5XMH

Crystal structure of an IgM rheumatoid factor YES8c in complex with IgG1 Fc


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.220 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-function analyses of a stereotypic rheumatoid factor unravel the structural basis for germline-encoded antibody autoreactivity.

Shiroishi, M.Ito, Y.Shimokawa, K.Lee, J.M.Kusakabe, T.Ueda, T.

(2018) J. Biol. Chem. 293: 7008-7016

  • DOI: 10.1074/jbc.M117.814475

  • PubMed Abstract: 
  • Rheumatoid factors (RFs) are autoantibodies against the fragment-crystallizable (Fc) region of immunoglobulin G (IgG). In individuals with hematological diseases such as cryoglobulinemia and certain B-cell lymphoma forms, the RFs derived from specifi ...

    Rheumatoid factors (RFs) are autoantibodies against the fragment-crystallizable (Fc) region of immunoglobulin G (IgG). In individuals with hematological diseases such as cryoglobulinemia and certain B-cell lymphoma forms, the RFs derived from specific heavy- and light-chain germline pairs, so-called "stereotypic RFs," are frequently produced in copious amounts and form immune complexes with IgG in serum. Of note, many structural details of the antigen-recognition mechanisms in RFs are unclear. Here, we report the crystal structure of the RF YES8c derived from the IGHV1-69/IGKV3-20 germline pair, the commonest of the stereotypic RFs, in complex with human IgG1-Fc at 2.8 Å resolution. We observed that YES8c binds to the CH2-CH3 elbow in the canonical antigen-binding manner involving a large antigen-antibody interface. On the basis of this observation combined with mutational analyses, we propose a recognition mechanism common to IGHV1-69/IGKV3-20 RFs: (1) the interaction of the Leu432-His435 region of Fc enables the highly variable complementarity-determining region (CDR)-H3 to participate in the binding, (2) the hydrophobic tip in the CDR-H2 typical of IGHV1-69 antibodies recognizes the hydrophobic patch on Fc, and (3) the interaction of the highly conserved RF light chain with Fc is important for RF activity. These features may determine the putative epitope common to the IGHV1-69/IGKV3-20 RFs. We also showed that some mutations in the binding site of RF increase the affinity to Fc, which may aggravate the hematological diseases. Our findings unravel the structural basis for germline-encoded antibody autoreactivity.


    Organizational Affiliation

    Kyushu University, Japan shiroish@phar.kyushu-u.ac.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Immunoglobulin gamma-1 heavy chain
A, B
208Homo sapiensMutation(s): 0 
Find proteins for P0DOX5 (Homo sapiens)
Go to UniProtKB:  P0DOX5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
YES8c light chain
L, C
216N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
YES8c heavy chain
H, D
226N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MAN
Query on MAN

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

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

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

Download SDF File 
Download CCD File 
A, B
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.220 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 189.895α = 90.00
b = 189.895β = 90.00
c = 79.602γ = 120.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
JSPS KAKENHIJapan23655160
JSPS KAKENHIJapan15K15184

Revision History 

  • Version 1.0: 2018-03-21
    Type: Initial release
  • Version 1.1: 2018-05-16
    Type: Data collection, Database references