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- PDB-3faa: Crystal structure of TGFbRI complexed with a 2-aminoimidazole inh... -

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Basic information

Entry
Database: PDB / ID: 3faa
TitleCrystal structure of TGFbRI complexed with a 2-aminoimidazole inhibitor
ComponentsTGF-beta receptor type-1
KeywordsTRANSFERASE / Kinase / TGFbeta / structure-based drug design / protein-inhibitor complex / ATP-binding / Craniosynostosis / Disease mutation / Glycoprotein / Magnesium / Manganese / Membrane / Metal-binding / Nucleotide-binding / Phosphoprotein / Polymorphism / Receptor / Serine/threonine-protein kinase / Transmembrane
Function / homology
Function and homology information


extracellular structure organization / epicardium morphogenesis / vascular endothelial cell proliferation / parathyroid gland development / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / myofibroblast differentiation / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity ...extracellular structure organization / epicardium morphogenesis / vascular endothelial cell proliferation / parathyroid gland development / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / myofibroblast differentiation / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity / ventricular compact myocardium morphogenesis / trophoblast cell migration / positive regulation of mesenchymal stem cell proliferation / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / TGFBR3 regulates TGF-beta signaling / positive regulation of tight junction disassembly / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / positive regulation of vasculature development / neuron fate commitment / activin receptor complex / positive regulation of extracellular matrix assembly / type II transforming growth factor beta receptor binding / transforming growth factor beta receptor activity, type I / activin receptor activity, type I / activin receptor activity, type II / BMP receptor activity / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / transforming growth factor beta receptor activity, type II / pharyngeal system development / TGFBR1 LBD Mutants in Cancer / transforming growth factor beta receptor activity, type III / activin binding / regulation of epithelial to mesenchymal transition / coronary artery morphogenesis / angiogenesis involved in coronary vascular morphogenesis / germ cell migration / filopodium assembly / ventricular trabecula myocardium morphogenesis / activin receptor signaling pathway / response to cholesterol / embryonic cranial skeleton morphogenesis / I-SMAD binding / transforming growth factor beta binding / collagen fibril organization / negative regulation of chondrocyte differentiation / endothelial cell activation / anterior/posterior pattern specification / skeletal system morphogenesis / lens development in camera-type eye / positive regulation of filopodium assembly / artery morphogenesis / ventricular septum morphogenesis / SMAD binding / negative regulation of endothelial cell proliferation / roof of mouth development / TGF-beta receptor signaling activates SMADs / positive regulation of SMAD protein signal transduction / blastocyst development / regulation of protein ubiquitination / epithelial to mesenchymal transition / bicellular tight junction / endothelial cell migration / positive regulation of epithelial to mesenchymal transition / cellular response to transforming growth factor beta stimulus / positive regulation of stress fiber assembly / positive regulation of endothelial cell proliferation / transforming growth factor beta receptor signaling pathway / negative regulation of cell migration / thymus development / Downregulation of TGF-beta receptor signaling / positive regulation of apoptotic signaling pathway / post-embryonic development / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development / skeletal system development / negative regulation of extrinsic apoptotic signaling pathway / cell motility / wound healing / cellular response to growth factor stimulus / male gonad development / UCH proteinases / nervous system development / peptidyl-serine phosphorylation / heart development / regulation of gene expression / positive regulation of cell growth / in utero embryonic development / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / protein kinase activity / regulation of cell cycle / endosome / Ub-specific processing proteases / intracellular signal transduction / cilium / positive regulation of cell migration / membrane raft
Similarity search - Function
GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Activin types I and II receptor domain / Activin types I and II receptor domain / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 ...GS domain / Transforming growth factor beta type I GS-motif / GS domain profile. / GS motif / Activin types I and II receptor domain / Activin types I and II receptor domain / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-55F / PHOSPHATE ION / TGF-beta receptor type-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.35 Å
AuthorsBoriack-Sjodin, P.A. / Fitch, C.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: 2-Aminoimidazoles inhibitors of TGF-beta receptor 1.
Authors: Bonafoux, D. / Chuaqui, C. / Boriack-Sjodin, P.A. / Fitch, C. / Hankins, G. / Josiah, S. / Black, C. / Hetu, G. / Ling, L. / Lee, W.C.
History
DepositionNov 16, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TGF-beta receptor type-1
B: TGF-beta receptor type-1
C: TGF-beta receptor type-1
D: TGF-beta receptor type-1
E: TGF-beta receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,65023
Polymers194,6035
Non-polymers3,04618
Water00
1
A: TGF-beta receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5685
Polymers38,9211
Non-polymers6474
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: TGF-beta receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5685
Polymers38,9211
Non-polymers6474
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: TGF-beta receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3783
Polymers38,9211
Non-polymers4572
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: TGF-beta receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5685
Polymers38,9211
Non-polymers6474
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: TGF-beta receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5685
Polymers38,9211
Non-polymers6474
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)174.861, 248.852, 138.628
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: 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: 38920.641 Da / Num. of mol.: 5 / Fragment: GS and Kinase domains: UNP residues 162-503
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: SF9 / Gene: TGFBR1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P36897, receptor protein serine/threonine kinase
#2: Chemical
ChemComp-55F / N-[4-(5-fluoro-6-methylpyridin-2-yl)-5-quinoxalin-6-yl-1H-imidazol-2-yl]acetamide


Mass: 362.360 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C19H15FN6O
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: PO4

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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: 3.87 Å3/Da / Density % sol: 68.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: Na/K phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 12, 2005
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 3.2→50 Å / Num. all: 51040 / Num. obs: 50127 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.127 / Χ2: 1.056 / Net I/σ(I): 13.38
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.755 / Num. unique all: 5043 / Χ2: 0.657 / % possible all: 99.7

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
CBASSdata collection
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.35→35 Å / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.271 2200 5 %random
Rwork0.228 ---
obs0.228 43683 99.8 %-
all-43769 --
Displacement parametersBiso max: 144.59 Å2 / Biso mean: 71.11 Å2 / Biso min: 7.15 Å2
Baniso -1Baniso -2Baniso -3
1-9.732 Å20 Å20 Å2
2---14.196 Å20 Å2
3---4.464 Å2
Refinement stepCycle: LAST / Resolution: 3.35→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13094 0 200 0 13294
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008529
X-RAY DIFFRACTIONc_angle_deg1.5053
X-RAY DIFFRACTIONc_mcbond_it1.5131.5
X-RAY DIFFRACTIONc_scbond_it1.7762
X-RAY DIFFRACTIONc_mcangle_it2.7472
X-RAY DIFFRACTIONc_scangle_it3.0242.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1MSI_CNX_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2bio16212.param
X-RAY DIFFRACTION3MSI_CNX_TOPPAR:ion.param
X-RAY DIFFRACTION4MSI_CNX_TOPPAR:water_rep.param

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