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 9JKR | pdb_00009jkr

human GM-CSF with Fabs from autoantibodies, F1 and C.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.1 of the entry. See complete history. 

Literature

Affinity- and epitope-dependent pathogenicity of GM-CSF autoantibodies in patients with autoimmune pulmonary alveolar proteinosis.

Futami, S., Kawai, C., Kishikawa, J.I., Hirose, M., Kida, H., Wang, P.H., Yamashita, K., Ishikawa, F., Kato, T., Inoue, Y., Kumanogoh, A., Kurosaki, T., Inoue, T.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-74717-2
  • Primary Citation Related Structures: 
    9JKR

  • PubMed Abstract: 

    Autoimmune pulmonary alveolar proteinosis (aPAP) is a rare lung disease caused by autoantibodies targeting granulocyte-macrophage colony-stimulating factor (GM-CSF). Although serum GM-CSF autoantibody levels are markedly increased in aPAP patients, total antibody titer does not correlate with disease severity. Here, we characterize 186 monoclonal anti-GM-CSF autoantibodies derived from GM-CSF-specific B cells in 28 aPAP patients with varying disease severity, including three longitudinal cohorts, to determine whether epitope specificity and affinity of the autoantibodies contribute to disease pathophysiology. We classify these antibodies into two groups based on their epitopes: class 1 (targeting A, BD, or D epitopes) and class 2 (targeting B or C epitopes). In class 1 antibodies, affinity strongly correlates with neutralization activity, whereas this relationship is weak or absent in class 2 antibodies. High-affinity class 1 antibodies are present at higher levels in patients with more severe disease and are sufficient to induce PAP symptoms in a humanized mouse model. Thus, these findings identify epitope specificity and affinity as key determinants of pathogenicity and provide a mechanistic framework for understanding why total serum autoantibody levels fail to reflect disease severity in aPAP.


  • Organizational Affiliation: 
    • Laboratory of Lymphocyte Differentiation, WPI Immunology Frontier Research Center, The University of Osaka, Osaka, Japan.

Macromolecule Content 

  • Total Structure Weight: 115.29 kDa 
  • Atom Count: 4,404 
  • Modeled Residue Count: 567 
  • Deposited Residue Count: 1,052 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab region of F1 antibody heavy chain231Homo sapiensMutation(s): 0 
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab region of F1 antibody light chain215Homo sapiensMutation(s): 0 
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab region of C antibody heavy chain236Homo sapiensMutation(s): 0 
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab region of C antibody light chain221Homo sapiensMutation(s): 0 
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Granulocyte-macrophage colony-stimulating factorE [auth I]149Homo sapiensMutation(s): 0 
Gene Names: CSF2, GMCSF
UniProt & NIH Common Fund Data Resources
Find proteins for P04141 (Homo sapiens)
Explore P04141 
Go to UniProtKB:  P04141
PHAROS:  P04141
GTEx:  ENSG00000164400 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04141
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.0.0
MODEL REFINEMENTServalcat

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan23K07625
Other privateJapan26-2-40

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-25
    Type: Initial release
  • Version 1.1: 2026-10-07
    Changes: Data collection, Database references