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- PDB-9r3s: pro-TGF-beta1 in complex with the third TB Domain from Latent Tra... -

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Basic information

Entry
Database: PDB / ID: 9r3s
Titlepro-TGF-beta1 in complex with the third TB Domain from Latent Transforming Growth Factor-beta Binding Protein-1
Components
  • Latent-transforming growth factor beta-binding protein 1
  • Transforming growth factor beta-1 proprotein
KeywordsSIGNALING PROTEIN / Latent transforming growth factor TGF-beta1 / LTBP1 / mechanobiology / extracellular matrix protein / disulphide / CYTOKINE
Function / homology
Function and homology information


: / establishment of protein localization to extracellular region / frontal suture morphogenesis / Influenza Virus Induced Apoptosis / 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 / positive regulation of primary miRNA processing / morphogenesis of a branching structure / negative regulation of skeletal muscle tissue development ...: / establishment of protein localization to extracellular region / frontal suture morphogenesis / Influenza Virus Induced Apoptosis / 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 / positive regulation of primary miRNA processing / morphogenesis of a branching structure / negative regulation of skeletal muscle tissue development / regulation of striated muscle tissue development / response to laminar fluid shear stress / embryonic liver development / heart valve morphogenesis / macrophage derived foam cell differentiation / TGFBR2 MSI Frameshift Mutants in Cancer / regulation of protein import into nucleus / regulation of blood vessel remodeling / transforming growth factor beta complex / cellular response to acetaldehyde / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of macrophage cytokine production / extracellular matrix assembly / negative regulation of hyaluronan biosynthetic process / microfibril binding / connective tissue replacement involved in inflammatory response wound healing / type III transforming growth factor beta receptor binding / microfibril / myofibroblast differentiation / transforming growth factor beta receptor activity / TGFBR2 Kinase Domain Mutants in Cancer / positive regulation of exit from mitosis / positive regulation of isotype switching to IgA isotypes / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / odontoblast differentiation / positive regulation of mesenchymal stem cell proliferation / positive regulation of receptor signaling pathway via STAT / membrane protein intracellular domain proteolysis / positive regulation of extracellular matrix assembly / negative regulation of myoblast differentiation / TGFBR3 regulates TGF-beta signaling / positive regulation of vasculature development / hyaluronan catabolic process / ATP biosynthetic process / negative regulation of extracellular matrix disassembly / type II transforming growth factor beta receptor binding / cell-cell junction organization / positive regulation of branching involved in ureteric bud morphogenesis / receptor catabolic process / positive regulation of cardiac muscle cell differentiation / response to salt / TGFBR1 LBD Mutants in Cancer / regulatory T cell differentiation / positive regulation of chemotaxis / negative regulation of cell-cell adhesion mediated by cadherin / negative regulation of biomineral tissue development / type I transforming growth factor beta receptor binding / receptor ligand inhibitor activity / positive regulation of vascular permeability / positive regulation of mononuclear cell migration / ureteric bud development / oligodendrocyte development / negative regulation of interleukin-17 production / phosphate-containing compound metabolic process / face morphogenesis / sprouting angiogenesis / response to cholesterol / digestive tract development / neural tube development / odontogenesis of dentin-containing tooth / transforming growth factor beta binding / positive regulation of chemokine (C-X-C motif) ligand 2 production / response to vitamin D / positive regulation of fibroblast migration / aortic valve morphogenesis / RUNX3 regulates CDKN1A transcription / negative regulation of release of sequestered calcium ion into cytosol / negative regulation of fat cell differentiation / positive regulation of regulatory T cell differentiation / Molecules associated with elastic fibres / negative regulation of neuroblast proliferation / Syndecan interactions / cellular response to insulin-like growth factor stimulus / inner ear development / negative regulation of phagocytosis / ventricular cardiac muscle tissue morphogenesis / positive regulation of interleukin-17 production / response to immobilization stress / cellular response to dexamethasone stimulus / negative regulation of cell cycle / chondrocyte differentiation / positive regulation of collagen biosynthetic process / TGF-beta receptor signaling activates SMADs / positive regulation of protein metabolic process / hematopoietic progenitor cell differentiation / negative regulation of blood vessel endothelial cell migration / positive regulation of cell division / positive regulation of SMAD protein signal transduction / epithelial to mesenchymal transition
Similarity search - Function
: / TB domain / TB domain / TGF-beta binding (TB) domain superfamily / TGF-beta binding (TB) domain profile. / Transforming growth factor beta-1 proprotein / Transforming growth factor-beta / Complement Clr-like EGF domain / Complement Clr-like EGF-like / TGF-beta, propeptide ...: / TB domain / TB domain / TGF-beta binding (TB) domain superfamily / TGF-beta binding (TB) domain profile. / Transforming growth factor beta-1 proprotein / Transforming growth factor-beta / Complement Clr-like EGF domain / Complement Clr-like EGF-like / 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. / : / Calcium-binding EGF domain / Cystine-knot cytokine / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
Transforming growth factor beta-1 proprotein / Latent-transforming growth factor beta-binding protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsBiggin, G. / Snee, M. / Godwin, A. / Roseman, A. / Baldock, C.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC) United Kingdom
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis for the contribution of latent TGF beta binding protein to TGF beta latency and activation
Authors: Biggin, G.
History
DepositionMay 6, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jul 22, 2026Data 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
B: Transforming growth factor beta-1 proprotein
A: Transforming growth factor beta-1 proprotein
C: Latent-transforming growth factor beta-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,1048
Polymers132,2443
Non-polymers2,8605
Water73941
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

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Protein , 2 types, 3 molecules BAC

#1: Protein Transforming growth factor beta-1 proprotein


Mass: 42320.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB1, TGFB / Production host: Homo sapiens (human) / Strain (production host): HEK293F / References: UniProt: P01137
#2: Protein Latent-transforming growth factor beta-binding protein 1 / LTBP-1 / Transforming growth factor beta-1-binding protein 1 / TGF-beta1-BP-1


Mass: 47603.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LTBP1 / Production host: Homo sapiens (human) / Strain (production host): HEK293F / References: UniProt: Q14766

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Sugars , 3 types, 5 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#5: 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.: 1 / Source method: obtained synthetically / 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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Non-polymers , 1 types, 41 molecules

#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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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: Complex of pro-Transforming growth factor beta 1 and the third TB Domain from Latent Transforming Growth Factor-beta Binding Protein-1
Type: COMPLEX
Details: This structure represents the resolvable portion of a sample containing pro-TGF-beta 1 disulphide bonded to a region of LTBP1. A fragment of fibrillin-1 was in the sample but fibrillin-1 was not resolved.
Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human) / Cell: HEK293F -EBNA
Buffer solutionpH: 7.4 / Details: 20mM HEPES, 150mM NaCl, pH 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMHEPESHEPES1
2150 mMsodium chlorideNaCl1
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: This sample was monodisperse
Specimen supportGrid material: COPPER / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K / Details: Vitrification carried out in liquid ethane

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 750 nm / Cs: 2.7 mm / C2 aperture diameter: 50 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 3.22 sec. / Electron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 30000
EM imaging opticsEnergyfilter name: TFS Selectris X / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
1Topazparticle selection
2PHENIX1.20.1_4487model refinement
3EPU3.3.1.5184RELimage acquisition
5CTFFINDCTF correction
10cryoSPARCinitial Euler assignment
12cryoSPARCclassification
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 92789 / Details: Automated blob picker - cryoSPARC
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 124397 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
RefinementHighest resolution: 3.06 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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