5MN2

Cocrystal structure of Fc gamma receptor IIIa interacting with Affimer G3, a specific binding protein which blocks IgG binding to the receptor.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Affimer proteins inhibit immune complex binding to Fc gamma RIIIa with high specificity through competitive and allosteric modes of action.

Robinson, J.I.Baxter, E.W.Owen, R.L.Thomsen, M.Tomlinson, D.C.Waterhouse, M.P.Win, S.J.Nettleship, J.E.Tiede, C.Foster, R.J.Owens, R.J.Fishwick, C.W.G.Harris, S.A.Goldman, A.McPherson, M.J.Morgan, A.W.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: E72-E81

  • DOI: 10.1073/pnas.1707856115
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Protein-protein interactions are essential for the control of cellular functions and are critical for regulation of the immune system. One example is the binding of Fc regions of IgG to the Fc gamma receptors (FcγRs). High sequence identity (98%) bet ...

    Protein-protein interactions are essential for the control of cellular functions and are critical for regulation of the immune system. One example is the binding of Fc regions of IgG to the Fc gamma receptors (FcγRs). High sequence identity (98%) between the genes encoding FcγRIIIa (expressed on macrophages and natural killer cells) and FcγRIIIb (expressed on neutrophils) has prevented the development of monospecific agents against these therapeutic targets. We now report the identification of FcγRIIIa-specific artificial binding proteins called "Affimer" that block IgG binding and abrogate FcγRIIIa-mediated downstream effector functions in macrophages, namely TNF release and phagocytosis. Cocrystal structures and molecular dynamics simulations have revealed the structural basis of this specificity for two Affimer proteins: One binds directly to the Fc binding site, whereas the other acts allosterically.


    Organizational Affiliation

    Leeds Institute of Rheumatic and Musculoskeletal Medicine, School of Medicine, University of Leeds, Leeds LS9 7TF, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Low affinity immunoglobulin gamma Fc region receptor III-A
A, B
175Homo sapiensMutation(s): 0 
Gene Names: FCGR3A (CD16A, FCG3, FCGR3, IGFR3)
Find proteins for P08637 (Homo sapiens)
Go to Gene View: FCGR3A
Go to UniProtKB:  P08637
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Affimer G3
C, D
101N/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
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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Download CCD File 
D
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
A, B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-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: 2.35 Å
  • R-Value Free: 0.244 
  • R-Value Work: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 64.985α = 90.00
b = 59.925β = 102.09
c = 100.001γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata processing
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Arthritis Research UKUnited Kingdom19764
Ann Wolks Memorial FundUnited Kingdom650810
NIHRUnited Kingdom--
Medical Research Council (United Kingdom)United KingdomMR/K018779/1

Revision History 

  • Version 1.0: 2017-12-13
    Type: Initial release
  • Version 1.1: 2017-12-27
    Type: Database references
  • Version 1.2: 2018-01-10
    Type: Database references
  • Version 1.3: 2018-01-31
    Type: Author supporting evidence