9N5P | pdb_00009n5p

CRYSTAL STRUCTURE OF HUMAN IGG2 FC FRAGMENT-FC-GAMMA RECEPTOR IIA COMPLEX H131 VARIANT

  • Classification: IMMUNE SYSTEM
  • Organism(s): Homo sapiens
  • Expression System: Homo sapiens
  • Mutation(s): No 

  • Deposited: 2025-02-04 Released: 2025-12-03 
  • Deposition Author(s): Tolbert, W.D., Pazgier, M.
  • Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free: 
    0.232 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.195 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


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Literature

Cross-species analysis of FcgRIIa/b (CD32a/b) polymorphisms at position 131: structural and functional insights into the mechanism of IgG- mediated phagocytosis in human and macaque.

Tolbert, W.D., Nhan, P.B., Conley, H.E., Ge, X., Chandravanshi, M., Lee, M., Veilleux, J., Korzeniowski, M., Gottumukkala, S., Ackerman, M.E., Pollara, J., Pazgier, M.

(2025) Front Immunol 


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Isoform 1 of Immunoglobulin heavy constant gamma 2
A, B
223Homo sapiensMutation(s): 0 
Gene Names: IGHG2
UniProt
Find proteins for Q6N093 (Homo sapiens)
Explore Q6N093 
Go to UniProtKB:  Q6N093
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6N093
Glycosylation
Glycosylation Sites: 1
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Low affinity immunoglobulin gamma Fc region receptor II-a H131 variant173Homo sapiensMutation(s): 0 
Gene Names: FCGR2A, CD32, FCG2, FCGR2A1, IGFR2
UniProt & NIH Common Fund Data Resources
Find proteins for P12318 (Homo sapiens)
Explore P12318 
Go to UniProtKB:  P12318
PHAROS:  P12318
GTEx:  ENSG00000143226 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP12318
Glycosylation
Glycosylation Sites: 2
Go to GlyGen: P12318-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
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
4N-Glycosylation
Entity ID: 4
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
E, F
8N-Glycosylation
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
G [auth C]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.01 Å
  • R-Value Free:  0.232 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.195 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.853α = 90
b = 66.949β = 94.18
c = 71.179γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01AI162242

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release