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- EMDB-19110: CryoEM structure of human GARP-lTGFbeta1 in complex with a Fab fr... -

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Basic information

Entry
Database: EMDB / ID: EMD-19110
TitleCryoEM structure of human GARP-lTGFbeta1 in complex with a Fab fragment derived from an activating antibody.
Map dataMain map: Sharpened map of human GARP-lTGFbeta1 in complex with Fab LHT-22, used for model refinement. Additional map: DeepEMhancer sharpened map, used for model building and map visualization.
Sample
  • Complex: human GAPR-lTGFbeta1 in complex with Fab LHT-22.
    • Protein or peptide: Transforming growth factor beta activator LRRC32
    • Protein or peptide: hFab LHT-22, Light Chain
    • Protein or peptide: hFab LHT-22, Heavy Chain
  • Protein or peptide: Transforming growth factor beta-1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsGARP / TGF-B1 / ACTIVATION / TREG / IMMUNE SYSTEM / ANTIBODY
Function / homology
Function and homology information


establishment of protein localization to extracellular region / cellular response to acetaldehyde / 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 / Influenza Virus Induced Apoptosis / negative regulation of skeletal muscle tissue development / regulation of branching involved in mammary gland duct morphogenesis ...establishment of protein localization to extracellular region / cellular response to acetaldehyde / 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 / Influenza Virus Induced Apoptosis / negative regulation of skeletal muscle tissue development / regulation of branching involved in mammary gland duct morphogenesis / macrophage derived foam cell differentiation / frontal suture morphogenesis / regulation of enamel mineralization / regulation of cartilage development / TGFBR2 MSI Frameshift Mutants in Cancer / regulation of striated muscle tissue development / regulatory T cell differentiation / tolerance induction to self antigen / regulation of blood vessel remodeling / regulation of protein import into nucleus / embryonic liver development / extracellular matrix assembly / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / columnar/cuboidal epithelial cell maturation / negative regulation of hyaluronan biosynthetic process / type III transforming growth factor beta receptor binding / positive regulation of cardiac muscle cell differentiation / myofibroblast differentiation / odontoblast differentiation / positive regulation of odontogenesis / connective tissue replacement involved in inflammatory response wound healing / Langerhans cell differentiation / negative regulation of macrophage cytokine production / positive regulation of smooth muscle cell differentiation / TGFBR2 Kinase Domain Mutants in Cancer / positive regulation of exit from mitosis / secondary palate development / positive regulation of isotype switching to IgA isotypes / positive regulation of mesenchymal stem cell proliferation / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / membrane protein intracellular domain proteolysis / positive regulation of receptor signaling pathway via STAT / heart valve morphogenesis / retina vasculature development in camera-type eye / TGFBR3 regulates TGF-beta signaling / mammary gland branching involved in thelarche / bronchiole development / hyaluronan catabolic process / positive regulation of vasculature development / response to laminar fluid shear stress / lens fiber cell differentiation / positive regulation of extracellular matrix assembly / negative regulation of extracellular matrix disassembly / ATP biosynthetic process / positive regulation of branching involved in ureteric bud morphogenesis / receptor catabolic process / type II transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / oligodendrocyte development / type I transforming growth factor beta receptor binding / receptor ligand inhibitor activity / response to salt / germ cell migration / negative regulation of biomineral tissue development / positive regulation of mononuclear cell migration / endoderm development / phospholipid homeostasis / negative regulation of myoblast differentiation / positive regulation of chemotaxis / negative regulation of cell-cell adhesion mediated by cadherin / cell-cell junction organization / response to vitamin D / response to cholesterol / positive regulation of vascular permeability / negative regulation of interleukin-17 production / surfactant homeostasis / deubiquitinase activator activity / transforming growth factor beta binding / phosphate-containing compound metabolic process / negative regulation of release of sequestered calcium ion into cytosol / positive regulation of chemokine (C-X-C motif) ligand 2 production / digestive tract development / positive regulation of fibroblast migration / aortic valve morphogenesis / sprouting angiogenesis / negative regulation of ossification / face morphogenesis / RUNX3 regulates CDKN1A transcription / neural tube development / positive regulation of regulatory T cell differentiation / negative regulation of cytokine production / ureteric bud development / Molecules associated with elastic fibres / positive regulation of epidermal growth factor receptor signaling pathway / negative regulation of phagocytosis / positive regulation of peptidyl-tyrosine phosphorylation / negative regulation of neuroblast proliferation / muscle cell cellular homeostasis / cellular response to insulin-like growth factor stimulus
Similarity search - Function
Transforming growth factor beta-1 proprotein / Transforming growth factor-beta / Leucine rich repeat N-terminal domain / 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 / Leucine-rich repeat N-terminal domain ...Transforming growth factor beta-1 proprotein / Transforming growth factor-beta / Leucine rich repeat N-terminal domain / 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 / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / 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-1 proprotein / Transforming growth factor beta activator LRRC32
Similarity search - Component
Biological speciesHomo sapiens (human) / Lama glama (llama)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 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 Belgium
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: To Be Published
Title: TGF-beta1 activating antibodies as novel immunotherapeutics for graft-versus-host disease.
Authors: Lambert F / Felix J / Wautier S / Gaignage M / Dupre E / Marien L / Lesage M / van der Woning B / Coulie PG / Savvides SN / Lucas S
History
DepositionDec 12, 2023-
Header (metadata) releaseMar 26, 2025-
Map releaseMar 26, 2025-
UpdateMar 26, 2025-
Current statusMar 26, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_19110.png

Downloads & links

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Map

FileDownload / File: emd_19110.map.gz / Format: CCP4 / Size: 325 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map: Sharpened map of human GARP-lTGFbeta1 in complex with Fab LHT-22, 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-0.27849072 - 0.47228703
Average (Standard dev.)-0.00011055857 (±0.007858034)
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_19110_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 human GARP-lTGFbeta1 in complex...

Fileemd_19110_additional_1.map
AnnotationDeepEMhancer sharpened map of human GARP-lTGFbeta1 in complex with Fab LHT-22, 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 1 of human GARP-lTGFbeta1 in complex with Fab LHT-22.

Fileemd_19110_half_map_1.map
AnnotationHalf map 1 of human GARP-lTGFbeta1 in complex with Fab LHT-22.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 of human GARP-lTGFbeta1 in complex with Fab LHT-22.

Fileemd_19110_half_map_2.map
AnnotationHalf map 2 of human GARP-lTGFbeta1 in complex with Fab LHT-22.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human GAPR-lTGFbeta1 in complex with Fab LHT-22.

EntireName: human GAPR-lTGFbeta1 in complex with Fab LHT-22.
Components
  • Complex: human GAPR-lTGFbeta1 in complex with Fab LHT-22.
    • Protein or peptide: Transforming growth factor beta activator LRRC32
    • Protein or peptide: hFab LHT-22, Light Chain
    • Protein or peptide: hFab LHT-22, Heavy Chain
  • Protein or peptide: Transforming growth factor beta-1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: human GAPR-lTGFbeta1 in complex with Fab LHT-22.

SupramoleculeName: human GAPR-lTGFbeta1 in complex with Fab LHT-22. / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#4
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 260 kDa/nm

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Macromolecule #1: Transforming growth factor beta-1

MacromoleculeName: Transforming growth factor beta-1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.383051 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MPPSGLRLLP LLLPLLWLLV LTPGRPAAGL STCKTIDMEL VKRKRIEAIR GQILSKLRLA SPPSQGEVPP GPLPEAVLAL YNSTRDRVA GESAEPEPEP EADYYAKEVT RVLMVETHNE IYDKFKQSTH SIYMFFNTSE LREAVPEPVL LSRAELRLLR L KLKVEQHV ...String:
MPPSGLRLLP LLLPLLWLLV LTPGRPAAGL STCKTIDMEL VKRKRIEAIR GQILSKLRLA SPPSQGEVPP GPLPEAVLAL YNSTRDRVA GESAEPEPEP EADYYAKEVT RVLMVETHNE IYDKFKQSTH SIYMFFNTSE LREAVPEPVL LSRAELRLLR L KLKVEQHV ELYQKYSNNS WRYLSNRLLA PSDSPEWLSF DVTGVVRQWL SRGGEIEGFR LSAHCSCDSR DNTLQVDING FT TGRRGDL ATIHGMNRPF LLLMATPLER AQHLQSSRHR RALDTNYCFS STEKNCCVRQ LYIDFRKDLG WKWIHEPKGY HAN FCLGPC PYIWSLDTQY SKVLALYNQH NPGASAAPCC 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: Homo sapiens (human)
Molecular weightTheoretical: 73.261523 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRPQILLLLA LLTLGLAAQH QDKVPCKMVD KKVSCQVLGL LQVPSVLPPD TETLDLSGNQ LRSILASPLG FYTALRHLDL STNEISFLQ PGAFQALTHL EHLSLAHNRL AMATALSAGG LGPLPRVTSL DLSGNSLYSG LLERLLGEAP SLHTLSLAEN S LTRLTRHT ...String:
MRPQILLLLA LLTLGLAAQH QDKVPCKMVD KKVSCQVLGL LQVPSVLPPD TETLDLSGNQ LRSILASPLG FYTALRHLDL STNEISFLQ PGAFQALTHL EHLSLAHNRL AMATALSAGG LGPLPRVTSL DLSGNSLYSG LLERLLGEAP SLHTLSLAEN S LTRLTRHT FRDMPALEQL DLHSNVLMDI EDGAFEGLPR LTHLNLSRNS LTCISDFSLQ QLRVLDLSCN SIEAFQTASQ PQ AEFQLTW LDLRENKLLH FPDLAALPRL IYLNLSNNLI RLPTGPPQDS KGIHAPSEGW SALPLSAPSG NASGRPLSQL LNL DLSYNE IELIPDSFLE HLTSLCFLNL SRNCLRTFEA RRLGSLPCLM LLDLSHNALE TLELGARALG SLRTLLLQGN ALRD LPPYT FANLASLQRL NLQGNRVSPC GGPDEPGPSG CVAFSGITSL RSLSLVDNEI ELLRAGAFLH TPLTELDLSS NPGLE VATG ALGGLEASLE VLALQGNGLM VLQVDLPCFI CLKRLNLAEN RLSHLPAWTQ AVSLEVLDLR NNSFSLLPGS AMGGLE TSL RRLYLQGNPL SCCGNGWLAA QLHQGRVDVD ATQDLICRFS SQEEVSLSHV RPEDCEKGGL KNINLEAAAE NLYFQGA AW SHPQFEKGAA WSHPQFEKGA AWSHPQFEKG AA

UniProtKB: Transforming growth factor beta activator LRRC32

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Macromolecule #3: hFab LHT-22, Light Chain

MacromoleculeName: hFab LHT-22, Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 25.104023 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSQ AVVTQEPSLS VSPGGTVTIT CGLSSGSVTR NNYPDWYQQT PGQAPRLLLY NTVARHSGVP SRFSGSISG NKAALTITGA QPEDEAGYYC ALYMYTGSNN GRVFGGGTLL TVLGQPKAAP SVTLFPPSSE ELQANKATLV C LISDFYPG ...String:
MGWSCIILFL VATATGVHSQ AVVTQEPSLS VSPGGTVTIT CGLSSGSVTR NNYPDWYQQT PGQAPRLLLY NTVARHSGVP SRFSGSISG NKAALTITGA QPEDEAGYYC ALYMYTGSNN GRVFGGGTLL TVLGQPKAAP SVTLFPPSSE ELQANKATLV C LISDFYPG AVTVAWKADS SPVKAGVETT TPSKQSNNKY AASSYLSLTP EQWKSHRSYS CQVTHEGSTV EKTVAPTECS

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Macromolecule #4: hFab LHT-22, Heavy Chain

MacromoleculeName: hFab LHT-22, Heavy Chain / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Lama glama (llama)
Molecular weightTheoretical: 26.268613 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MGWSCIILFL VATATGVHSE LQLVESGGGL VQPGGSLRLS CAASGFTFDD YTMNWVRQAP GKGLEWVSAI RWNGVTTYYA ESMKGRFTV SRDNGQNTLY LQMNSLKAED TAVYYCAKGG SIDLTYGMDY WGKGTLVTVS SASTKGPSVF PLAPSSKSTS G GTAALGCL ...String:
MGWSCIILFL VATATGVHSE LQLVESGGGL VQPGGSLRLS CAASGFTFDD YTMNWVRQAP GKGLEWVSAI RWNGVTTYYA ESMKGRFTV SRDNGQNTLY LQMNSLKAED TAVYYCAKGG SIDLTYGMDY WGKGTLVTVS SASTKGPSVF PLAPSSKSTS G GTAALGCL VKDYFPEPVT VSWNSGALTS GVHTFPAVLQ SSGLYSLSSV VTVPSSSLGT QTYICNVNHK PSNTKVDKKV EP KSCDKTH

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 5 / 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

Concentration0.13 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 / Pretreatment - Type: GLOW DISCHARGE
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: 2 / Number real images: 13898 / Average exposure time: 3.37 sec. / Average electron dose: 61.8 e/Å2
Details: A total of 6678 untilted movies were collected with a defocus of 0.8 to 2 micrometer. Following untilted data collection, 4020 movies were collected at 16 degree tilt and 3200 movies were ...Details: A total of 6678 untilted movies were collected with a defocus of 0.8 to 2 micrometer. Following untilted data collection, 4020 movies were collected at 16 degree tilt and 3200 movies were collected at 35 degree tilt, all using similar microscope settings.
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

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6gff

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 320551
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6gff


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

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

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