nat Struct Biol, 3, 752-757.
PDB code: 1hcv
  7556106 I.M.Tomlinson, J.P.Cox, E.Gherardi, A.M.Lesk, and C.Chothia (1995).
The structural repertoire of the human V kappa domain.
  EMBO J, 14, 4628-4638.  
7764904 A.R.Rees, D.Staunton, D.M.Webster, S.J.Searle, A.H.Henry, and J.T.Pedersen (1994).
Antibody design: beyond the natural limits.
  Trends Biotechnol, 12, 199-206.  
7944332 D.M.Webster, J.Pedersen, D.Staunton, A.Jones, and A.R.Rees (1994).
Antibody-combining sites. Extending the natural limits.
  Appl Biochem Biotechnol, 47, 119.  
7994573 R.L.Malby, W.R.Tulip, V.R.Harley, J.L.McKimm-Breschkin, W.G.Laver, R.G.Webster, and P.M.Colman (1994).
The structure of a complex between the NC10 antibody and influenza virus neuraminidase and comparison with the overlapping binding site of the NC41 antibody.
  Structure, 2, 733-746.
PDB code: 1nmb
7765075 R.L.Stanfield, and I.A.Wilson (1994).
Antigen-induced conformational changes in antibodies: a problem for structural prediction and design.
  Trends Biotechnol, 12, 275-279.  
8346191 A.B.Edmundson, D.L.Harris, Z.C.Fan, L.W.Guddat, B.T.Schley, B.L.Hanson, G.Tribbick, and H.M.Geysen (1993).
Principles and pitfalls in designing site-directed peptide ligands.
  Proteins, 16, 246-267.
PDB codes: 1mcb 1mcc 1mcd 1mce 1mcf 1mch 1mci 1mcj 1mck 1mcl 1mcn 1mcq 1mcr 1mcs
8507403 A.Skerra (1993).
Bacterial expression of immunoglobulin fragments.
  Curr Opin Immunol, 5, 256-262.  
1286869 A.Plückthun (1992).
Mono- and bivalent antibody fragments produced in Escherichia coli: engineering, folding and antigen binding.
  Immunol Rev, 130, 151-188.  
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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