6EAQ

Glycosylated FCGR3B / CD16b in complex with afucosylated IgG1 Fc

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): 

  • Deposited: 2018-08-03 Released: 2018-11-07 
  • Deposition Author(s): Roberts, J.T., Barb, A.W.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences; Department of Energy (United States) 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A single amino acid distorts the Fc gamma receptor IIIb / CD16b structure upon binding immunoglobulin G1 and reduces affinity relative to CD16a.

Roberts, J.T.Barb, A.W.

(2018) J. Biol. Chem. --: --

  • DOI: 10.1074/jbc.RA118.005273

  • PubMed Abstract: 
  • Therapeutic mAbs engage Fc γ receptor III (CD16) to elicit a protective cell-mediated response and destroy the target tissue. Newer drugs designed to bind CD16a with increased affinity surprisingly also elicit protective CD16b-mediated responses. How ...

    Therapeutic mAbs engage Fc γ receptor III (CD16) to elicit a protective cell-mediated response and destroy the target tissue. Newer drugs designed to bind CD16a with increased affinity surprisingly also elicit protective CD16b-mediated responses. However, it is unclear why immunoglobulin G (IgG) binds CD16a with more than 10-fold higher affinity than CD16b even though these receptors share > 97% identity. Here, we identified one residue, Gly129, that contributes to the greater IgG-binding affinity of CD16a. The CD16b variant D129G bound IgG1 Fc with two-fold higher affinity than CD16a and with 90-fold higher affinity than WT. Conversely, the binding affinity of CD16a-G129D was decreased 128-fold relative to WT CD16a and comparably to that of WT CD16b. The interaction of IgG1 Fc with CD16a, but not with CD16b, is known to be sensitive to the composition of the asparagine-linked carbohydrates (N-glycans) attached to the receptor. CD16a and CD16b-D129G displaying minimally processed oligomannose N-glycans bound to IgG1 Fc with about 5.2-fold increased affinity compared with variants with highly processed complex-type N-glycans. CD16b and the CD16a-G129D variant exhibited a smaller 1.9-fold affinity increase with oligomannose N-glycans. A model of glycosylated CD16b bound to IgG1 Fc determined to 2.2 Å resolution combined with a 250-ns all-atom molecular dynamics simulation showed that the larger Asp129 residue deformed the Fc-binding surface. These results reveal how Asp-129 in CD16b affects its binding affinity for IgG1 Fc and suggest that antibodies engineered to engage CD16b with high affinity must accommodate the Asp-129 sidechain.


    Organizational Affiliation

    Iowa State University, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Immunoglobulin gamma-1 heavy chain
A, B
220Homo sapiensMutation(s): 0 
Find proteins for P0DOX5 (Homo sapiens)
Go to UniProtKB:  P0DOX5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Low affinity immunoglobulin gamma Fc region receptor III-B
C
175Homo sapiensMutation(s): 4 
Gene Names: FCGR3B (CD16B, FCG3, FCGR3, IGFR3)
Find proteins for O75015 (Homo sapiens)
Go to Gene View: FCGR3B
Go to UniProtKB:  O75015
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
GAL
Query on GAL

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

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

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.22 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.213 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 123.629α = 90.00
b = 49.388β = 103.04
c = 139.415γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data reduction
PHENIXrefinement
PHASERphasing
HKL-3000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01 GM115489
Department of Energy (United States)United StatesGUP-48455

Revision History 

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-11-14
    Type: Data collection, Database references