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- PDB-3kfd: Ternary complex of TGF-b1 reveals isoform-specific ligand recogni... -

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Basic information

Entry
Database: PDB / ID: 3kfd
TitleTernary complex of TGF-b1 reveals isoform-specific ligand recognition and receptor recruitment in the superfamily
Components
  • TGF-beta receptor type-1
  • TGF-beta receptor type-2
  • Transforming growth factor beta-1
KeywordsCYTOKINE/CYTOKINE RECEPTOR / TGF-beta / TGF-b1 / TGF-beta receptor type-1 / TGF-beta receptor type-2 / TbRII / TbRI / Growth factor / Receptor / Serine/threonine-protein kinase / CYTOKINE-CYTOKINE RECEPTOR complex
Function / homology
Function and homology information


positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / inferior endocardial cushion morphogenesis / transforming growth factor beta receptor activity, type II / 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 / transforming growth factor beta complex ...positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / inferior endocardial cushion morphogenesis / transforming growth factor beta receptor activity, type II / 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 / transforming growth factor beta complex / positive regulation of primary miRNA processing / morphogenesis of a branching structure / negative regulation of skeletal muscle tissue development / response to laminar fluid shear stress / extracellular structure organization / epicardium morphogenesis / tricuspid valve morphogenesis / vascular endothelial cell proliferation / embryonic liver development / transforming growth factor beta ligand-receptor complex / macrophage derived foam cell differentiation / TGFBR2 MSI Frameshift Mutants in Cancer / regulation of striated muscle tissue development / parathyroid gland development / positive regulation of T cell tolerance induction / miRNA transport / regulation of protein import into nucleus / regulation of blood vessel remodeling / regulation of cardiac muscle cell proliferation / cellular response to acetaldehyde / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / extracellular matrix assembly / negative regulation of hyaluronan biosynthetic process / type III transforming growth factor beta receptor binding / aorta morphogenesis / myofibroblast differentiation / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / negative regulation of macrophage cytokine production / connective tissue replacement involved in inflammatory response wound healing / transforming growth factor beta receptor activity / TGFBR2 Kinase Domain Mutants in Cancer / positive regulation of exit from mitosis / cardiac left ventricle morphogenesis / trophoblast cell migration / secondary palate development / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / angiogenesis involved in coronary vascular morphogenesis / odontoblast differentiation / positive regulation of mesenchymal stem cell proliferation / endocardial cushion fusion / positive regulation of receptor signaling pathway via STAT / membrane protein intracellular domain proteolysis / ventricular compact myocardium morphogenesis / positive regulation of isotype switching to IgA isotypes / positive regulation of extracellular matrix assembly / positive regulation of tight junction disassembly / positive regulation of NK T cell differentiation / cardiac epithelial to mesenchymal transition / membranous septum morphogenesis / transforming growth factor beta receptor activity, type I / mesenchymal cell differentiation / heart valve morphogenesis / TGFBR3 regulates TGF-beta signaling / neuron fate commitment / positive regulation of vasculature development / hyaluronan catabolic process / activin receptor activity, type I / activin receptor complex / primordial germ cell migration / regulation of epithelial to mesenchymal transition / ATP biosynthetic process / negative regulation of extracellular matrix disassembly / pharyngeal system development / type II transforming growth factor beta receptor binding / receptor protein serine/threonine kinase / activin binding / myeloid dendritic cell differentiation / positive regulation of branching involved in ureteric bud morphogenesis / transmembrane receptor protein serine/threonine kinase activity / receptor catabolic process / positive regulation of cardiac muscle cell differentiation / TGFBR1 LBD Mutants in Cancer / cell-cell junction organization / negative regulation of myoblast differentiation / response to salt / regulatory T cell differentiation / filopodium assembly / coronary artery morphogenesis / embryonic cranial skeleton morphogenesis / negative regulation of cell-cell adhesion mediated by cadherin / ventricular trabecula myocardium morphogenesis / glycosaminoglycan binding / activin receptor signaling pathway / negative regulation of biomineral tissue development / type I transforming growth factor beta receptor binding / positive regulation of CD4-positive, alpha-beta T cell proliferation / anterior/posterior pattern specification / positive regulation of chemotaxis / positive regulation of vascular permeability
Similarity search - Function
Transforming growth factor beta receptor 2 ectodomain / Transforming growth factor-beta receptor, type II / Transforming growth factor beta receptor 2 ectodomain / Transforming growth factor beta-1 proprotein / Transforming growth factor-beta / GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / TGF-beta, propeptide ...Transforming growth factor beta receptor 2 ectodomain / Transforming growth factor-beta receptor, type II / Transforming growth factor beta receptor 2 ectodomain / Transforming growth factor beta-1 proprotein / Transforming growth factor-beta / GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / TGF-beta, propeptide / TGF-beta propeptide / Activin types I and II receptor domain / Transforming growth factor beta, conserved site / Activin types I and II receptor domain / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / CD59 / CD59 / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Ser/Thr protein kinase, TGFB receptor / Cystine-knot cytokine / Snake toxin-like superfamily / Ribbon / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Mainly Beta
Similarity search - Domain/homology
Transforming growth factor beta-1 proprotein / TGF-beta receptor type-1 / TGF-beta receptor type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.995 Å
AuthorsRadaev, S. / Sun, P.D.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: Ternary complex of transforming growth factor-beta1 reveals isoform-specific ligand recognition and receptor recruitment in the superfamily.
Authors: Radaev, S. / Zou, Z. / Huang, T. / Lafer, E.M. / Hinck, A.P. / Sun, P.D.
History
DepositionOct 27, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
B: Transforming growth factor beta-1
E: TGF-beta receptor type-2
F: TGF-beta receptor type-2
I: TGF-beta receptor type-1
J: TGF-beta receptor type-1
C: Transforming growth factor beta-1
D: Transforming growth factor beta-1
G: TGF-beta receptor type-2
H: TGF-beta receptor type-2
K: TGF-beta receptor type-1
L: TGF-beta receptor type-1


Theoretical massNumber of molelcules
Total (without water)141,46212
Polymers141,46212
Non-polymers00
Water1,67593
1
A: Transforming growth factor beta-1
B: Transforming growth factor beta-1
E: TGF-beta receptor type-2
F: TGF-beta receptor type-2
I: TGF-beta receptor type-1
J: TGF-beta receptor type-1


Theoretical massNumber of molelcules
Total (without water)70,7316
Polymers70,7316
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9310 Å2
ΔGint-64 kcal/mol
Surface area28420 Å2
MethodPISA
2
C: Transforming growth factor beta-1
D: Transforming growth factor beta-1
G: TGF-beta receptor type-2
H: TGF-beta receptor type-2
K: TGF-beta receptor type-1
L: TGF-beta receptor type-1


Theoretical massNumber of molelcules
Total (without water)70,7316
Polymers70,7316
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9400 Å2
ΔGint-66 kcal/mol
Surface area28470 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20380 Å2
ΔGint-131 kcal/mol
Surface area55220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.70, 99.35, 102.7
Angle α, β, γ (deg.)64.01, 84.47, 84.34
Int Tables number1
Space group name H-MP1
DetailsHexamer

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Components

#1: Protein
Transforming growth factor beta-1 / TGF-beta-1 / Latency-associated peptide / LAP


Mass: 12809.812 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB1, TGFB / Organ (production host): ovary cells / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO-lec3.2.8.1 / References: UniProt: P01137
#2: Protein
TGF-beta receptor type-2 / Transforming growth factor-beta receptor type II / TGF-beta receptor type II / TGF-beta type II ...Transforming growth factor-beta receptor type II / TGF-beta receptor type II / TGF-beta type II receptor / TbetaR-II / TGFR-2


Mass: 13225.042 Da / Num. of mol.: 4 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBR2 / Production host: Escherichia coli (E. coli) / References: UniProt: P37173
#3: Protein
TGF-beta receptor type-1 / Transforming growth factor-beta receptor type I / TGF-beta receptor type I / TGF-beta type I ...Transforming growth factor-beta receptor type I / TGF-beta receptor type I / TGF-beta type I receptor / TbetaR-I / TGFR-1 / Serine/threonine-protein kinase receptor R4 / SKR4 / Activin receptor-like kinase 5 / ALK-5


Mass: 9330.697 Da / Num. of mol.: 4 / Fragment: extracellular domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P36897
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7
Details: 8-15% Peg 4000-8000, pH 7.0, VAPOR DIFFUSION, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 10, 2007 / Details: mirrors
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 23426 / Observed criterion σ(I): -3 / Redundancy: 1.9 % / Rsym value: 0.08 / Net I/σ(I): 9.2
Reflection shellResolution: 3→3.11 Å / Redundancy: 1.6 % / Mean I/σ(I) obs: 2 / Num. unique all: 1223 / Rsym value: 0.245

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Processing

Software
NameVersionClassification
PHASERphasing
EPMRphasing
PHENIX(phenix.refine)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2TGI, 1M9Z, 1REW

2tgi

1m9z

1rew


Resolution: 2.995→46.08 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.763 / SU ML: 0.41 / Isotropic thermal model: Isotropic / σ(F): 0.06 / Phase error: 30.61 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1062 4.8 %Random
Rwork0.217 21063 --
obs0.22 22125 82.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.915 Å2 / ksol: 0.322 e/Å3
Displacement parametersBiso max: 164.87 Å2 / Biso mean: 73.45 Å2 / Biso min: 16.27 Å2
Baniso -1Baniso -2Baniso -3
1-3.635 Å2-2.728 Å20.206 Å2
2---6.662 Å28.384 Å2
3----31.29 Å2
Refinement stepCycle: LAST / Resolution: 2.995→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9058 0 0 93 9151
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0039334
X-RAY DIFFRACTIONf_angle_d0.63112563
X-RAY DIFFRACTIONf_dihedral_angle_d20.0353375
X-RAY DIFFRACTIONf_chiral_restr0.0441396
X-RAY DIFFRACTIONf_plane_restr0.0031613
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.995-3.13120.3876620.30011234X-RAY DIFFRACTION38
3.1312-3.29630.3283960.2891990X-RAY DIFFRACTION63
3.2963-3.50270.33921380.26052695X-RAY DIFFRACTION85
3.5027-3.77310.31651310.22223016X-RAY DIFFRACTION93
3.7731-4.15260.24821640.20212968X-RAY DIFFRACTION94
4.1526-4.75290.22231590.16383048X-RAY DIFFRACTION95
4.7529-5.98610.21931610.18193048X-RAY DIFFRACTION96
5.9861-46.08540.25571510.23283064X-RAY DIFFRACTION96

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