6MJ3

CRYSTAL STRUCTURE OF RHESUS MACAQUE (MACACA MULATTA) IGG1 Fc Fragment-Fc-GAMMA RECEPTOR III complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.278 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Decoding human-macaque interspecies differences in Fc-effector functions: The structural basis for CD16-dependent effector function in Rhesus macaques.

Tolbert, W.D.Gohain, N.Kremer, P.G.Hederman, A.P.Nguyen, D.N.Van, V.Sherburn, R.Lewis, G.K.Finzi, A.Pollara, J.Ackerman, M.E.Barb, A.W.Pazgier, M.

(2022) Front Immunol 13: 960411-960411

  • DOI: https://doi.org/10.3389/fimmu.2022.960411
  • Primary Citation of Related Structures:  
    6MJ3, 6MJO, 7KCZ

  • PubMed Abstract: 

    Fc mediated effector functions of antibodies play important roles in immunotherapies and vaccine efficacy but assessing those functions in animal models can be challenging due to species differences. Rhesus macaques, Macaca mulatta (Mm) share approximately 93% sequence identity with humans but display important differences in their adaptive immune system that complicates their use in validating therapeutics and vaccines that rely on Fc effector functions. In contrast to humans, macaques only have one low affinity FcγRIII receptor, CD16, which shares a polymorphism at position 158 with human FcγRIIIa with Ile 158 and Val 158 variants. Here we describe structure-function relationships of the Ile/Val 158 polymorphism in Mm FcγRIII. Our data indicate that the affinity of the allelic variants of Mm FcγRIII for the macaque IgG subclasses vary greatly with changes in glycan composition both on the Fc and the receptor. However, unlike the human Phe/Val 158 polymorphism in FcγRIIIa, the higher affinity variant corresponds to the larger, more hydrophobic side chain, Ile, even though it is not directly involved in the binding interface. Instead, this side chain appears to modulate glycan-glycan interactions at the Fc/FcγRIII interface. Furthermore, changes in glycan composition on the receptor have a greater effect for the Val 158 variant such that with oligomannose type glycans and with glycans only on Asn 45 and Asn 162 , Val 158 becomes the variant with higher affinity to Fc. These results have implications not only for the better interpretation of nonhuman primate studies but also for studies performed with human effector cells carrying different FcγRIIIa alleles.


  • Organizational Affiliation

    Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Igg1 FcA,
B,
C [auth D],
D [auth E]
224Macaca mulattaMutation(s): 0 
UniProt
Find proteins for F6RL33 (Macaca mulatta)
Explore F6RL33 
Go to UniProtKB:  F6RL33
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupF6RL33
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Low affinity immunoglobulin gamma Fc region receptor IIIE [auth C],
F
192Macaca mulattaMutation(s): 2 
Gene Names: FCGR3
UniProt
Find proteins for A3RFZ7 (Macaca mulatta)
Explore A3RFZ7 
Go to UniProtKB:  A3RFZ7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA3RFZ7
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
G, H, I, J
8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G80858MF
GlyCosmos:  G80858MF
GlyGen:  G80858MF
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.324 
  • R-Value Work: 0.276 
  • R-Value Observed: 0.278 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 213.108α = 90
b = 71.27β = 119.72
c = 135.521γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI16274
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01AI120756
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI129769

Revision History  (Full details and data files)

  • Version 1.0: 2019-08-21
    Type: Initial release
  • Version 1.1: 2019-12-18
    Changes: Author supporting evidence, Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2022-10-26
    Changes: Database references, Derived calculations, Structure summary
  • Version 2.2: 2023-10-18
    Changes: Data collection, Refinement description