8DJ7 | pdb_00008dj7

The complex structure between human IgG1 Fc and its high affinity receptor FcgRI H174R variant


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 
    0.266 (Depositor), 0.266 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 
    0.217 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Fc gamma RI FG-loop functions as a pH sensitive switch for IgG binding and release.

Lu, J.Spencer, M.Zou, Z.Traver, M.Brzostowski, J.Sun, P.D.

(2023) Front Immunol 14: 1100499-1100499

  • DOI: https://doi.org/10.3389/fimmu.2023.1100499
  • Primary Citation Related Structures: 
    8DIN, 8DIR, 8DJ7

  • PubMed Abstract: 

    Understanding the molecular mechanism underlying the hierarchic binding between FcγRs and IgG antibodies is critical for therapeutic antibody engineering and FcγR functions. The recent determination of crystal structures of FcγRI-Fc complexes, however, resulted in two controversial mechanisms for the high affinity receptor binding to IgG. Here, we describe high resolution structures of a bovine FG-loop variant of FcγRI in complex with the Fc fragment of IgG 1 crystallized in three different conditions at neutral pH, confirming the characteristic FG loop-Fc interaction is critical to the high affinity immunoglobulin binding. We showed that the FcγRI D2-domain FG-loop functioned as a pH-sensing switch for IgG binding. Further live cell imaging of FcγRI-mediated internalization of immune complexes showed a pH sensitive temporal-spatial antibody-antigen uptake and release. Taken together, we demonstrate that the structures of FcγRI-Fc crystallized at neutral and acidic pH, respectively, represent the high and low affinity binding states of the receptor for IgG uptake and release. These results support a role for FcγRI in antigen delivery, highlight the importance of Fc glycan in antibody binding to the high affinity receptor and provide new insights to future antibody engineering.


  • Organizational Affiliation
    • Structural Immunology Section, Lab of Immunogenetics, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD, United States.

Macromolecule Content 

  • Total Structure Weight: 83.88 kDa 
  • Atom Count: 5,663 
  • Modeled Residue Count: 669 
  • Deposited Residue Count: 715 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ig gamma-1 Fc chainA [auth B],
B [auth A]
219Homo sapiensMutation(s): 0 
Gene Names: IGHG1
UniProt & NIH Common Fund Data Resources
Find proteins for P01857 (Homo sapiens)
Explore P01857 
Go to UniProtKB:  P01857
PHAROS:  P01857
GTEx:  ENSG00000211896 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01857
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P01857-2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
High affinity immunoglobulin gamma Fc receptor I277Homo sapiensMutation(s): 0 
Gene Names: FCGR1AFCG1FCGR1IGFR1
UniProt & NIH Common Fund Data Resources
Find proteins for P12314 (Homo sapiens)
Explore P12314 
Go to UniProtKB:  P12314
PHAROS:  P12314
GTEx:  ENSG00000150337 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12314
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

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Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD 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
D
8N-Glycosylation
Glycosylation Resources
GlyTouCan: G80858MF
GlyCosmos: G80858MF
GlyGen: G80858MF
Entity ID: 4
MoleculeChains Length2D Diagram GlycosylationD Interactions
beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]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
E
9N-Glycosylation
Glycosylation Resources
GlyTouCan: G27919IH
GlyCosmos: G27919IH
GlyGen: G27919IH

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free:  0.266 (Depositor), 0.266 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.214 (DCC) 
  • R-Value Observed: 0.217 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 206.371α = 90
b = 89.037β = 96.81
c = 56.191γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

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 StatesDivision of ntramural research

Revision History  (Full details and data files)

  • Version 1.0: 2023-05-10
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description
  • Version 1.2: 2024-11-13
    Changes: Structure summary