Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 47414.77 
• Atom Count: 3333 
• Residue Count: 436 
• Unique protein chains: 2

1L7I

Crystal Structure of the anti-ErbB2 Fab2C4

• DOI: 10.2210/pdb1L7I/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2002-03-15 Released: 2002-07-10 
• Deposition Author(s): Vajdos, F.F., Adams, C.W., Breece, T.N., Presta, L.G., de Vos, A.M., Sidhu, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.230 
• R-Value Work: 0.197 

Literature

Comprehensive functional maps of the antigen-binding site of an anti-ErbB2 antibody obtained with shotgun scanning mutagenesis.

Vajdos, F.F., Adams, C.W., Breece, T.N., Presta, L.G., de Vos, A.M., Sidhu, S.S.

(2002) J.Mol.Biol. 320: 415-428

• PubMed: 12079396 
• DOI: 10.1016/S0022-2836(02)00264-4
• Also Cited By: 1S78


• PubMed Abstract: 
  

Shotgun scanning combinatorial mutagenesis was used to study the antigen-binding site of Fab2C4, a humanized monoclonal antibody fragment that binds to the extracellular domain of the human oncogene product ErbB2. Essentially all the residues in the Fab2C4 complementarity determining regions (CDRs) were alanine-scanned using phage-displayed libraries that preferentially allowed side-chains to vary as the wild-type or alanine. A separate homolog-scan was performed using libraries that allowed side-chains to vary only as the wild-type or a similar amino acid residue. Following binding selections to isolate functional clones, DNA sequencing was used to determine the wild-type/mutant ratios at each varied position, and these ratios were used to assess the contributions of each side-chain to antigen binding. The alanine-scan revealed that most of the side-chains that contribute to antigen binding are located in the heavy chain, and the Fab2C4 three-dimensional structure revealed that these residues fall into two groups. The first group consists of solvent-exposed residues which likely make energetically favorable contacts with the antigen and thus comprise the functional-binding epitope. The second group consists of buried residues with side-chains that pack against other CDR residues and apparently act as scaffolding to maintain the functional epitope in a binding-competent conformation. The homolog-scan involved subtle mutations, and as a result, only a subset of the side-chains that were intolerant to alanine substitutions were also intolerant to homologous substitutions. In particular, the 610 A2 functional epitope surface revealed by alanine-scanning shrunk to only 369 A2 when mapped with homologous substitutions, suggesting that this smaller subset of side-chains may be involved in more precise contacts with the antigen. The results validate shotgun scanning as a rapid and accurate method for determining the functional contributions of individual side-chains involved in protein-protein interactions.

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Organizational Affiliation: 

Department of Protein Engineering, Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
chimera of Fab2C4: "humanized" murine monoclonal antibody	L	214	Homo sapiens	Mutation(s): 0
Find proteins for Q7Z3Y4 (Homo sapiens) Go to UniProtKB:  Q7Z3Y4

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
chimera of Fab2C4: "humanized" murine monoclonal antibody	H	222	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	L	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.230 
• R-Value Work: 0.197 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 41.966	α = 90.00
b = 64.249	β = 105.44
c = 79.445	γ = 90.00

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing
CCP4	data scaling
CNX	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-03-15 
• Released Date: 2002-07-10 
• Deposition Author(s): Vajdos, F.F., Adams, C.W., Breece, T.N., Presta, L.G., de Vos, A.M., Sidhu, S.S.

Revision History 

• Version 1.0: 2002-07-10
  Type: Initial release
• Version 1.1: 2008-04-28
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance