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- EMDB-61568: human GM-CSF with Fabs from autoantibodies, F1 and BD. -

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Basic information

Entry
Database: EMDB / ID: EMD-61568
Titlehuman GM-CSF with Fabs from autoantibodies, F1 and BD.
Map data
Sample
  • Complex: the complex of human GM-CSF with Fabs from its autoantibodies, F1 and BD.
    • Complex: human GM-CSF
    • Complex: F1 autoantibody for human GM-CSF
    • Complex: BD autoantibody for human GM-CSF
KeywordsAutoimmune pulmonary alveolar proteinosis / autoantibody / IMMUNE SYSTEM
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 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_61568.png

Downloads & links

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Map

FileDownload / File: emd_61568.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)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.0125 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-2.3641918 - 3.5795176
Average (Standard dev.)-0.0012752231 (±0.05820801)
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_61568_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_61568_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_61568_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

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 BD.
Components
  • Complex: the complex of human GM-CSF with Fabs from its autoantibodies, F1 and BD.
    • Complex: human GM-CSF
    • Complex: F1 autoantibody for human GM-CSF
    • Complex: BD autoantibody for human GM-CSF

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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 BD.
type: complex / ID: 1 / Parent: 0
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
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
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: BD autoantibody for human GM-CSF

SupramoleculeName: BD autoantibody for human GM-CSF / type: complex / ID: 4 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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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: 10764 / 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: 0.032 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: 939335 / 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: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0.0) / Number images used: 50310
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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