+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16459 | |||||||||
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Title | Cryo-EM Map of the latTGF-beta 12G2B4 Fab complex | |||||||||
Map data | Cryo-EM map sharp | |||||||||
Sample |
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Keywords | Fab-complex / GARP / lat-TGF-beta / IMMUNE SYSTEM | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Ebenhoch R / Nar H | |||||||||
Funding support | 1 items
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Citation | Journal: Immunohorizons / Year: 2023 Title: Anti-GARP Antibodies Inhibit Release of TGF-β by Regulatory T Cells via Different Modes of Action, but Do Not Influence Their Function In Vitro. Authors: Frederik H Igney / Rebecca Ebenhoch / Felix Schiele / Herbert Nar / Abstract: Regulatory T cells (Treg) play a critical role in controlling immune responses in diseases such as cancer or autoimmunity. Activated Treg express the membrane protein GARP (LRRC32) in complex with ...Regulatory T cells (Treg) play a critical role in controlling immune responses in diseases such as cancer or autoimmunity. Activated Treg express the membrane protein GARP (LRRC32) in complex with the latent form of the immunosuppressive cytokine TGF-β (L-TGF-β). In this study, we confirmed that active TGF-β was generated from its latent form in an integrin-dependent manner and induced TGF-β receptor signaling in activated human Treg. We studied a series of Abs targeting the L-TGF-β/GARP complex with distinct binding modes. We found that TGF-β receptor signaling could be inhibited by anti-TGF-β and by some, but not all, Abs against the L-TGF-β/GARP complex. Cryogenic electron microscopy structures of three L-TGF-β/GARP complex-targeting Abs revealed their distinct epitopes and allowed us to elucidate how they achieve blockade of TGF-β activation. Three different modes of action were identified, including a novel unusual mechanism of a GARP-binding Ab. However, blockade of GARP or TGF-β by Abs did not influence the suppressive activity of human Treg in vitro. We were also not able to confirm a prominent role of GARP in other functions of human Treg, such as FOXP3 induction and Treg stability. These data show that the GARP/TGF-β axis can be targeted pharmacologically in different ways, but further studies are necessary to understand its complexity and to unleash its therapeutic potential. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16459.map.gz | 96.9 MB | EMDB map data format | |
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Header (meta data) | emd-16459-v30.xml emd-16459.xml | 12.1 KB 12.1 KB | Display Display | EMDB header |
Images | emd_16459.png | 68.1 KB | ||
Filedesc metadata | emd-16459.cif.gz | 3.9 KB | ||
Others | emd_16459_half_map_1.map.gz emd_16459_half_map_2.map.gz | 95.3 MB 95.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16459 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16459 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_16459.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM map sharp | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Cryo-EM half map B
File | emd_16459_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM half map A
File | emd_16459_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM half map A | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : latTGF-beta in complex with Fab 28G11
Entire | Name: latTGF-beta in complex with Fab 28G11 |
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Components |
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-Supramolecule #1: latTGF-beta in complex with Fab 28G11
Supramolecule | Name: latTGF-beta in complex with Fab 28G11 / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 4 K / Instrument: LEICA EM GP |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY PDB model - PDB ID: |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 613675 |