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- EMDB-47130: cryoEM map of avb8/mutant-L-TGF-b1/GARP/28G11 -

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Basic information

Entry
Database: EMDB / ID: EMD-47130
TitlecryoEM map of avb8/mutant-L-TGF-b1/GARP/28G11
Map datamap of avb8/L-TGF-b1/GARP/28G11
Sample
  • Complex: avb8/mutant-L-TGF-b1/GARP/28G11
    • Complex: avb8 complex
    • Complex: mutant-L-TGF-b1/GARP complex
    • Complex: 28G11
KeywordsIntegrin / Complex / SIGNALING PROTEIN
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.22 Å
AuthorsJin M / Cheng Y / Nishimura SL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01HL134183 and R01HL165175 United States
CitationJournal: To Be Published
Title: cryoEM map of avb8/mutant-L-TGF-b1/GARP/28G11
Authors: Jin M / Cheng Y / Nishimura SL
History
DepositionSep 26, 2024-
Header (metadata) releaseAug 6, 2025-
Map releaseAug 6, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47130.png

Downloads & links

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Map

FileDownload / File: emd_47130.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap of avb8/L-TGF-b1/GARP/28G11
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 512 pix.
= 442.368 Å		0.86 Å/pix.
x 512 pix.
= 442.368 Å		0.86 Å/pix.
x 512 pix.
= 442.368 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.864 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.40361768 - 0.716942
Average (Standard dev.)-0.00062284985 (±0.024837023)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 442.368 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map of avb8/L-TGF-b1/GARP/28G11

Fileemd_47130_half_map_1.map
Annotationhalf map of avb8/L-TGF-b1/GARP/28G11
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map of avb8/L-TGF-b1/GARP/28G11

Fileemd_47130_half_map_2.map
Annotationhalf map of avb8/L-TGF-b1/GARP/28G11
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : avb8/mutant-L-TGF-b1/GARP/28G11

EntireName: avb8/mutant-L-TGF-b1/GARP/28G11
Components
  • Complex: avb8/mutant-L-TGF-b1/GARP/28G11
    • Complex: avb8 complex
    • Complex: mutant-L-TGF-b1/GARP complex
    • Complex: 28G11

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Supramolecule #1: avb8/mutant-L-TGF-b1/GARP/28G11

SupramoleculeName: avb8/mutant-L-TGF-b1/GARP/28G11 / type: complex / ID: 1 / Parent: 0
Details: mixture of avb8 and mutant-L-TGF-b1/GARP with 28G11
Molecular weightTheoretical: 150 KDa

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Supramolecule #2: avb8 complex

SupramoleculeName: avb8 complex / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: mutant-L-TGF-b1/GARP complex

SupramoleculeName: mutant-L-TGF-b1/GARP complex / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #4: 28G11

SupramoleculeName: 28G11 / type: complex / ID: 4 / Parent: 1 / Details: commercial antibody
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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Detailsmicroscope model is Thermofisher Glacios 200 kV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 63.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.1 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.22 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 20159
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE

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