4B53 | pdb_00004b53

Crystal structure of the isolated IgG4 CH3 domain

• PDB DOI: https://doi.org/10.2210/pdb4B53/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2012-08-02 Released: 2012-12-05 
• Deposition Author(s): Davies, A.M., Rispens, T., den Bleker, T.H., McDonnell, J.M., Gould, H.J., Aalberse, R.C., Sutton, B.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.237 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.183 (Depositor) 
• R-Value Observed: 
  0.185 (Depositor) 

Starting Model: experimental

Literature

Crystal Structure of the Human Igg4 C(H)3 Dimer Reveals the Role of Arg409 in the Mechanism of Fab-Arm Exchange.

Davies, A.M., Rispens, T., Den Bleker, T.H., Mcdonnell, J.M., Gould, H.J., Aalberse, R.C., Sutton, B.J.

(2012) Mol Immunol 54: 1

• PubMed: 23164605 
• DOI: https://doi.org/10.1016/j.molimm.2012.10.029
• Primary Citation Related Structures: 
  4B53


• PubMed Abstract: 
  

  Antibodies of the human IgG4 subclass uniquely undergo a process of Fab-arm exchange in which the heavy-chains of antibodies of different specificities can dissociate and then recombine. The mechanism by which the resulting functionally monovalent but bi-specific antibodies are formed is not only key to understanding their biological role, but is also important for the design of therapeutic monoclonal antibodies. Both the hinge region and the C(H)3 domain interface are known to be involved, and of the residues that differ between human IgG1 and IgG4 in C(H)3, residue 409, the only difference at the interface itself, has been implicated. We report the high resolution (1.8Å) structure of the C(H)3 domain dimer of IgG4, and find that Arg409 in IgG4, when compared with Lys409 observed in high resolution IgG1 structures, disrupts a network of water-mediated hydrogen bonding that is conserved in IgG1. Other conformational differences were detected that are a consequence of the presence of Arg409, such as a widening of the separation between residues Asn390 in one domain and Ser 400 in the other, which opens up a groove at the edge of the interface in IgG4 compared with IgG1. The effect of all these differences on the C(H)3 interface, doubled as a result of the interface's two-fold symmetry, is weakening of the inter-domain interaction in IgG4 compared with IgG1. This suggests a mechanism by which Arg409 weakens the C(H)3 interface in IgG4, predisposing this human antibody subclass to Fab-arm exchange.

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Organizational Affiliation: 
• King's College London, Randall Division of Cell and Molecular Biophysics, London, SE1 1UL, United Kingdom.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 25.04 kDa 
• Atom Count: 1,941 
• Modeled Residue Count: 206 
• Deposited Residue Count: 212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
IG GAMMA-4 CHAIN C REGION	A, B	106	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P01861 (Homo sapiens) Explore P01861  Go to UniProtKB:  P01861
PHAROS:  P01861 GTEx:  ENSG00000211892

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TRS	H [auth A]	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C4 H12 N O3 LENZDBCJOHFCAS-UHFFFAOYSA-O
PEG	F [auth A], G [auth A], I [auth A], M [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO	C [auth A], D [auth A], E [auth A], K [auth B], L [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT	J [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA	A, B	L-PEPTIDE LINKING	C5 H7 N O3		GLN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.237 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.183 (Depositor) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 4₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.09	α = 90
b = 57.09	β = 90
c = 138.436	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-05 
Deposition Author(s): Davies, A.M., Rispens, T., den Bleker, T.H., McDonnell, J.M., Gould, H.J., Aalberse, R.C., Sutton, B.J.

Revision History  

• Version 1.0: 2012-12-05
  Type: Initial release
  
• Version 1.1: 2013-07-31
  Changes: Derived calculations, Other
• Version 1.2: 2013-09-04
  Changes: Atomic model, Derived calculations, Non-polymer description
• Version 1.3: 2019-05-08
  Changes: Data collection, Derived calculations, Experimental preparation, Other
• Version 1.4: 2019-05-22
  Changes: Data collection, Experimental preparation
• Version 2.0: 2020-03-04
  Changes: Derived calculations, Other, Polymer sequence
• Version 2.1: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 2.2: 2024-11-06
  Changes: Structure summary