Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 44.79 kDa 
• Atom Count: 3151 
• Modelled Residue Count: 407 
• Deposited Residue Count: 407 
• Unique protein chains: 2

2KH2

Solution structure of a scFv-IL-1B complex

• PDB DOI: 10.2210/pdb2KH2/pdb

• Classification: Cytokine/IMMUNE SYSTEM
• Organism(s): Homo sapiens, Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-03-23 Released: 2009-09-08 
• Deposition Author(s): Wilkinson, I.C., Hall, C.J., Veverka, V., Muskett, F.W., Stephens, P.E., Taylor, R.J., Henry, A.J., Carr, M.D.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 77 
• Conformers Submitted: 77 
• Selection Criteria: all calculated structures submitted 

Literature

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.

Wilkinson, I.C., Hall, C.J., Veverka, V., Shi, J.Y., Muskett, F.W., Stephens, P.E., Taylor, R.J., Henry, A.J., Carr, M.D.

(2009) J Biol Chem 284: 31928-31935

• PubMed: 19776018 
• DOI: 10.1074/jbc.M109.025304
• Primary Citation of Related Structures:  
  2KH2


• PubMed Abstract: 
  

Monoclonal antibodies have recently started to deliver on their promise as highly specific and active drugs; however, a more effective, knowledge-based approach to the selection, design, and optimization of potential therapeutic antibodies is currently limited by the surprising lack of detailed structural information for complexes formed with target proteins. Here we show that complexes formed with minimal antigen binding single chain variable fragments (scFv) reliably reflect all the features of the binding interface present in larger Fab fragments, which are commonly used as therapeutics, and report the development of a robust, reliable, and relatively rapid approach to the determination of high resolution models for scFv-target protein complexes. This NMR spectroscopy-based approach combines experimental determination of the interaction surfaces and relative orientations of the scFv and target protein, with NMR restraint-driven, semiflexible docking of the proteins to produce a reliable and highly informative model of the complex. Experience with scFvs and Fabs targeted at a number of secreted regulatory proteins suggests that the approach will be applicable to many therapeutic antibodies targeted at proteins, and its application is illustrated for a potential therapeutic antibody targeted at the cytokine IL-1beta. The detailed structural information that can be obtained by this approach has the potential to have a major impact on the rational design and development of an increasingly important class of biological pharmaceuticals.

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Organizational Affiliation: 

Department of Biochemistry, University of Leicester, Leicester LE1 9HN, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Interleukin-1 beta	A	153	Homo sapiens	Mutation(s): 0  Gene Names: IL1B, IL1F2
UniProt & NIH Common Fund Data Resources
Find proteins for P01584 (Homo sapiens) Explore P01584  Go to UniProtKB:  P01584
PHAROS:  P01584

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
scFv	B	254	Mus musculus	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 77 
• Conformers Submitted: 77 
• Selection Criteria: all calculated structures submitted 
• OLDERADO: 2KH2 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-03-23 
• Released Date: 2009-09-08 
Deposition Author(s): Wilkinson, I.C., Hall, C.J., Veverka, V., Muskett, F.W., Stephens, P.E., Taylor, R.J., Henry, A.J., Carr, M.D.

Revision History  

• Version 1.0: 2009-09-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-16
  Changes: Data collection, Database references, Derived calculations