9JKR | pdb_00009jkr

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

• PDB DOI: https://doi.org/10.2210/pdb9JKR/pdb
• EM Map EMD-61569: EMDB EMDataResource

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


• Deposited: 2024-09-17 Released: 2026-03-25 
• Deposition Author(s): Kishikawa, J., Kato, T., Kurosaki, T., Inoue, T.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS), Other private

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Experimental Data Snapshot

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

Starting Model: experimental

Literature

Mechanism of GM-CSF autoantibody-induced pathogenicity in autoimmune pulmonary alveolar proteinosis

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

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A1B1C1D1E1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 5-mer - A4B1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab region of F1 antibody heavy chain	A	231	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab region of F1 antibody light chain	B	215	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab region of C antibody heavy chain	C	236	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab region of C antibody light chain	D	221	Homo sapiens	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Granulocyte-macrophage colony-stimulating factor	E [auth I]	149	Homo sapiens	Mutation(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

Experimental Data & Validation

Experimental Data

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

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.0.0
MODEL REFINEMENT	Servalcat

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-03-25 
Deposition Author(s): Kishikawa, J., Kato, T., Kurosaki, T., Inoue, T.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	23K07625
Other private	Japan	26-2-40

Revision History  

• Version 1.0: 2026-03-25
  Type: Initial release