+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16460 | |||||||||
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Title | Cryo-EM Map of the latTGF-beta 28G11 Fab complex | |||||||||
Map data | Sharpened map | |||||||||
Sample |
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Function / homology | Function and homology information : / positive regulation of primary miRNA processing / positive regulation of microglia differentiation / Influenza Virus Induced Apoptosis / negative regulation of skeletal muscle tissue development / TGFBR2 MSI Frameshift Mutants in Cancer / regulatory T cell differentiation / regulation of blood vessel remodeling / regulation of striated muscle tissue development / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target ...: / positive regulation of primary miRNA processing / positive regulation of microglia differentiation / Influenza Virus Induced Apoptosis / negative regulation of skeletal muscle tissue development / TGFBR2 MSI Frameshift Mutants in Cancer / regulatory T cell differentiation / regulation of blood vessel remodeling / regulation of striated muscle tissue development / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / regulation of protein import into nucleus / extracellular matrix assembly / embryonic liver development / type III transforming growth factor beta receptor binding / negative regulation of hyaluronan biosynthetic process / positive regulation of cardiac muscle cell differentiation / myofibroblast differentiation / connective tissue replacement involved in inflammatory response wound healing / odontoblast differentiation / negative regulation of macrophage cytokine production / positive regulation of receptor signaling pathway via STAT / TGFBR2 Kinase Domain Mutants in Cancer / : / positive regulation of isotype switching to IgA isotypes / positive regulation of mesenchymal stem cell proliferation / secondary palate development / membrane protein intracellular domain proteolysis / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / heart valve morphogenesis / positive regulation of vasculature development / hyaluronan catabolic process / regulation of transforming growth factor beta receptor signaling pathway / ATP biosynthetic process / receptor catabolic process / negative regulation of extracellular matrix disassembly / positive regulation of extracellular matrix assembly / type II transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / positive regulation of chemotaxis / negative regulation of biomineral tissue development / type I transforming growth factor beta receptor binding / cell-cell junction organization / negative regulation of myoblast differentiation / positive regulation of vascular permeability / deubiquitinase activator activity / transforming growth factor beta binding / response to cholesterol / positive regulation of endothelial cell apoptotic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / aortic valve morphogenesis / positive regulation of fibroblast migration / phosphate-containing compound metabolic process / negative regulation of protein localization to plasma membrane / sprouting angiogenesis / neural tube development / Molecules associated with elastic fibres / RUNX3 regulates CDKN1A transcription / negative regulation of cytokine production / positive regulation of epidermal growth factor receptor signaling pathway / ventricular cardiac muscle tissue morphogenesis / macrophage derived foam cell differentiation / negative regulation of fat cell differentiation / Syndecan interactions / negative regulation of cell-cell adhesion / positive regulation of interleukin-17 production / TGF-beta receptor signaling activates SMADs / plasma membrane => GO:0005886 / negative regulation of activated T cell proliferation / negative regulation of cell differentiation / positive regulation of SMAD protein signal transduction / RUNX3 regulates p14-ARF / positive regulation of cell division / cellular response to low-density lipoprotein particle stimulus / negative regulation of blood vessel endothelial cell migration / negative regulation of cell cycle / ECM proteoglycans / positive regulation of vascular endothelial growth factor production / positive regulation of collagen biosynthetic process / epithelial to mesenchymal transition / positive regulation of epithelial to mesenchymal transition / positive regulation of blood vessel endothelial cell migration / vasculogenesis / lymph node development / chondrocyte differentiation / hematopoietic progenitor cell differentiation / salivary gland morphogenesis / extrinsic apoptotic signaling pathway / positive regulation of protein dephosphorylation / regulation of cell migration / cellular response to transforming growth factor beta stimulus / antigen binding / positive regulation of protein metabolic process / protein export from nucleus / Downregulation of TGF-beta receptor signaling / extracellular matrix / transforming growth factor beta receptor signaling pathway / positive regulation of superoxide anion generation / negative regulation of miRNA transcription / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 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_16460.map.gz | 8.3 MB | EMDB map data format | |
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Header (meta data) | emd-16460-v30.xml emd-16460.xml | 18 KB 18 KB | Display Display | EMDB header |
Images | emd_16460.png | 73 KB | ||
Others | emd_16460_half_map_1.map.gz emd_16460_half_map_2.map.gz | 95.5 MB 95.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16460 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16460 | HTTPS FTP |
-Related structure data
Related structure data | 8c7hMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_16460.map.gz / Format: CCP4 / Size: 8.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. generated in cubic-lattice coordinate | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Half map B
File | emd_16460_half_map_1.map | ||||||||||||
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Annotation | Half map B | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map A
File | emd_16460_half_map_2.map | ||||||||||||
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Annotation | 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 / Chimera: Yes / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Transforming growth factor beta-1
Macromolecule | Name: Transforming growth factor beta-1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 28.531488 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: LSTCKTIDME LVKRKRIEAI RGQILSKLRL ASPPSQGEVP PGPLPEAVLA LYNSTRDRVA GESAEPEPEP EADYYAKEVT RVLMVETHN EIYDKFKQST HSIYMFFNTS ELREAVPEPV LLSRAELRLL RLKLKVEQHV ELYQKYSNNS WRYLSNRLLA P SDSPEWLS ...String: LSTCKTIDME LVKRKRIEAI RGQILSKLRL ASPPSQGEVP PGPLPEAVLA LYNSTRDRVA GESAEPEPEP EADYYAKEVT RVLMVETHN EIYDKFKQST HSIYMFFNTS ELREAVPEPV LLSRAELRLL RLKLKVEQHV ELYQKYSNNS WRYLSNRLLA P SDSPEWLS FDVTGVVRQW LSRGGEIEGF RLSAHCSCDS RDNTLQVDIN GFTTGRRGDL ATIHGMNRPF LLLMATPLER AQ HLQSSRH RR |
-Macromolecule #2: Transforming growth factor beta-1
Macromolecule | Name: Transforming growth factor beta-1 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 12.809812 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: ALDTNYCFSS TEKNCCVRQL YIDFRKDLGW KWIHEPKGYH ANFCLGPCPY IWSLDTQYSK VLALYNQHNP GASAAPCCVP QALEPLPIV YYVGRKPKVE QLSNMIVRSC KCS |
-Macromolecule #3: Transforming growth factor beta activator LRRC32
Macromolecule | Name: Transforming growth factor beta activator LRRC32 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 65.358488 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: HQDKVPCKMV DKKVSCQVLG LLQVPSVLPP DTETLDLSGN QLRSILASPL GFYTALRHLD LSTNEISFLQ PGAFQALTHL EHLSLAHNR LAMATALSAG GLGPLPRVTS LDLSGNSLYS GLLERLLGEA PSLHTLSLAE NSLTRLTRHT FRDMPALEQL D LHSNVLMD ...String: HQDKVPCKMV DKKVSCQVLG LLQVPSVLPP DTETLDLSGN QLRSILASPL GFYTALRHLD LSTNEISFLQ PGAFQALTHL EHLSLAHNR LAMATALSAG GLGPLPRVTS LDLSGNSLYS GLLERLLGEA PSLHTLSLAE NSLTRLTRHT FRDMPALEQL D LHSNVLMD IEDGAFEGLP RLTHLNLSRN SLTCISDFSL QQLRVLDLSC NSIEAFQTAS QPQAEFQLTW LDLRENKLLH FP DLAALPR LIYLNLSNNL IRLPTGPPQD SKGIHAPSEG WSALPLSAPS GNASGRPLSQ LLNLDLSYNE IELIPDSFLE HLT SLCFLN LSRNCLRTFE ARRLGSLPCL MLLDLSHNAL ETLELGARAL GSLRTLLLQG NALRDLPPYT FANLASLQRL NLQG NRVSP CGGPDEPGPS GCVAFSGITS LRSLSLVDNE IELLRAGAFL HTPLTELDLS SNPGLEVATG ALGGLEASLE VLALQ GNGL MVLQVDLPCF ICLKRLNLAE NRLSHLPAWT QAVSLEVLDL RNNSFSLLPG SAMGGLETSL RRLYLQGNPL SCCGNG WLA AQLHQGRVDV DATQDLICRF SSQEEVSLSH VRPEDCEK |
-Macromolecule #4: 28G11 Fab heavy chain
Macromolecule | Name: 28G11 Fab heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 24.529211 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: EVQLVQPGAE LRNSGASVKV SCKASGYRFT SYYIDWVRQA PGQGLEWMGR IDPEDGGTKY AQKFQGRVTF TADTSTSTAY VELSSLRSE DTAVYYCARN EWETVVVGDL MYEYEYWGQG TQVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN ...String: EVQLVQPGAE LRNSGASVKV SCKASGYRFT SYYIDWVRQA PGQGLEWMGR IDPEDGGTKY AQKFQGRVTF TADTSTSTAY VELSSLRSE DTAVYYCARN EWETVVVGDL MYEYEYWGQG TQVTVSSAST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKRVEPK |
-Macromolecule #5: 28G11 Fab light chain
Macromolecule | Name: 28G11 Fab light chain / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 23.091578 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DIQMTQSPSS LSASLGDRVT ITCQASQSIS SYLAWYQQKP GQAPNILIYG ASRLKTGVPS RFSGSGSGTS FTLTISGLEA EDAGTYYCQ QYASVPVTFG QGTKVELKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String: DIQMTQSPSS LSASLGDRVT ITCQASQSIS SYLAWYQQKP GQAPNILIYG ASRLKTGVPS RFSGSGSGTS FTLTISGLEA EDAGTYYCQ QYASVPVTFG QGTKVELKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC |
-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 / Pretreatment - Type: GLOW DISCHARGE |
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: 2.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 418886 |