1IGT

STRUCTURE OF IMMUNOGLOBULIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Refined structure of an intact IgG2a monoclonal antibody.

Harris, L.J.Larson, S.B.Hasel, K.W.McPherson, A.

(1997) Biochemistry 36: 1581-1597

  • DOI: 10.1021/bi962514+

  • PubMed Abstract: 
  • The structure of an intact, anti-canine lymphoma monoclonal antibody (Mab231) was determined by molecular replacement and refined in a triclinic cell to an R-value of 20.9%, using synchrotron diffraction data from 2.8 to 20 A resolution. All segments ...

    The structure of an intact, anti-canine lymphoma monoclonal antibody (Mab231) was determined by molecular replacement and refined in a triclinic cell to an R-value of 20.9%, using synchrotron diffraction data from 2.8 to 20 A resolution. All segments of the antibody, including the hinge region and carbohydrate component, are visible in electron density maps. There is no overall symmetry to the antibody, as the Fc is disposed in an entirely oblique manner with respect to the Fabs. The CH2 and CH3 domains do, however, possess a nearly exact, local 2-fold relationship. The Fab segments are related by a second, independent, local dyad axis, exact only with respect to constant domains. Variable domains exhibit no symmetry relationship as a consequence of the 16 degrees difference in Fab elbow angles. Variable domain pair associations VL:VH for the Fabs are virtually the same, and corresponding CDRs of the two Fabs also are nearly identical in structure. CDR-H3 displays the greatest difference. Hypervariable loops of both Fabs are involved in contacts with symmetry-related Fc segments at the CH2-CH3 switch junction, suggesting a "complex" structure. The hinge segment connecting Fabs with the Fc is quite extended and exhibits thermal factors indicative of a high degree of mobility. It consists of a well-defined upper hinge that partially maintains dyad symmetry and a fairly rigid core bounded above and below by fluid polypeptides that provide segmental flexibility. This structure represents the first visualization by X-ray analysis of a murine Fc segment, and its CH2 domains exhibit substantial rigid body conformational changes with respect to the human Fc used as an initial molecular replacement model. The oligosaccharides were found by difference Fourier syntheses to be very similar to those of the free human Fc fragment, although differences are present in the terminal residues. The detailed structure of the IgG presented here, and the distribution of effector binding sites, appears consistent with effector activation mechanisms involving translocation and/or aggregation of the Fc following antigen binding by the Fabs.


    Related Citations: 
    • The Three-Dimensional Structure of an Intact Monoclonal Antibody for Canine Lymphoma
      Harris, L.J.,Larson, S.B.,Hasel, K.W.,Day, J.,Greenwood, A.,McPherson, A.
      (1992) Nature 360: 369


    Organizational Affiliation

    Department of Biochemistry, University of California, Riverside 92521, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IGG2A INTACT ANTIBODY - MAB231
A, C
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IGG2A INTACT ANTIBODY - MAB231
B, D
444N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

Download SDF File 
Download CCD File 
B, D
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
D
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
GAL
Query on GAL

Download SDF File 
Download CCD File 
B, D
BETA-D-GALACTOSE
C6 H12 O6
WQZGKKKJIJFFOK-FPRJBGLDSA-N
 Ligand Interaction
BMA
Query on BMA

Download SDF File 
Download CCD File 
B, D
BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
B, D
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
FUL
Query on FUL

Download SDF File 
Download CCD File 
B
BETA-L-FUCOSE
6-DEOXY-BETA-L-GALACTOSE
C6 H12 O5
SHZGCJCMOBCMKK-KGJVWPDLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.297 
  • R-Value Work: 0.209 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 65.820α = 88.05
b = 76.770β = 92.35
c = 100.640γ = 97.23
Software Package:
Software NamePurpose
HOWARDdata reduction
NIELSENdata reduction
X-PLORmodel building
NIELSENdata collection
XENGENdata reduction
XUONG)data reduction
XENGENdata scaling
HOWARDdata collection
X-PLORrefinement
X-PLORphasing
NIELSENdata scaling
XUONG)data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1997-07-07
    Type: Initial release
  • Version 1.1: 2008-03-03
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance