9MI6 | pdb_00009mi6

Crystal structure of human FcRn in complex with nipocalimab Fab fragment


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free: 
    0.248 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.206 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 
    0.208 (Depositor) 

Starting Models: experimental
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This is version 1.1 of the entry. See complete history


Literature

Nipocalimab, an immunoselective FcRn blocker that lowers IgG and has unique molecular properties.

Seth, N.P.Xu, R.DuPrie, M.Choudhury, A.Sihapong, S.Tyler, S.Meador, J.Avery, W.Cochran, E.Daly, T.Brown, J.Rutitzky, L.Markowitz, L.Kumar, S.Beavers, T.Bhattacharya, S.Chen, H.Parge, V.Price, K.Wang, Y.Sukumaran, S.Pao, Y.Abouzahr, K.Elwood, F.Duffner, J.Roy, S.Narayanaswami, P.Hubbard, J.J.Ling, L.E.

(2025) MAbs 17: 2461191-2461191

  • DOI: https://doi.org/10.1080/19420862.2025.2461191
  • Primary Citation of Related Structures:  
    9MI6

  • PubMed Abstract: 

    Nipocalimab is a human immunoglobulin G (IgG)1 monoclonal antibody that binds to the neonatal Fc receptor (FcRn) with high specificity and high affinity at both neutral (extracellular) and acidic (intracellular) pH, resulting in the reduction of circulating IgG levels, including those of pathogenic IgG antibodies. Here, we present the molecular, cellular, and nonclinical characteristics of nipocalimab that support the reported clinical pharmacology and potential clinical application in IgG-driven, autoantibody- and alloantibody-mediated diseases. The crystal structure of the nipocalimab antigen binding fragment (Fab)/FcRn complex reveals its binding to a unique epitope on the IgG binding site of FcRn that supports the observed pH-independent high-binding affinity to FcRn. Cell-based and in vivo studies demonstrate concentration/dose- and time-dependent FcRn occupancy and IgG reduction. Nipocalimab selectively reduces circulating IgG levels without detectable effects on other adaptive and innate immune functions. In vitro experiments and in vivo studies in mice and cynomolgus monkeys generated data that align with observations from clinical studies of nipocalimab in IgG autoantibody- and alloantibody-mediated diseases.


  • Organizational Affiliation

    Johnson & Johnson, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
IgG receptor FcRn large subunit p51280Homo sapiensMutation(s): 0 
Gene Names: FCGRTFCRN
UniProt & NIH Common Fund Data Resources
Find proteins for P55899 (Homo sapiens)
Explore P55899 
Go to UniProtKB:  P55899
PHAROS:  P55899
GTEx:  ENSG00000104870 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55899
Glycosylation
Glycosylation Sites: 1Go to GlyGen: P55899-1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-2-microglobulin99Homo sapiensMutation(s): 0 
Gene Names: B2MCDABP0092HDCMA22P
UniProt & NIH Common Fund Data Resources
Find proteins for P61769 (Homo sapiens)
Explore P61769 
Go to UniProtKB:  P61769
PHAROS:  P61769
GTEx:  ENSG00000166710 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61769
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
nipocalimab Fab heavy chainC [auth H]220Homo sapiensMutation(s): 0 
Entity Groups  
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Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
nipocalimab Fab light chainD [auth L]216Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
E [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.41 Å
  • R-Value Free:  0.248 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.206 (Depositor), 0.207 (DCC) 
  • R-Value Observed: 0.208 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.282α = 90
b = 67.644β = 104.879
c = 105.303γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-02-12
    Type: Initial release
  • Version 1.1: 2025-02-26
    Changes: Database references