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- PDB-9jkr: human GM-CSF with Fabs from autoantibodies, F1 and C. -

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Basic information

Entry
Database: PDB / ID: 9jkr
Titlehuman GM-CSF with Fabs from autoantibodies, F1 and C.
Components
  • Fab region of C antibody heavy chain
  • Fab region of C antibody light chain
  • Fab region of F1 antibody heavy chain
  • Fab region of F1 antibody light chain
  • Granulocyte-macrophage colony-stimulating factor
KeywordsIMMUNE SYSTEM / Autoimmune pulmonary alveolar proteinosis / autoantibody
Function / homology
Function and homology information


granulocyte macrophage colony-stimulating factor receptor binding / histamine secretion / response to silicon dioxide / neutrophil differentiation / epithelial fluid transport / positive regulation of interleukin-23 production / dendritic cell differentiation / regulation of circadian sleep/wake cycle, sleep / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway ...granulocyte macrophage colony-stimulating factor receptor binding / histamine secretion / response to silicon dioxide / neutrophil differentiation / epithelial fluid transport / positive regulation of interleukin-23 production / dendritic cell differentiation / regulation of circadian sleep/wake cycle, sleep / granulocyte macrophage colony-stimulating factor receptor complex / granulocyte-macrophage colony-stimulating factor signaling pathway / positive regulation of leukocyte proliferation / myeloid dendritic cell differentiation / response to fluid shear stress / cellular response to granulocyte macrophage colony-stimulating factor stimulus / myeloid cell differentiation / positive regulation of macrophage derived foam cell differentiation / cell surface receptor signaling pathway via STAT / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / positive regulation of podosome assembly / Interleukin-10 signaling / macrophage differentiation / Interleukin-3, Interleukin-5 and GM-CSF signaling / Interleukin receptor SHC signaling / monocyte differentiation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / embryonic placenta development / cell surface receptor signaling pathway via JAK-STAT / cytokine activity / growth factor activity / RAF/MAP kinase cascade / cellular response to lipopolysaccharide / cell population proliferation / positive regulation of cell migration / immune response / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of gene expression / : / extracellular region / plasma membrane
Similarity search - Function
Granulocyte-macrophage colony-stimulating factor / Granulocyte-macrophage colony-stimulating factor / Granulocyte-macrophage colony-stimulating factor signature. / Granulocyte-macrophage colony-simulating factor (GM-CSF) / Four-helical cytokine-like, core
Similarity search - Domain/homology
Granulocyte-macrophage colony-stimulating factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKishikawa, J. / Kato, T. / Kurosaki, T. / Inoue, T.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)23K07625 Japan
Other private26-2-40 Japan
CitationJournal: To Be Published
Title: Mechanism of GM-CSF autoantibody-induced pathogenicity in autoimmune pulmonary alveolar proteinosis
Authors: 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.
History
DepositionSep 17, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab region of F1 antibody heavy chain
B: Fab region of F1 antibody light chain
C: Fab region of C antibody heavy chain
D: Fab region of C antibody light chain
I: Granulocyte-macrophage colony-stimulating factor


Theoretical massNumber of molelcules
Total (without water)115,2945
Polymers115,2945
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Antibody Fab region of F1 antibody heavy chain


Mass: 24706.588 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C-terminal is His x6 tag for purification / Source: (gene. exp.) Homo sapiens (human) / Cell (production host): expi293 / Production host: Homo sapiens (human)
#2: Antibody Fab region of F1 antibody light chain


Mass: 23494.256 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): expi293 / Production host: Homo sapiens (human)
#3: Antibody Fab region of C antibody heavy chain


Mass: 25442.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: C terminal is His x6 tag for purification / Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Expi293 / Production host: Homo sapiens (human)
#4: Antibody Fab region of C antibody light chain


Mass: 24459.273 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): Expi293 / Production host: Homo sapiens (human)
#5: Protein Granulocyte-macrophage colony-stimulating factor / GM-CSF / Colony-stimulating factor / CSF / Molgramostin / Sargramostim


Mass: 17191.404 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: 1-17 residues are signal peptides cleaved in purified protein. 145-159 residues are avi-tag for purification 160 is a linker 161-166 residues are his-tag for purification
Source: (gene. exp.) Homo sapiens (human) / Gene: CSF2, GMCSF / Cell (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: P04141
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1the complex of human GM-CSF with Fabs from its autoantibodies, F1 and C.COMPLEXall0RECOMBINANT
2human GM-CSFCOMPLEX#51RECOMBINANT
3F1 autoantibody for human GM-CSFCOMPLEX#1-#21RECOMBINANT
4C autoantibody for human GM-CSFCOMPLEX#3-#41RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.12 MDaNO
210.015 MDaNO
3150 kDa/nmNO
4150 kDa/nmNO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
11Homo sapiens (human)9606
22Homo sapiens (human)9606
33Homo sapiens (human)9606
44Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCellPlasmid
11Homo sapiens (human)9606Expi293pcDNA3.4
22Homo sapiens (human)9606Expi293pcDNA3.4
33Homo sapiens (human)9606Expi293pcDNA3.4
44Homo sapiens (human)9606Expi293pcDNA3.4
Buffer solutionpH: 7.5
SpecimenConc.: 0.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 0.054 mm / C2 aperture diameter: 50 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 65 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 3467
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2SerialEM4image acquisition
4cryoSPARC4.0.0CTF correction
7Cootmodel fitting
9cryoSPARC4.0.0initial Euler assignment
10cryoSPARC4.0.0final Euler assignment
11cryoSPARC4.0.0classification
12cryoSPARC4.0.03D reconstruction
13Servalcatmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 601878 / Details: topaz extraction
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 189815 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 6BFQ

6bfq


Accession code: 6BFQ / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0054505
ELECTRON MICROSCOPYf_angle_d0.6576113
ELECTRON MICROSCOPYf_dihedral_angle_d9.7712672
ELECTRON MICROSCOPYf_chiral_restr0.045676
ELECTRON MICROSCOPYf_plane_restr0.004784

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