spacer
spacer

PDBsum entry 1nmc

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Complex (single-chain antibody/antigen) PDB id
1nmc
Jmol
Contents
Protein chains
388 a.a. *
122 a.a. *
109 a.a. *
Ligands
NAG-NAG-BMA-MAN-
MAN-MAN
×2
MAN ×2
NAG ×4
Metals
_CA ×2
Waters ×180
* Residue conservation analysis
PDB id:
1nmc
Name: Complex (single-chain antibody/antigen)
Title: Complex between nc10 anti-influenza virus neuraminidase sing antibody with a 15 residue linker and influenza virus neura
Structure: Neuraminidase. Chain: n, a. Fragment: residues 82 - 468. Engineered: yes. Single chain antibody. Chain: h, b. Fragment: vh and vl domains of anti-neuraminidase antibody covalently joined by a fifteen residue polypeptide linker. Engineered: yes.
Source: Influenza a virus. Organism_taxid: 11320. Strain: n9. Variant: a/tern/australia/g70c/75. Expressed in: gallus gallus. Expression_system_taxid: 9031. Expression_system_cell: egg. Mus musculus. House mouse.
Biol. unit: Hexamer (from PQS)
Resolution:
2.50Å     R-factor:   0.220     R-free:   0.260
Authors: R.L.Malby,A.J.Mccoy,A.A.Kortt,P.J.Hudson,P.M.Colman
Key ref:
R.L.Malby et al. (1998). Three-dimensional structures of single-chain Fv-neuraminidase complexes. J Mol Biol, 279, 901-910. PubMed id: 9642070 DOI: 10.1006/jmbi.1998.1794
Date:
21-Dec-97     Release date:   23-Sep-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P03472  (NRAM_I75A5) -  Neuraminidase
Seq:
Struc:
470 a.a.
388 a.a.
Protein chains
No UniProt id for this chain
Struc: 122 a.a.
Protein chains
No UniProt id for this chain
Struc: 109 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   3 terms 
  Biological process     carbohydrate metabolic process   1 term 
  Biochemical function     exo-alpha-sialidase activity     1 term  

 

 
DOI no: 10.1006/jmbi.1998.1794 J Mol Biol 279:901-910 (1998)
PubMed id: 9642070  
 
 
Three-dimensional structures of single-chain Fv-neuraminidase complexes.
R.L.Malby, A.J.McCoy, A.A.Kortt, P.J.Hudson, P.M.Colman.
 
  ABSTRACT  
 
The structure of the complex between a recombinant single-chain Fv construct of antibody NC10 with a five-residue peptide linker between VH and VL (termed scFv(5)), and its antigen, tetrameric neuraminidase from influenza virus (NA), has been determined and refined at 2.5 A resolution. The antibody-antigen binding interface is very similar to that of a similar NC10 scFv-NA complex in which the scFv has a 15-residue peptide linker (scFv(15)), and the NC10 Fab-NA complex. However, scFv(5) and scFv(15) have different stoichiometries in solution. While scFv(15) is predominantly monomeric in solution, scFv(5) forms dimers exclusively, because the five-residue linker is not long enough to permit VH and VL domains from the same polypeptide associating and forming an antigen-binding site. Upon forming a complex with NA, scFv(15) forms a approximately 300 kDa complex corresponding to one NA tetramer binding four scFv(15) monomers, while scFv(5) forms a approximately 590 kDa complex, corresponding to two NA tetramers crosslinked by four bivalent scFv(5) dimers. However, the dimeric scFv(5) in the scFv(5)-NA crystals does not crosslink NA tetramers, and modelling studies indicate that it is not possible to pack four dimeric and simultaneously bivalent scFvs between the NA tetramers with only a five-residue linker between VH and VL. The inability arises from the exacting requirement to orient the two antigen-binding surfaces to bind the tetrameric NA antigen while avoiding steric clashes with NC10 scFv(5) dimers bound to other sites on the NA tetramer. The utility of bivalent or bifunctional scFvs with short linkers may therefore be restricted by the steric constraints imposed by binding multivalent antigens.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. Model of the vert, similar 590 kDa complex observed in solution studies of the NC10 scFv(5)-NA, in which the scFv(5) is dimeric and bivalent [Kortt et al 1997]. Model is shown as a bold C^╬▒trace. The NA tetramers (green and purple) are crosslinked by scFv(5) molecules. The Fv domain bound to the green NA is shown with V[L]yellow and V[H]orange, while the Fv domain bound to the purple NA is shown with V[L]light blue and V[H]dark blue. The scFv(5) is thus shown with one V[L]yellow and the other light blue, and one V[H]orange and the other dark-blue. The complex has point group 422 symmetry. Drawn with MOLSCRIPT [Kraulis 1991] and RASTER3D [Bacon and Anderson 1989 and Merritt and Murphy 1994]. (a) View with the molecular 4-fold axis vertical. (b) View with the molecular 4-fold axis out of the page.
Figure 3.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 279, 901-910) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19776018 I.C.Wilkinson, C.J.Hall, V.Veverka, J.Y.Shi, F.W.Muskett, P.E.Stephens, R.J.Taylor, A.J.Henry, and M.D.Carr (2009).
High resolution NMR-based model for the structure of a scFv-IL-1beta complex: potential for NMR as a key tool in therapeutic antibody design and development.
  J Biol Chem, 284, 31928-31935.
PDB code: 2kh2
12021428 Y.Liu, and D.Eisenberg (2002).
3D domain swapping: as domains continue to swap.
  Protein Sci, 11, 1285-1299.  
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.