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- PDB-1b6c: CRYSTAL STRUCTURE OF THE CYTOPLASMIC DOMAIN OF THE TYPE I TGF-BET... -

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Basic information

Entry
Database: PDB / ID: 1b6c
TitleCRYSTAL STRUCTURE OF THE CYTOPLASMIC DOMAIN OF THE TYPE I TGF-BETA RECEPTOR IN COMPLEX WITH FKBP12
Components
  • FK506-BINDING PROTEIN
  • TGF-B SUPERFAMILY RECEPTOR TYPE I
KeywordsCOMPLEX (ISOMERASE/PROTEIN KINASE) / COMPLEX (ISOMERASE-PROTEIN KINASE) / RECEPTOR SERINE/THREONINE KINASE / COMPLEX (ISOMERASE-PROTEIN KINASE) complex
Function / homology
Function and homology information


extracellular structure organization / epicardium morphogenesis / parathyroid gland development / myofibroblast differentiation / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / positive regulation of tight junction disassembly / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / TGFBR2 Kinase Domain Mutants in Cancer / positive regulation of mesenchymal stem cell proliferation ...extracellular structure organization / epicardium morphogenesis / parathyroid gland development / myofibroblast differentiation / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / positive regulation of tight junction disassembly / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / TGFBR2 Kinase Domain Mutants in Cancer / positive regulation of mesenchymal stem cell proliferation / transforming growth factor beta receptor activity / ventricular compact myocardium morphogenesis / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / macrolide binding / positive regulation of vasculature development / regulation of epithelial to mesenchymal transition / activin receptor activity, type I / activin receptor binding / cytoplasmic side of membrane / cardiac epithelial to mesenchymal transition / transforming growth factor beta receptor activity, type I / activin receptor complex / mesenchymal cell differentiation / neuron fate commitment / positive regulation of extracellular matrix assembly / germ cell migration / transforming growth factor beta receptor binding / type II transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / angiogenesis involved in coronary vascular morphogenesis / signaling receptor inhibitor activity / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / type I transforming growth factor beta receptor binding / pharyngeal system development / activin binding / coronary artery morphogenesis / activin receptor signaling pathway / filopodium assembly / ventricular trabecula myocardium morphogenesis / negative regulation of activin receptor signaling pathway / regulation of amyloid precursor protein catabolic process / heart trabecula formation / transforming growth factor beta binding / embryonic cranial skeleton morphogenesis / response to cholesterol / terminal cisterna / ryanodine receptor complex / I-SMAD binding / endothelial cell proliferation / artery morphogenesis / negative regulation of chondrocyte differentiation / collagen fibril organization / endothelial cell activation / skeletal system morphogenesis / lens development in camera-type eye / anterior/posterior pattern specification / protein maturation by protein folding / positive regulation of filopodium assembly / 'de novo' protein folding / ventricular cardiac muscle tissue morphogenesis / negative regulation of phosphoprotein phosphatase activity / FK506 binding / ventricular septum morphogenesis / negative regulation of endothelial cell proliferation / roof of mouth development / mTORC1-mediated signalling / SMAD binding / TGF-beta receptor signaling activates SMADs / positive regulation of SMAD protein signal transduction / blastocyst development / regulation of protein ubiquitination / Calcineurin activates NFAT / bicellular tight junction / endothelial cell migration / epithelial to mesenchymal transition / positive regulation of epithelial to mesenchymal transition / regulation of immune response / protein peptidyl-prolyl isomerization / supramolecular fiber organization / heart morphogenesis / positive regulation of apoptotic signaling pathway / regulation of ryanodine-sensitive calcium-release channel activity / positive regulation of stress fiber assembly / cellular response to transforming growth factor beta stimulus / sarcoplasmic reticulum membrane / positive regulation of endothelial cell proliferation / T cell activation / Downregulation of TGF-beta receptor signaling / post-embryonic development / transforming growth factor beta receptor signaling pathway / negative regulation of cell migration / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / thymus development / sarcoplasmic reticulum / peptidylprolyl isomerase / kidney development / skeletal system development / peptidyl-prolyl cis-trans isomerase activity
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 / Chitinase A; domain 3 - #40 / Snake toxin-like superfamily / Chitinase A; domain 3 ...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 / Chitinase A; domain 3 - #40 / Snake toxin-like superfamily / Chitinase A; domain 3 / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Roll / 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
TGF-beta receptor type-1 / Peptidyl-prolyl cis-trans isomerase FKBP1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.6 Å
AuthorsHuse, M. / Chen, Y.-G. / Massague, J. / Kuriyan, J.
CitationJournal: Cell(Cambridge,Mass.) / Year: 1999
Title: Crystal structure of the cytoplasmic domain of the type I TGF beta receptor in complex with FKBP12.
Authors: Huse, M. / Chen, Y.G. / Massague, J. / Kuriyan, J.
History
DepositionJan 13, 1999Processing site: BNL
Revision 1.0Jun 15, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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: FK506-BINDING PROTEIN
B: TGF-B SUPERFAMILY RECEPTOR TYPE I
C: FK506-BINDING PROTEIN
D: TGF-B SUPERFAMILY RECEPTOR TYPE I
E: FK506-BINDING PROTEIN
F: TGF-B SUPERFAMILY RECEPTOR TYPE I
G: FK506-BINDING PROTEIN
H: TGF-B SUPERFAMILY RECEPTOR TYPE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,41312
Polymers203,0298
Non-polymers3844
Water1,58588
1
A: FK506-BINDING PROTEIN
B: TGF-B SUPERFAMILY RECEPTOR TYPE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8533
Polymers50,7572
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1980 Å2
ΔGint-28 kcal/mol
Surface area19670 Å2
MethodPISA
2
C: FK506-BINDING PROTEIN
D: TGF-B SUPERFAMILY RECEPTOR TYPE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8533
Polymers50,7572
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-28 kcal/mol
Surface area19640 Å2
MethodPISA
3
E: FK506-BINDING PROTEIN
F: TGF-B SUPERFAMILY RECEPTOR TYPE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8533
Polymers50,7572
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-28 kcal/mol
Surface area19810 Å2
MethodPISA
4
G: FK506-BINDING PROTEIN
H: TGF-B SUPERFAMILY RECEPTOR TYPE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8533
Polymers50,7572
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1950 Å2
ΔGint-29 kcal/mol
Surface area19670 Å2
MethodPISA
5
A: FK506-BINDING PROTEIN
B: TGF-B SUPERFAMILY RECEPTOR TYPE I
hetero molecules

G: FK506-BINDING PROTEIN
H: TGF-B SUPERFAMILY RECEPTOR TYPE I
hetero molecules

C: FK506-BINDING PROTEIN
D: TGF-B SUPERFAMILY RECEPTOR TYPE I
hetero molecules

E: FK506-BINDING PROTEIN
F: TGF-B SUPERFAMILY RECEPTOR TYPE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,41312
Polymers203,0298
Non-polymers3844
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation1_546x,y-1,z+11
crystal symmetry operation1_544x,y-1,z-11
Buried area11700 Å2
ΔGint-142 kcal/mol
Surface area74980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.580, 81.060, 90.530
Angle α, β, γ (deg.)86.23, 81.86, 63.92
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999639, -0.026418, -0.004965), (-0.026378, 0.999619, -0.008128), (0.005178, -0.007994, -0.999955)
Vector: -4.30666, -0.7216, -0.03192)

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Components

#1: Protein
FK506-BINDING PROTEIN / FKBP12


Mass: 11836.508 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: PLYS S / Plasmid: PFASTBAC / Cell line (production host): SF9 / Cellular location (production host): CYTOPLASM / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62942, peptidylprolyl isomerase
#2: Protein
TGF-B SUPERFAMILY RECEPTOR TYPE I / SERINE/THREONINE-PROTEIN KINASE RECEPTOR R4


Mass: 38920.641 Da / Num. of mol.: 4 / Fragment: CYTOPLASMIC PORTION
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: PLYS S / Plasmid: PET23 / Cell line (production host): PLYS S / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P36897, EC: 2.7.1.37
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 88 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 6

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52 %
Crystal growpH: 8.5 / Details: pH 8.5
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMTris-HCl1reservoir
21.40-1.53 Mammonium sulfate1reservoir
32 mMAMP-PNP1drop
410 mM1dropMgCl2
50.5 M1dropNal

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Feb 1, 1998 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 57740 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Rsym value: 0.08 / Net I/σ(I): 18
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 6 / Rsym value: 0.24 / % possible all: 97.7
Reflection
*PLUS
Rmerge(I) obs: 0.08
Reflection shell
*PLUS
% possible obs: 97.7 % / Rmerge(I) obs: 0.243

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Processing

Software
NameVersionClassification
CCP4model building
CNS0.3Crefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: MIR / Resolution: 2.6→30 Å / Data cutoff high rms absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.269 5883 10 %RANDOM
Rwork0.249 ---
obs0.249 57740 98.4 %-
Solvent computationSolvent model: FLAT
Displacement parametersBiso mean: 37.29 Å2
Baniso -1Baniso -2Baniso -3
1--4.616 Å23.262 Å24.942 Å2
2---2.271 Å21.013 Å2
3---6.887 Å2
Refinement stepCycle: LAST / Resolution: 2.6→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13732 0 20 88 13840
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.66
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Refine LS restraints NCSNCS model details: RESTRAINTS
LS refinement shellResolution: 2.6→2.62 Å / Total num. of bins used: 50
RfactorNum. reflection% reflection
Rfree0.3114 126 10 %
Rwork0.3448 1138 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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