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- PDB-8rex: CryoEM structure of mouse GARP-lTGFbeta1 in complex with a Fab fr... -

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Basic information

Entry
Database: PDB / ID: 8rex
TitleCryoEM structure of mouse GARP-lTGFbeta1 in complex with a Fab fragment derived from an activating antibody.
Components
  • (Transforming growth factor ...) x 2
  • (mFab LMT-12, ...) x 2
KeywordsIMMUNE SYSTEM / GARP / TGF-B1 / ACTIVATION / TREG / 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 / TGF-beta receptor signaling activates SMADs / cellular response to acetaldehyde / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / 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 / negative regulation of skeletal muscle tissue development / regulation of branching involved in mammary gland duct morphogenesis / frontal suture 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 / 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 / odontoblast differentiation / positive regulation of odontogenesis / Langerhans cell differentiation / negative regulation of macrophage cytokine production / positive regulation of smooth muscle cell differentiation / mononuclear cell proliferation / positive regulation of exit from mitosis / regulation of regulatory T cell differentiation / secondary palate development / 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 / heart valve morphogenesis / retina vasculature development in camera-type eye / mammary gland branching involved in thelarche / bronchiole development / hyaluronan catabolic process / positive regulation of vasculature development / response to laminar fluid shear stress / Platelet degranulation / negative regulation of T cell activation / lens fiber cell differentiation / positive regulation of extracellular matrix assembly / transforming growth factor beta receptor binding / ATP biosynthetic process / positive regulation of branching involved in ureteric bud morphogenesis / type II transforming growth factor beta receptor binding / receptor catabolic process / cell activation / oligodendrocyte development / receptor ligand inhibitor activity / response to salt / type I transforming growth factor beta receptor binding / 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 / mammary gland development / 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 / phosphate-containing compound metabolic process / transforming growth factor beta binding / 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 / neural tube development / positive regulation of regulatory T cell differentiation
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å
AuthorsFelix, J. / Lambert, F. / Marien, L. / van der Woning, B. / Savvides, S.N. / Lucas, S.
Funding support Belgium, 5items
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: 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, P.G. / Savvides, S.N. / Lucas, S.
History
DepositionDec 12, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 25, 2025Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Jun 25, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transforming growth factor beta-1 proprotein
B: Transforming growth factor beta-1 proprotein
C: Transforming growth factor beta-1 proprotein
D: Transforming growth factor beta-1 proprotein
E: Transforming growth factor beta activator LRRC32
F: mFab LMT-12, Light Chain
G: mFab LMT-12, Heavy Chain
H: mFab LMT-12, Heavy Chain
I: mFab LMT-12, Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)354,60914
Polymers352,8939
Non-polymers1,7165
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23250 Å2
ΔGint-80 kcal/mol
Surface area64510 Å2
MethodPISA

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Components

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Transforming growth factor ... , 2 types, 5 molecules ABCDE

#1: Protein
Transforming growth factor beta-1 proprotein


Mass: 44369.926 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tgfb1 / Production host: Homo sapiens (human) / References: UniProt: P04202
#2: Protein Transforming growth factor beta activator LRRC32 / Garpin / Glycoprotein A repetitions predominant / GARP / Leucine-rich repeat-containing protein 32


Mass: 73699.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Lrrc32 / Production host: Homo sapiens (human) / References: UniProt: G3XA59

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Antibody , 2 types, 4 molecules FIGH

#3: Antibody mFab LMT-12, Light Chain


Mass: 24713.555 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#4: Antibody mFab LMT-12, Heavy Chain


Mass: 26143.363 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Sugars , 2 types, 5 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#6: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: mouse GAPR-lTGFbeta1 in complex with Fab LMT-12. / Type: COMPLEX / Entity ID: #2-#4 / Source: RECOMBINANT
Molecular weightValue: 0.2599 MDa / Experimental value: NO
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESC8H18N2O4S1
2150 mMsodium chlorideNaCl1
SpecimenConc.: 0.12 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Grids were acquired via PUXANO (https://puxano.com)
Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R0.6/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: OTHER / Nominal defocus max: 2000 nm / Nominal defocus min: 800 nm
Image recordingAverage exposure time: 3.37 sec. / Electron dose: 61.8 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 13898
Details: A total of 6605 untilted movies were collected followed by 3508 movies at 20 degree tilt.

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Processing

EM software
IDNameVersionCategory
2SerialEMimage acquisition
4cryoSPARC4.2.1CTF correction
7UCSF Chimeramodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIX1.19.2-4158model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 288887 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model building
ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11AF-G3XA59-F11AlphaFoldin silico model
21AF-P040202-F12AlphaFoldin silico model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00412626
ELECTRON MICROSCOPYf_angle_d0.74617161
ELECTRON MICROSCOPYf_dihedral_angle_d4.9861764
ELECTRON MICROSCOPYf_chiral_restr0.0461963
ELECTRON MICROSCOPYf_plane_restr0.0062205

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