2QL1

Structural Characterization of a Mutated, ADCC-Enhanced Human Fc Fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.235 

wwPDB Validation   3D Report Full Report


This is version 2.2 of the entry. See complete history


Literature

Structural characterization of a mutated, ADCC-enhanced human Fc fragment

Oganesyan, V.Damschroder, M.M.Leach, W.Wu, H.Dall'Acqua, W.F.

(2008) Mol Immunol 45: 1872-1882

  • DOI: https://doi.org/10.1016/j.molimm.2007.10.042
  • Primary Citation of Related Structures:  
    2QL1

  • PubMed Abstract: 

    We report here the three-dimensional structure of a human Fc fragment engineered for enhanced antibody dependent cell mediated cytotoxicity (ADCC). The triple mutation S239D/A330L/I332E ('3M') was introduced into the C(H)2 portion of a human immunoglobulin G1 (IgG1) Fc. These three substitutions typically result in an about 10-100-fold increase in human IgG1 binding to human Fc gamma RIIIA (CD16). The recombinantly produced Fc/3M fragment was crystallized and its structure solved at a resolution of 2.5A using molecular replacement. No dramatic structural changes were observed in Fc/3M when compared with unmutated human Fc fragments. However, we found that the relative positions of its C(H)2 domains allowed for an unusually 'open' conformation of the entire fragment. Although this particular structural feature could be due to crystallization artifacts or intrinsic variability, we propose that molecular mechanisms at the basis of the enhanced interaction between Fc/3M and CD16 could include enhanced Fc openness as well as the introduction of additional hydrophobic contacts, hydrogen bonds and/or electrostatic interactions at the corresponding interface. The existence of a more pronounced cleft between the two Fc chains as well as of repulsive, electrostatic intra-chain interactions may also account in part for the decreased thermostability of both Fc/3M and a 3M-modified humanized anti-human EphA2 IgG1 when compared with their respective unmutated counterparts.


  • Organizational Affiliation

    Department of Antibody Discovery and Protein Engineering, MedImmune, Inc., One MedImmune Way, Gaithersburg, MD 20878, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IGHM protein225Homo sapiensMutation(s): 3 
Gene Names: IGHM
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens)
Explore P01857 
Go to UniProtKB:  P01857
PHAROS:  P01857
GTEx:  ENSG00000211896 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01857
Sequence Annotations
Expand
  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseB [auth C]9N-Glycosylation
Glycosylation Resources
GlyTouCan:  G27919IH
GlyCosmos:  G27919IH
GlyGen:  G27919IH
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.53 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.235 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 49.869α = 90
b = 147.492β = 90
c = 74.315γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-10-20
    Changes: Database references, Structure summary
  • Version 2.2: 2023-08-30
    Changes: Data collection, Refinement description