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- EMDB-61569: human GM-CSF with Fabs from autoantibodies, F1 and C. -

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Basic information

Entry
Database: EMDB / ID: EMD-61569
Titlehuman GM-CSF with Fabs from autoantibodies, F1 and C.
Map data
Sample
  • Complex: the complex of human GM-CSF with Fabs from its autoantibodies, F1 and C.
    • Complex: human GM-CSF
      • Protein or peptide: Granulocyte-macrophage colony-stimulating factor
    • Complex: F1 autoantibody for human GM-CSF
      • Protein or peptide: Fab region of F1 antibody heavy chain
      • Protein or peptide: Fab region of F1 antibody light chain
    • Complex: C autoantibody for human GM-CSF
      • Protein or peptide: Fab region of C antibody heavy chain
      • Protein or peptide: Fab region of C antibody light chain
KeywordsAutoimmune pulmonary alveolar proteinosis / autoantibody / IMMUNE SYSTEM
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsKishikawa J / Kato T / Kurosaki T / Inoue T
Funding support Japan, 2 items
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 PH / Yamashita K / Ishikawa F / Kato T / Inoue Y / Kumanogoh A / Kurosaki T / Inoue T
History
DepositionSep 17, 2024-
Header (metadata) releaseMar 25, 2026-
Map releaseMar 25, 2026-
UpdateMar 25, 2026-
Current statusMar 25, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_61569.png

Downloads & links

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Map

FileDownload / File: emd_61569.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.01 Å/pix.
x 300 pix.
= 303.75 Å		1.01 Å/pix.
x 300 pix.
= 303.75 Å		1.01 Å/pix.
x 300 pix.
= 303.75 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0125 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.7103071 - 0.80907893
Average (Standard dev.)-0.000009117716 (±0.02063241)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 303.75 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_61569_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_61569_additional_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61569_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61569_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : the complex of human GM-CSF with Fabs from its autoantibodies, F1...

EntireName: the complex of human GM-CSF with Fabs from its autoantibodies, F1 and C.
Components
  • Complex: the complex of human GM-CSF with Fabs from its autoantibodies, F1 and C.
    • Complex: human GM-CSF
      • Protein or peptide: Granulocyte-macrophage colony-stimulating factor
    • Complex: F1 autoantibody for human GM-CSF
      • Protein or peptide: Fab region of F1 antibody heavy chain
      • Protein or peptide: Fab region of F1 antibody light chain
    • Complex: C autoantibody for human GM-CSF
      • Protein or peptide: Fab region of C antibody heavy chain
      • Protein or peptide: Fab region of C antibody light chain

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Supramolecule #1: the complex of human GM-CSF with Fabs from its autoantibodies, F1...

SupramoleculeName: the complex of human GM-CSF with Fabs from its autoantibodies, F1 and C.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50 kDa/nm

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Supramolecule #2: human GM-CSF

SupramoleculeName: human GM-CSF / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: F1 autoantibody for human GM-CSF

SupramoleculeName: F1 autoantibody for human GM-CSF / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: C autoantibody for human GM-CSF

SupramoleculeName: C autoantibody for human GM-CSF / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Fab region of F1 antibody heavy chain

MacromoleculeName: Fab region of F1 antibody heavy chain / type: protein_or_peptide / ID: 1 / Details: C-terminal is His x6 tag for purification / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.706588 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MAQLQESGPG VVKPSETLSL TCSVSDSAIR KYYWSWIRQP PGQGLEYIGY IYASGSSFYN PSFKSRVSMS VDATNNQFYL KLTSVTAAD TAVYYCAAIT GTTDLWGRGT LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP EPVTVSWNSG A LTSGVHTF ...String:
MAQLQESGPG VVKPSETLSL TCSVSDSAIR KYYWSWIRQP PGQGLEYIGY IYASGSSFYN PSFKSRVSMS VDATNNQFYL KLTSVTAAD TAVYYCAAIT GTTDLWGRGT LVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP EPVTVSWNSG A LTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKRVEPKSC DKTHTNGHHH HHH

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Macromolecule #2: Fab region of F1 antibody light chain

MacromoleculeName: Fab region of F1 antibody light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.494256 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDIQMTQSPS SVSASVGDRV TITCRASQGI NRRLAWYQQK PGKAPKRLIY AVSTLQSGVP SRFNGSGSGT DFTLTVNNVQ PDDLAMYFC LQSNNYPLTF GGGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD ...String:
MDIQMTQSPS SVSASVGDRV TITCRASQGI NRRLAWYQQK PGKAPKRLIY AVSTLQSGVP SRFNGSGSGT DFTLTVNNVQ PDDLAMYFC LQSNNYPLTF GGGTKVEIKR TVAAPSVFIF PPSDEQLKSG TASVVCLLNN FYPREAKVQW KVDNALQSGN S QESVTEQD SKDSTYSLSS TLTLSKADYE KHKVYACEVT HQGLSSPVTK SFNRGEC

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Macromolecule #3: Fab region of C antibody heavy chain

MacromoleculeName: Fab region of C antibody heavy chain / type: protein_or_peptide / ID: 3 / Details: C terminal is His x6 tag for purification / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.442504 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MQVQLVQSGA EVKKPGSSMK VSCKTSGGTF DNYAFSWLRQ APGQGFEWMG SIMPILDFPQ YAEKFQGRLT ITADKSTNTA FIELSSLRP DDTAVYYCAR EGIAVGDVLA EYFQHWGHGT TVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS ...String:
MQVQLVQSGA EVKKPGSSMK VSCKTSGGTF DNYAFSWLRQ APGQGFEWMG SIMPILDFPQ YAEKFQGRLT ITADKSTNTA FIELSSLRP DDTAVYYCAR EGIAVGDVLA EYFQHWGHGT TVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKKVENLYF QGHHHHHH

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Macromolecule #4: Fab region of C antibody light chain

MacromoleculeName: Fab region of C antibody light chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.459273 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDIVMTQSPD SLAVSLGGRA TINCKSSQSV FYGSRNKNFL AWYQQKPGQP PKLLFYWAST RESGVPDRFR SSGSGTEFTL TINSLQVED VAIYYCQQYY GHPLTFGGGT KVDIKRTVAA PSVFIFPPSD EQLKSGTASV VCLLNNFYPR EAKVQWKVDN A LQSGNSQE ...String:
MDIVMTQSPD SLAVSLGGRA TINCKSSQSV FYGSRNKNFL AWYQQKPGQP PKLLFYWAST RESGVPDRFR SSGSGTEFTL TINSLQVED VAIYYCQQYY GHPLTFGGGT KVDIKRTVAA PSVFIFPPSD EQLKSGTASV VCLLNNFYPR EAKVQWKVDN A LQSGNSQE SVTEQDSKDS TYSLSSTLTL SKADYEKHKV YACEVTHQGL SSPVTKSFNR GEC

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Macromolecule #5: Granulocyte-macrophage colony-stimulating factor

MacromoleculeName: Granulocyte-macrophage colony-stimulating factor / type: protein_or_peptide / ID: 5
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
Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.191404 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
APARSPSPST QPWEHVNAIQ EARRLLNLSR DTAAEMNETV EVISEMFDLQ EPTCLQTRLE LYKQGLRGSL TKLKGPLTMM ASHYKQHCP PTPETSCATQ IITFESFKEN LKDFLLVIPF DCWEPVQEGL NDIFEAQKIE WHEGHHHHHH

UniProtKB: Granulocyte-macrophage colony-stimulating factor

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.2 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 3467 / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.054 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 601878 / Details: topaz extraction
CTF correctionSoftware - Name: cryoSPARC (ver. 4.0.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: ab initio reconstruction job in cryosparc
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0.0) / Number images used: 189815
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.0.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.0.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6bfq


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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