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- PDB-2pjy: Structural basis for cooperative assembly of the TGF-beta signali... -

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Basic information

Entry
Database: PDB / ID: 2pjy
TitleStructural basis for cooperative assembly of the TGF-beta signaling complex
Components
  • TGF-beta receptor type-1
  • TGF-beta receptor type-2
  • Transforming growth factor beta-3
KeywordsCYTOKINE/CYTOKINE RECEPTOR / ternary complex / three finger toxin / 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 / uterine wall breakdown / inferior endocardial cushion morphogenesis / transforming growth factor beta receptor activity, type II / bronchus morphogenesis / mammary gland morphogenesis / detection of hypoxia / lens fiber cell apoptotic process / growth plate cartilage chondrocyte growth ...positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / uterine wall breakdown / inferior endocardial cushion morphogenesis / transforming growth factor beta receptor activity, type II / bronchus morphogenesis / mammary gland morphogenesis / detection of hypoxia / lens fiber cell apoptotic process / growth plate cartilage chondrocyte growth / extracellular structure organization / epicardium morphogenesis / tricuspid valve morphogenesis / vascular endothelial cell proliferation / TGFBR2 MSI Frameshift Mutants in Cancer / miRNA transport / parathyroid gland development / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / type III transforming growth factor beta receptor binding / aorta morphogenesis / myofibroblast differentiation / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / Langerhans cell differentiation / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity / cardiac left ventricle morphogenesis / secondary palate development / negative regulation of macrophage cytokine production / trophoblast cell migration / angiogenesis involved in coronary vascular morphogenesis / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / positive regulation of mesenchymal stem cell proliferation / endocardial cushion fusion / ventricular compact myocardium morphogenesis / positive regulation of extracellular matrix assembly / positive regulation of T cell tolerance induction / membranous septum morphogenesis / positive regulation of tight junction disassembly / positive regulation of NK T cell differentiation / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / TGFBR3 regulates TGF-beta signaling / transforming growth factor beta receptor activity, type I / positive regulation of vasculature development / neuron fate commitment / activin receptor complex / activin receptor activity, type I / regulation of epithelial to mesenchymal transition / lung lobe morphogenesis / type II transforming growth factor beta receptor binding / pharyngeal system development / transmembrane receptor protein serine/threonine kinase activity / receptor protein serine/threonine kinase / regulation of stem cell proliferation / activin binding / TGFBR1 LBD Mutants in Cancer / SMAD protein signal transduction / type I transforming growth factor beta receptor binding / germ cell migration / myeloid dendritic cell differentiation / filopodium assembly / coronary artery morphogenesis / embryonic cranial skeleton morphogenesis / glycosaminoglycan binding / activin receptor signaling pathway / ventricular trabecula myocardium morphogenesis / positive regulation of CD4-positive, alpha-beta T cell proliferation / regulation of stem cell differentiation / response to cholesterol / mammary gland development / outflow tract septum morphogenesis / cell-cell junction organization / I-SMAD binding / transforming growth factor beta binding / collagen fibril organization / negative regulation of chondrocyte differentiation / kinase activator activity / lens development in camera-type eye / aortic valve morphogenesis / atrioventricular valve morphogenesis / face morphogenesis / endothelial cell activation / odontogenesis / anterior/posterior pattern specification / positive regulation of mesenchymal cell proliferation / positive regulation of filopodium assembly / artery morphogenesis / embryonic hemopoiesis / Molecules associated with elastic fibres / skeletal system morphogenesis / trachea formation / lung alveolus development / smoothened signaling pathway / branching involved in blood vessel morphogenesis / ventricular septum morphogenesis / blood vessel development / SMAD binding / heart looping
Similarity search - Function
Transforming growth factor beta-3 / 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 / GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / TGF-beta, propeptide ...Transforming growth factor beta-3 / 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 / GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Activin types I and II receptor domain / Transforming growth factor-beta-related / Activin types I and II receptor domain / Transforming growth factor-beta (TGF-beta) family / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Cystine-knot cytokine / Snake toxin-like superfamily / Ribbon / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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-3 proprotein / TGF-beta receptor type-1 / TGF-beta receptor type-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / MAD / Resolution: 3 Å
AuthorsGroppe, J. / Zubieta, C.
CitationJournal: Mol.Cell / Year: 2008
Title: Cooperative assembly of TGF-beta superfamily signaling complexes is mediated by two disparate mechanisms and distinct modes of receptor binding.
Authors: Groppe, J. / Hinck, C.S. / Samavarchi-Tehrani, P. / Zubieta, C. / Schuermann, J.P. / Taylor, A.B. / Schwarz, P.M. / Wrana, J.L. / Hinck, A.P.
History
DepositionApr 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 5, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.4Nov 20, 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-3
B: TGF-beta receptor type-2
C: TGF-beta receptor type-1


Theoretical massNumber of molelcules
Total (without water)33,6953
Polymers33,6953
Non-polymers00
Water1629
1
A: Transforming growth factor beta-3
B: TGF-beta receptor type-2
C: TGF-beta receptor type-1

A: Transforming growth factor beta-3
B: TGF-beta receptor type-2
C: TGF-beta receptor type-1


Theoretical massNumber of molelcules
Total (without water)67,3896
Polymers67,3896
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555x-y,-y,-z1
Buried area8880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.920, 66.920, 254.360
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein Transforming growth factor beta-3 / TGF-beta-3


Mass: 12734.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB3 / Production host: Escherichia coli (E. coli) / References: UniProt: P10600
#2: Protein TGF-beta receptor type-2 / TGF-beta receptor type II / TGFR-2 / TGF-beta type II receptor / Transforming growth factor-beta ...TGF-beta receptor type II / TGFR-2 / TGF-beta type II receptor / Transforming growth factor-beta receptor type II / TbetaR-II


Mass: 12244.113 Da / Num. of mol.: 1 / Fragment: extracellular domain / Mutation: N42A
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, receptor protein serine/threonine kinase
#3: Protein TGF-beta receptor type-1 / TGF-beta receptor type I / TGFR-1 / TGF-beta type I receptor / Transforming growth factor-beta ...TGF-beta receptor type I / TGFR-1 / TGF-beta type I receptor / Transforming growth factor-beta receptor type I / TbetaR-I / Serine/threonine-protein kinase receptor R4 / SKR4 / Activin receptor-like kinase 5 / ALK-5


Mass: 8715.943 Da / Num. of mol.: 1 / Fragment: extracellular domain / Mutation: M70S
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, receptor protein serine/threonine kinase
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / 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: 2.44 Å3/Da / Density % sol: 49.56 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10-20% PEG 3350, 0.4-0.65 M calcium acetate, 0.1-0.25M NaCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 6, 2006 / Details: mirrors
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 6710 / % possible obs: 90.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 8.7 % / Biso Wilson estimate: 75.056 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.078 / Net I/σ(I): 26.2
Reflection shellResolution: 3→3.29 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.598 / Mean I/σ(I) obs: 4.2 / Num. measured obs: 17731 / Num. unique all: 1724 / Rsym value: 0.63 / % possible all: 100

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Phasing

PhasingMethod: MAD
Phasing MRRfactor: 0.525 / Cor.coef. Fo:Fc: 0.267
Highest resolutionLowest resolution
Rotation3 Å38.35 Å
Translation3 Å38.35 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
MOLREPphasing
SOLVEphasing
REFMACrefinement
PDB_EXTRACT2data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1KTZ

1ktz


Resolution: 3→28.8 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.906 / SU B: 63.761 / SU ML: 0.508 / TLS residual ADP flag: LIKELY RESIDUAL / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.566 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.297 312 4.7 %RANDOM
Rwork0.242 ---
obs0.244 6701 90.43 %-
all-7427 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.645 Å2
Baniso -1Baniso -2Baniso -3
1-0.14 Å20.07 Å20 Å2
2--0.14 Å20 Å2
3----0.21 Å2
Refinement stepCycle: LAST / Resolution: 3→28.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2328 0 0 9 2337
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222396
X-RAY DIFFRACTIONr_angle_refined_deg0.8091.9583264
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.645296
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.33725.146103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.56915399
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.433158
X-RAY DIFFRACTIONr_chiral_restr0.0550.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.021798
X-RAY DIFFRACTIONr_nbd_refined0.1520.2934
X-RAY DIFFRACTIONr_nbtor_refined0.290.21616
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0890.267
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2430.270
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.24
X-RAY DIFFRACTIONr_mcbond_it0.1011.51549
X-RAY DIFFRACTIONr_mcangle_it0.18622456
X-RAY DIFFRACTIONr_scbond_it0.143958
X-RAY DIFFRACTIONr_scangle_it0.2474.5808
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 38 -
Rwork0.353 491 -
obs-529 100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.44251.2651.981710.7537-1.20432.23160.1158-0.0723-0.05960.0088-0.14520.67670.3098-0.2540.02940.61710.2118-0.00470.24550.01110.1784-13.4939.751-12.885
25.4893-2.57125.4944.017-1.88938.75820.96390.39820.7434-1.2105-0.29160.86840.9989-0.6442-0.67230.8137-0.0939-0.16040.30550.1050.4862-12.812-12.940.034
33.22514.3224-1.251412.4868-4.55413.39050.2704-0.3088-0.13480.5077-0.421-0.18040.18960.12150.15060.64070.1525-0.10150.3068-0.00140.2161-6.14610.172-7.374
432.249811.616440.32484.184214.52550.42181.1703-0.1358-1.04420.29020.49810.73611.5223-0.5878-1.66841.51910.2416-0.18910.45290.2673-0.1206-4.58133.0684.36
54.32470.60072.88840.286-1.035812.1226-0.84410.03291.1909-0.27630.7373-0.8082-0.19220.65430.10680.8230.1196-0.04450.1985-0.16790.2947-7.62943.436-16.971
67.5661-2.2751-1.74189.2049-1.06216.23620.28820.30820.6632-0.4569-0.1139-0.2627-0.64990.2581-0.17430.56820.0502-0.09170.1791-0.23060.3147-9.69945.835-13.172
79.272-6.0855-3.77748.6272-3.54819.3798-0.1598-0.27621.83760.13340.6143-0.7614-0.94360.5289-0.45440.97550.0192-0.19690.2329-0.42630.5319-8.71252.931-4.969
87.2152-9.117-0.932421.4467-7.74629.8327-0.3552-0.88090.19490.4920.31811.235-0.1545-0.67780.03710.43310.184-0.13390.1886-0.21160.1238-14.80444.393-7.565
91.6044-1.41463.27129.6792-3.665410.27-0.1809-0.1712-0.5597-0.0648-0.1878-0.02370.4261-0.30680.36870.5362-0.1161-0.05710.3144-0.05330.2339-0.25516.27515.592
1015.96662.03033.508911.7998-4.83234.51570.5592-0.1942-0.1448-0.3345-0.66570.48110.34090.12120.10650.5877-0.049-0.190.1121-0.10310.1802-4.83319.9387.043
110.5823-0.24492.2897.3465-4.470310.69640.2156-0.73910.64370.28150.26591.5607-1.453-2.0077-0.48160.970.23040.11240.4977-0.10180.5083-7.21624.28812.723
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 481 - 48
22AA49 - 6849 - 68
33AA69 - 11269 - 112
44BB20 - 272 - 9
55BB28 - 3810 - 20
66BB39 - 7721 - 59
77BB78 - 11060 - 92
88BB111 - 12693 - 108
99CC10 - 372 - 29
1010CC38 - 6030 - 52
1111CC61 - 8753 - 79

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