3DJ9

Crystal Structure of an isolated, unglycosylated antibody CH2 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.201 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of an isolated unglycosylated antibody C(H)2 domain.

Prabakaran, P.Vu, B.K.Gan, J.Feng, Y.Dimitrov, D.S.Ji, X.

(2008) Acta Crystallogr.,Sect.D 64: 1062-1067

  • DOI: 10.1107/S0907444908025274

  • PubMed Abstract: 
  • The C(H)2 (C(H)3 for IgM and IgE) domain of an antibody plays an important role in mediating effector functions and preserving antibody stability. It is the only domain in human immunoglobulins (Igs) which is involved in weak interchain protein-prote ...

    The C(H)2 (C(H)3 for IgM and IgE) domain of an antibody plays an important role in mediating effector functions and preserving antibody stability. It is the only domain in human immunoglobulins (Igs) which is involved in weak interchain protein-protein interactions with another C(H)2 domain solely through sugar moieties. The N-linked glycosylation at Asn297 is conserved in mammalian IgGs as well as in homologous regions of other antibody isotypes. To examine the structural details of the C(H)2 domain in the absence of glycosylation and other antibody domains, the crystal structure of an isolated unglycosylated antibody gamma1 C(H)2 domain was determined at 1.7 A resolution and compared with corresponding C(H)2 structures from intact Fc, IgG and Fc receptor complexes. Furthermore, the oligomeric state of the protein in solution was studied using size-exclusion chromatography. The results suggested that the unglycosylated human antibody C(H)2 domain is a monomer and that its structure is similar to that found in the intact Fc, IgG and Fc receptor complex structures. However, certain structural variations were observed in the Fc receptor-binding sites. Owing to its small size, stability and non-immunogenic Ig template, the C(H)2-domain structure could be useful for the development by protein design of antibody domains exerting effector functions and/or antigen specificity and as a robust scaffold in protein-engineering applications.


    Organizational Affiliation

    Protein Interactions Group, Center for Cancer Research Nanobiology Program, National Cancer Institute, NIH, Frederick, MD 21702, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ig gamma-1 chain C region
A
107Homo sapiensMutation(s): 0 
Gene Names: IGHG1
Find proteins for P01857 (Homo sapiens)
Go to UniProtKB:  P01857
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.201 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 36.144α = 90.00
b = 40.678β = 106.74
c = 39.131γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
HKL-2000data reduction
SCALEPACKdata scaling
CNSrefinement
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2012-09-05
    Type: Database references
  • Version 1.3: 2016-12-21
    Type: Structure summary