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- PDB-5tx4: Derivative of mouse TGF-beta2, with a deletion of residues 52-71 ... -

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Basic information

Entry
Database: PDB / ID: 5tx4
TitleDerivative of mouse TGF-beta2, with a deletion of residues 52-71 and K25R, R26K, L51R, A74K, C77S, L89V, I92V, K94R T95K, I98V single amino acid substitutions, bound to human TGF-beta type II receptor ectodomain residues 15-130
Components
  • TGF-beta receptor type-2
  • Transforming growth factor beta-2
KeywordsTRANSFERASE/CYTOKINE / TGF-beta / TGF-beta type II receptor / TRANSFERASE-CYTOKINE complex
Function / homology
Function and homology information


regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / substantia propria of cornea development / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / ascending aorta morphogenesis / inferior endocardial cushion morphogenesis / transforming growth factor beta receptor activity, type II / uterine wall breakdown ...regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / substantia propria of cornea development / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / positive regulation of tolerance induction to self antigen / positive regulation of B cell tolerance induction / ascending aorta morphogenesis / inferior endocardial cushion morphogenesis / transforming growth factor beta receptor activity, type II / uterine wall breakdown / bronchus morphogenesis / cardioblast differentiation / mammary gland morphogenesis / lens fiber cell apoptotic process / positive regulation of timing of catagen / growth plate cartilage chondrocyte growth / positive regulation of cardioblast differentiation / tricuspid valve morphogenesis / TGFBR2 MSI Frameshift Mutants in Cancer / activin receptor activity / positive regulation of heart contraction / cardiac right ventricle morphogenesis / miRNA transport / pharyngeal arch artery morphogenesis / type III transforming growth factor beta receptor binding / transforming growth factor beta ligand-receptor complex / regulation of transforming growth factor beta2 production / Langerhans cell differentiation / atrial septum morphogenesis / aorta morphogenesis / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / negative regulation of macrophage cytokine production / TGFBR2 Kinase Domain Mutants in Cancer / signaling / transforming growth factor beta receptor activity / secondary palate development / cardiac left ventricle morphogenesis / glial cell migration / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / somatic stem cell division / heart valve morphogenesis / endocardial cushion fusion / positive regulation of T cell tolerance induction / atrial septum primum morphogenesis / membranous septum morphogenesis / lung lobe morphogenesis / positive regulation of integrin biosynthetic process / positive regulation of NK T cell differentiation / cardiac epithelial to mesenchymal transition / eye development / cranial skeletal system development / neural retina development / positive regulation of stress-activated MAPK cascade / embryonic digestive tract development / transforming growth factor beta receptor binding / type II transforming growth factor beta receptor binding / regulation of stem cell proliferation / TGFBR1 LBD Mutants in Cancer / myeloid dendritic cell differentiation / receptor protein serine/threonine kinase / pulmonary valve morphogenesis / transmembrane receptor protein serine/threonine kinase activity / activin binding / type I transforming growth factor beta receptor binding / positive regulation of CD4-positive, alpha-beta T cell proliferation / outflow tract septum morphogenesis / SMAD protein signal transduction / regulation of stem cell differentiation / ventricular trabecula myocardium morphogenesis / cell-cell junction organization / glycosaminoglycan binding / kinase activator activity / negative regulation of Ras protein signal transduction / transforming growth factor beta binding / response to cholesterol / embryonic cranial skeleton morphogenesis / aortic valve morphogenesis / collagen fibril organization / positive regulation of cell adhesion mediated by integrin / embryonic limb morphogenesis / embryo development ending in birth or egg hatching / odontogenesis / dopamine biosynthetic process / lens development in camera-type eye / Molecules associated with elastic fibres / atrioventricular valve morphogenesis / embryonic hemopoiesis / positive regulation of mesenchymal cell proliferation / cardiac muscle cell proliferation / trachea formation / artery morphogenesis / endocardial cushion morphogenesis / smoothened signaling pathway / branching involved in blood vessel morphogenesis / hair follicle morphogenesis / generation of neurons / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / activation of protein kinase activity
Similarity search - Function
Transforming growth factor beta-2 proprotein / 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 / 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-2 proprotein / 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 / 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. / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / CD59 / CD59 / Ser/Thr protein kinase, TGFB receptor / Snake toxin-like superfamily / Cystine-knot cytokine / 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. / 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
TGF-beta receptor type-2 / Transforming growth factor beta-2 proprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.876 Å
AuthorsHinck, A.P. / Kim, S.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM58670 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA172886 United States
Robert A. Welch FoundationAQ1842 United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: An engineered transforming growth factor beta (TGF-beta ) monomer that functions as a dominant negative to block TGF-beta signaling.
Authors: Kim, S.K. / Barron, L. / Hinck, C.S. / Petrunak, E.M. / Cano, K.E. / Thangirala, A. / Iskra, B. / Brothers, M. / Vonberg, M. / Leal, B. / Richter, B. / Kodali, R. / Taylor, A.B. / Du, S. / ...Authors: Kim, S.K. / Barron, L. / Hinck, C.S. / Petrunak, E.M. / Cano, K.E. / Thangirala, A. / Iskra, B. / Brothers, M. / Vonberg, M. / Leal, B. / Richter, B. / Kodali, R. / Taylor, A.B. / Du, S. / Barnes, C.O. / Sulea, T. / Calero, G. / Hart, P.J. / Hart, M.J. / Demeler, B. / Hinck, A.P.
History
DepositionNov 15, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 8, 2017Group: Database references
Revision 1.2May 10, 2017Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: TGF-beta receptor type-2
B: Transforming growth factor beta-2


Theoretical massNumber of molelcules
Total (without water)23,7262
Polymers23,7262
Non-polymers00
Water1,47782
1
A: TGF-beta receptor type-2


Theoretical massNumber of molelcules
Total (without water)13,2251
Polymers13,2251
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Transforming growth factor beta-2


Theoretical massNumber of molelcules
Total (without water)10,5011
Polymers10,5011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.019, 70.772, 77.116
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein TGF-beta receptor type-2 / TGFR-2 / TGF-beta type II receptor / Transforming growth factor-beta receptor type II / TbetaR-II


Mass: 13225.042 Da / Num. of mol.: 1 / Fragment: UNP residues 38-153
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
#2: Protein Transforming growth factor beta-2 / TGF-beta-2 / BSC-1 cell growth inhibitor / Cetermin / Glioblastoma-derived T-cell suppressor factor ...TGF-beta-2 / BSC-1 cell growth inhibitor / Cetermin / Glioblastoma-derived T-cell suppressor factor / G-TSF / Polyergin


Mass: 10501.184 Da / Num. of mol.: 1 / Fragment: UNP residues 303-414
Mutation: deletion of residues 52-71 and K25R, R26K, L51R, A74K, C77S, L89V, I92V, K94R T95K, I98V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB2 / Production host: Escherichia coli (E. coli) / References: UniProt: P61812
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.24 Å3/Da / Density % sol: 45.18 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1 M Hepes, pH 7.5, 60 % v/v (+/-)-2-Methyl-2,4-pentanediol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Apr 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.876→35.39 Å / Num. obs: 17715 / % possible obs: 99.6 % / Redundancy: 6.8 % / Rsym value: 0.143 / Net I/σ(I): 15.17

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1M9Z,5TX2

1m9z

5tx2


Resolution: 1.876→35.386 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2222 883 4.98 %
Rwork0.1935 --
obs0.195 17714 97.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.876→35.386 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1575 0 0 82 1657
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111621
X-RAY DIFFRACTIONf_angle_d1.0862195
X-RAY DIFFRACTIONf_dihedral_angle_d13.3871026
X-RAY DIFFRACTIONf_chiral_restr0.064234
X-RAY DIFFRACTIONf_plane_restr0.007281
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8761-1.99360.27391390.232472X-RAY DIFFRACTION89
1.9936-2.14750.26351460.20512836X-RAY DIFFRACTION100
2.1475-2.36360.22941260.18952823X-RAY DIFFRACTION100
2.3636-2.70550.25791480.18692851X-RAY DIFFRACTION100
2.7055-3.40820.21931540.19862874X-RAY DIFFRACTION100
3.4082-35.39230.20521700.18852975X-RAY DIFFRACTION99

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