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- EMDB-53558: pro-TGF-beta1 in complex with the third TB Domain from Latent Tra... -

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Basic information

Entry
Database: EMDB / ID: EMD-53558
Titlepro-TGF-beta1 in complex with the third TB Domain from Latent Transforming Growth Factor-beta Binding Protein-1
Map data
Sample
  • Complex: Complex of pro-Transforming growth factor beta 1 and the third TB Domain from Latent Transforming Growth Factor-beta Binding Protein-1
    • Protein or peptide: Transforming growth factor beta-1 proprotein
    • Protein or peptide: Latent-transforming growth factor beta-binding protein 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water
KeywordsLatent transforming growth factor TGF-beta1 / LTBP1 / mechanobiology / extracellular matrix protein / disulphide / CYTOKINE / SIGNALING PROTEIN
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.06 Å
AuthorsBiggin G / Snee M / Godwin A / Roseman A / Baldock C
Funding support United Kingdom, 1 items
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, 2025-
Header (metadata) releaseJul 22, 2026-
Map releaseJul 22, 2026-
UpdateJul 22, 2026-
Current statusJul 22, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53558.png

Downloads & links

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Map

FileDownload / File: emd_53558.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å		1.08 Å/pix.
x 256 pix.
= 276.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.08 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0821
Minimum - Maximum-0.56432754 - 1.2312499
Average (Standard dev.)-0.00044123438 (±0.02005487)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_53558_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53558_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of pro-Transforming growth factor beta 1 and the third TB...

EntireName: Complex of pro-Transforming growth factor beta 1 and the third TB Domain from Latent Transforming Growth Factor-beta Binding Protein-1
Components
  • Complex: Complex of pro-Transforming growth factor beta 1 and the third TB Domain from Latent Transforming Growth Factor-beta Binding Protein-1
    • Protein or peptide: Transforming growth factor beta-1 proprotein
    • Protein or peptide: Latent-transforming growth factor beta-binding protein 1
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: water

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Supramolecule #1: Complex of pro-Transforming growth factor beta 1 and the third TB...

SupramoleculeName: Complex of pro-Transforming growth factor beta 1 and the third TB Domain from Latent Transforming Growth Factor-beta Binding Protein-1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
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.
Source (natural)Organism: Homo sapiens (human)

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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: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 42.320191 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DYKDDDDKLS TCKTIDMELV KRKRIEAIRG QILSKLRLAS PPSQGEVPPG PLPEAVLALY NSTRDRVAGE SAEPEPEPEA DYYAKEVTR VLMVETHNEI YDKFKQSTHS IYMFFNTSEL REAVPEPVLL SRAELRLLRL KLKVEQHVEL YQKYSNNSWR Y LSNRLLAP ...String:
DYKDDDDKLS TCKTIDMELV KRKRIEAIRG QILSKLRLAS PPSQGEVPPG PLPEAVLALY NSTRDRVAGE SAEPEPEPEA DYYAKEVTR VLMVETHNEI YDKFKQSTHS IYMFFNTSEL REAVPEPVLL SRAELRLLRL KLKVEQHVEL YQKYSNNSWR Y LSNRLLAP SDSPEWLSFD VTGVVRQWLS RGGEIEGFRL SAHCSCDSRD NTLQVDINGF TTGRRGDLAT IHGMNRPFLL LM ATPLERA QHLQSSRHRR ALDTNYCFSS TEKNCCVRQL YIDFRKDLGW KWIHEPKGYH ANFCLGPCPY IWSLDTQYSK VLA LYNQHN PGASAAPCCV PQALEPLPIV YYVGRKPKVE QLSNMIVRSC KCS

UniProtKB: Transforming growth factor beta-1 proprotein

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Macromolecule #2: Latent-transforming growth factor beta-binding protein 1

MacromoleculeName: Latent-transforming growth factor beta-binding protein 1
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.603562 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: APLALDVDVD QPKEEKKECY YNLNDASLCD NVLAPNVTKQ ECCCTSGVGW GDNCEIFPCP VLGTAEFTEM CPKGKGFVPA GESSSEAGG ENYKDADECL LFGQEICKNG FCLNTRPGYE CYCKQGTYYD PVKLQCFDMD ECQDPSSCID GQCVNTEGSY N CFCTHPMV ...String:
APLALDVDVD QPKEEKKECY YNLNDASLCD NVLAPNVTKQ ECCCTSGVGW GDNCEIFPCP VLGTAEFTEM CPKGKGFVPA GESSSEAGG ENYKDADECL LFGQEICKNG FCLNTRPGYE CYCKQGTYYD PVKLQCFDMD ECQDPSSCID GQCVNTEGSY N CFCTHPMV LDASEKRCIR PAESNEQIEE TDVYQDLCWE HLSDEYVCSR PLVGKQTTYT ECCCLYGEAW GMQCALCPLK DS DDYAQLC NIPVTGRRQP YGRDALVDFS EQYTPEADPY FIQDRFLNSF EELQAEECGI LNGCENGRCV RVQEGYTCDC FDG YHLDTA KMTCVDVNEC DELNNRMSLC KNAKCINTDG SYKCLCLPGY VPSDKPNYCT PLNTALNLEK DSDLTGGGGS GGGG SGGGG SAWSHPQFEK GGGSGGGSGG SAWSHPQFEK

UniProtKB: Latent-transforming growth factor beta-binding protein 1

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

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

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 41 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration1 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
20.0 mMHEPESHEPES
150.0 mMNaClsodium chloride

Details: 20mM HEPES, 150mM NaCl, pH 7.4
GridModel: Quantifoil R2/2 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK II / Details: Vitrification carried out in liquid ethane.
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 30000 / Average exposure time: 3.22 sec. / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.75 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 92789 / Details: Automated blob picker - cryoSPARC
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 124397
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Details: ab initio
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 50 / Avg.num./class: 1670 / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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