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- EMDB-19111: CryoEM structure of mouse GARP-lTGFbeta1 in complex with a Fab fr... -

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Basic information

Entry
Database: EMDB / ID: EMD-19111
TitleCryoEM structure of mouse GARP-lTGFbeta1 in complex with a Fab fragment derived from an activating antibody.
Map dataMain map: Sharpened map of mouse GARP-lTGFbeta1 in complex with Fab LMT-12, used for model refinement. Additional map: DeepEMhancer sharpened map, used for model building and map visualization.
Sample
  • Complex: mouse GAPR-lTGFbeta1 in complex with Fab LMT-12.
    • Protein or peptide: Transforming growth factor beta activator LRRC32
    • Protein or peptide: mFab LMT-12, Light Chain
    • Protein or peptide: mFab LMT-12, Heavy Chain
  • Protein or peptide: Transforming growth factor beta-1 proprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsGARP / TGF-B1 / ACTIVATION / TREG / IMMUNE SYSTEM / ANTIBODY
Function / homology
Function and homology information


regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / Syndecan interactions / TGFBR3 regulates TGF-beta signaling / CD4-positive, CD25-positive, alpha-beta regulatory T cell lineage commitment / RUNX3 regulates CDKN1A transcription / RUNX3 regulates p14-ARF / Molecules associated with elastic fibres / establishment of protein localization to extracellular region / leukocyte proliferation / connective tissue development ...regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation / Syndecan interactions / TGFBR3 regulates TGF-beta signaling / CD4-positive, CD25-positive, alpha-beta regulatory T cell lineage commitment / RUNX3 regulates CDKN1A transcription / RUNX3 regulates p14-ARF / Molecules associated with elastic fibres / establishment of protein localization to extracellular region / leukocyte proliferation / connective tissue development / cellular response to acetaldehyde / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / frontal suture morphogenesis / TGF-beta receptor signaling activates SMADs / adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains / positive regulation of microglia differentiation / regulation of interleukin-23 production / branch elongation involved in mammary gland duct branching / positive regulation of primary miRNA processing / columnar/cuboidal epithelial cell maturation / negative regulation of skeletal muscle tissue development / embryonic liver development / response to laminar fluid shear stress / regulation of branching involved in mammary gland duct morphogenesis / regulation of enamel mineralization / regulation of cartilage development / regulation of striated muscle tissue development / regulatory T cell differentiation / tolerance induction to self antigen / Regulation of RUNX3 expression and activity / regulation of protein import into nucleus / extracellular matrix assembly / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of hyaluronan biosynthetic process / type III transforming growth factor beta receptor binding / positive regulation of cardiac muscle cell differentiation / positive regulation of odontogenesis / Langerhans cell differentiation / positive regulation of smooth muscle cell differentiation / positive regulation of exit from mitosis / odontoblast differentiation / mononuclear cell proliferation / secondary palate development / negative regulation of macrophage cytokine production / positive regulation of isotype switching to IgA isotypes / positive regulation of mesenchymal stem cell proliferation / Cell surface interactions at the vascular wall / membrane protein intracellular domain proteolysis / positive regulation of receptor signaling pathway via STAT / T-helper 17 cell lineage commitment / positive regulation of extracellular matrix assembly / retina vasculature development in camera-type eye / heart valve morphogenesis / mammary gland branching involved in thelarche / bronchiole development / hyaluronan catabolic process / regulation of regulatory T cell differentiation / Platelet degranulation / positive regulation of vasculature development / lens fiber cell differentiation / negative regulation of T cell activation / transforming growth factor beta receptor binding / ATP biosynthetic process / type II transforming growth factor beta receptor binding / receptor catabolic process / cell activation / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of chemotaxis / receptor ligand inhibitor activity / type I transforming growth factor beta receptor binding / positive regulation of mononuclear cell migration / response to salt / germ cell migration / negative regulation of biomineral tissue development / endoderm development / phospholipid homeostasis / negative regulation of cell-cell adhesion mediated by cadherin / negative regulation of myoblast differentiation / positive regulation of vascular permeability / response to cholesterol / mammary gland development / oligodendrocyte development / negative regulation of interleukin-17 production / cell-cell junction organization / phosphate-containing compound metabolic process / surfactant homeostasis / transforming growth factor beta binding / sprouting angiogenesis / deubiquitinase activator activity / negative regulation of release of sequestered calcium ion into cytosol / negative regulation of ossification / positive regulation of chemokine (C-X-C motif) ligand 2 production / aortic valve morphogenesis / digestive tract development / response to vitamin D / face morphogenesis / positive regulation of fibroblast migration / ureteric bud development / neural tube development
Similarity search - Function
Transforming growth factor beta-1 proprotein / Transforming growth factor-beta / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain ...Transforming growth factor beta-1 proprotein / Transforming growth factor-beta / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Leucine rich repeat, ribonuclease inhibitor type / Leucine-rich repeats, bacterial type / Cystine-knot cytokine / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily
Similarity search - Domain/homology
Transforming growth factor beta activator LRRC32 / Transforming growth factor beta-1 proprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsFelix J / Lambert F / Marien L / van der Woning B / Savvides SN / Lucas S
Funding support Belgium, 5 items
OrganizationGrant numberCountry
Other privateFondation contre le Cancer / 2020-079
Other governmentARC / 19/24-098
Fonds National de la Recherche Scientifique (FNRS)PDR / T.0145.21 Belgium
Fonds National de la Recherche Scientifique (FNRS)WELBIO / CR2019A-02R Belgium
Other privateSalus Sanguinis
CitationJournal: Cell Rep / Year: 2025
Title: Antibody-mediated TGF-β1 activation for the treatment of diseases caused by deleterious T cell activity.
Authors: Fanny Lambert / Jan Felix / Séverine Wautier / Emilie Dupré / Mathieu Jamez / Camille Michiels / Mélanie Gaignage / Lore Mariën / Manon Lesage / Bas van der Woning / Savvas N Savvides / Sophie Lucas /
Abstract: Transforming growth factor β1 (TGF-β1) is an immunosuppressive cytokine produced as a latent homodimer, in which mature TGF-β1 is encapsulated and kept inactive by the latency-associated peptide ...Transforming growth factor β1 (TGF-β1) is an immunosuppressive cytokine produced as a latent homodimer, in which mature TGF-β1 is encapsulated and kept inactive by the latency-associated peptide (LAP). The transmembrane protein GARP presents latent TGF-β1 on the surface of regulatory T cells (Tregs) to enable activation and release of mature TGF-β1 by integrins. Here, we derived monoclonal antibodies (mAbs) that activate latent TGF-β1 anchored on cells by a transmembrane protein. Biochemical and structural studies by electron cryo-microscopy (cryo-EM) reveal that such mAb-mediated activation requires bivalent binding close to the LAP dimerization interface and crosslinking of two membrane-bound GARP:TGF-β1 complexes on the same cell or across different cells. Administration of mAbs to mice with graft versus host disease reduced disease severity and increased survival. The therapeutic effect required Tregs. Collectively, our findings demonstrate that activation of membrane-bound TGF-β1 in vivo is achievable with mAbs, introducing new immunotherapeutic options for allo- or autoimmune diseases characterized by deleterious T cell activity insufficiently controlled by Tregs.
History
DepositionDec 12, 2023-
Header (metadata) releaseJun 25, 2025-
Map releaseJun 25, 2025-
UpdateOct 8, 2025-
Current statusOct 8, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19111.png

Downloads & links

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Map

FileDownload / File: emd_19111.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map: Sharpened map of mouse GARP-lTGFbeta1 in complex with Fab LMT-12, used for model refinement. Additional map: DeepEMhancer sharpened map, used for model building and map visualization.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.72 Å/pix.
x 440 pix.
= 316.8 Å		0.72 Å/pix.
x 440 pix.
= 316.8 Å		0.72 Å/pix.
x 440 pix.
= 316.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.72 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.06
Minimum - Maximum-0.3829911 - 0.6301
Average (Standard dev.)0.00006955558 (±0.009160325)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions440440440
Spacing440440440
CellA=B=C: 316.80002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_19111_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: DeepEMhancer sharpened map of mouse GARP-lTGFbeta1 in complex...

Fileemd_19111_additional_1.map
AnnotationDeepEMhancer sharpened map of mouse GARP-lTGFbeta1 in complex with Fab LMT-12, used for model building and map visualization.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 of mouse GARP-lTGFbeta1 in complex with Fab LMT-12.

Fileemd_19111_half_map_1.map
AnnotationHalf map 2 of mouse GARP-lTGFbeta1 in complex with Fab LMT-12.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 of mouse GARP-lTGFbeta1 in complex with Fab LMT-12.

Fileemd_19111_half_map_2.map
AnnotationHalf map 1 of mouse GARP-lTGFbeta1 in complex with Fab LMT-12.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : mouse GAPR-lTGFbeta1 in complex with Fab LMT-12.

EntireName: mouse GAPR-lTGFbeta1 in complex with Fab LMT-12.
Components
  • Complex: mouse GAPR-lTGFbeta1 in complex with Fab LMT-12.
    • Protein or peptide: Transforming growth factor beta activator LRRC32
    • Protein or peptide: mFab LMT-12, Light Chain
    • Protein or peptide: mFab LMT-12, Heavy Chain
  • Protein or peptide: Transforming growth factor beta-1 proprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: mouse GAPR-lTGFbeta1 in complex with Fab LMT-12.

SupramoleculeName: mouse GAPR-lTGFbeta1 in complex with Fab LMT-12. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#4
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 259.9 KDa

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Macromolecule #1: Transforming growth factor beta-1 proprotein

MacromoleculeName: Transforming growth factor beta-1 proprotein / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 44.369926 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPPSGLRLLP LLLPLPWLLV LTPGRPAAGL STCKTIDMEL VKRKRIEAIR GQILSKLRLA SPPSQGEVPP GPLPEAVLAL YNSTRDRVA GESADPEPEP EADYYAKEVT RVLMVDRNNA IYEKTKDISH SIYMFFNTSD IREAVPEPPL LSRAELRLQR L KSSVEQHV ...String:
MPPSGLRLLP LLLPLPWLLV LTPGRPAAGL STCKTIDMEL VKRKRIEAIR GQILSKLRLA SPPSQGEVPP GPLPEAVLAL YNSTRDRVA GESADPEPEP EADYYAKEVT RVLMVDRNNA IYEKTKDISH SIYMFFNTSD IREAVPEPPL LSRAELRLQR L KSSVEQHV ELYQKYSNNS WRYLGNRLLT PTDTPEWLSF DVTGVVRQWL NQGDGIQGFR FSAHCSCDSK DNKLHVEING IS PKRRGDL GTIHDMNRPF LLLMATPLER AQHLHSSRHR RALDTNYCFS STEKNCCVRQ LYIDFRKDLG WKWIHEPKGY HAN FCLGPC PYIWSLDTQY SKVLALYNQH NPGASASPCC VPQALEPLPI VYYVGRKPKV EQLSNMIVRS CKCS

UniProtKB: Transforming growth factor beta-1 proprotein

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Macromolecule #2: Transforming growth factor beta activator LRRC32

MacromoleculeName: Transforming growth factor beta activator LRRC32 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 73.699914 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSHQILLLLA MLTLGLAISQ RREQVPCRTV NKEALCHGLG LLQVPSVLSL DIQALYLSGN QLQSILVSPL GFYTALRHLD LSDNQISFL QAGVFQALPY LEHLNLAHNR LATGMALNSG GLGRLPLLVS LDLSGNSLHG NLVERLLGET PRLRTLSLAE N SLTRLARH ...String:
MSHQILLLLA MLTLGLAISQ RREQVPCRTV NKEALCHGLG LLQVPSVLSL DIQALYLSGN QLQSILVSPL GFYTALRHLD LSDNQISFL QAGVFQALPY LEHLNLAHNR LATGMALNSG GLGRLPLLVS LDLSGNSLHG NLVERLLGET PRLRTLSLAE N SLTRLARH TFWGMPAVEQ LDLHSNVLMD IEDGAFEALP HLTHLNLSRN SLTCISDFSL QQLQVLDLSC NSIEAFQTAP EP QAQFQLA WLDLRENKLL HFPDLAVFPR LIYLNVSNNL IQLPAGLPRG SEDLHAPSEG WSASPLSNPS RNASTHPLSQ LLN LDLSYN EIELVPASFL EHLTSLRFLN LSRNCLRSFE ARQVDSLPCL VLLDLSHNVL EALELGTKVL GSLQTLLLQD NALQ ELPPY TFASLASLQR LNLQGNQVSP CGGPAEPGPP GCVDFSGIPT LHVLNMAGNS MGMLRAGSFL HTPLTELDLS TNPGL DVAT GALVGLEASL EVLELQGNGL TVLRVDLPCF LRLKRLNLAE NQLSHLPAWT RAVSLEVLDL RNNSFSLLPG NAMGGL ETS LRRLYLQGNP LSCCGNGWLA AQLHQGRVDV DATQDLICRF GSQEELSLSL VRPEDCEKGG LKNVNLEAAA ENLYFQG AA WSHPQFEKGA AWSHPQFEKG AAWSHPQFEK GAA

UniProtKB: Transforming growth factor beta activator LRRC32

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Macromolecule #3: mFab LMT-12, Light Chain

MacromoleculeName: mFab LMT-12, Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 24.713555 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSQ PALTQLSSMS GSPGQTVTIT CTGSSSNIGG GYYLNWYQQL PGAAPKLVIY NANNRASGVP DRFSGSKSG NLASLTITGL QAEDEAVYFC GCYDSSLSSV VFGGGTHLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL I SDFYPGAV ...String:
MGWSCIILFL VATATGVHSQ PALTQLSSMS GSPGQTVTIT CTGSSSNIGG GYYLNWYQQL PGAAPKLVIY NANNRASGVP DRFSGSKSG NLASLTITGL QAEDEAVYFC GCYDSSLSSV VFGGGTHLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL I SDFYPGAV TVAWKADSSP VKAGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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Macromolecule #4: mFab LMT-12, Heavy Chain

MacromoleculeName: mFab LMT-12, Heavy Chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 26.143363 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSE VQLVESGGGL VQPGGSLRLS CAASGFTFSS YYMYWVRQAP GKGLEWVSGT SIGGGSTWYA DSVKGRFTI SRDNAKNTLY LQMNNLKSED TAVYYCAKDL NSRSYKGMGD WGQGTQVTVS SASTKGPSVF PLAPSSKSTS G GTAALGCL ...String:
MGWSCIILFL VATATGVHSE VQLVESGGGL VQPGGSLRLS CAASGFTFSS YYMYWVRQAP GKGLEWVSGT SIGGGSTWYA DSVKGRFTI SRDNAKNTLY LQMNNLKSED TAVYYCAKDL NSRSYKGMGD WGQGTQVTVS SASTKGPSVF PLAPSSKSTS G GTAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EP KSCDKTH

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Macromolecule #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 2 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration0.12 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
GridModel: Quantifoil R0.6/1 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE / Support film - topology: CONTINUOUS / Support film - Film thickness: 1
Details: Grids were acquired via PUXANO (https://puxano.com)
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 13898 / Average exposure time: 3.37 sec. / Average electron dose: 61.8 e/Å2
Details: A total of 6605 untilted movies were collected followed by 3508 movies at 20 degree tilt.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Alphafold models of mouse GARP and mouse transforming growth factor beta 1 pro-protein
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 288887
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 2 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

9-f1

source_name: AlphaFold, initial_model_type: in silico model

2-f1

source_name: AlphaFold, initial_model_type: in silico model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8rex:
CryoEM structure of mouse GARP-lTGFbeta1 in complex with a Fab fragment derived from an activating antibody.

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