[English] 日本語
Yorodumi
- PDB-8yhf: The Crystal Structure of the Type I TGF beta receptor from Biortus. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8yhf
TitleThe Crystal Structure of the Type I TGF beta receptor from Biortus.
ComponentsTGF-beta receptor type-1
KeywordsTRANSFERASE / Serine/threonine-protein kinase / apoptosis / ATP-binding
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 / trophoblast cell migration / angiogenesis involved in coronary vascular morphogenesis / positive regulation of mesenchymal stem cell proliferation / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / ventricular compact myocardium morphogenesis / positive regulation of extracellular matrix assembly / TGFBR3 regulates TGF-beta signaling / positive regulation of tight junction disassembly / cardiac epithelial to mesenchymal transition / mesenchymal cell differentiation / positive regulation of vasculature development / transforming growth factor beta receptor activity, type I / neuron fate commitment / activin receptor complex / activin receptor activity, type I / regulation of epithelial to mesenchymal transition / type II transforming growth factor beta receptor binding / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / pharyngeal system development / TGFBR1 LBD Mutants in Cancer / activin binding / germ cell migration / filopodium assembly / coronary artery morphogenesis / embryonic cranial skeleton morphogenesis / activin receptor signaling pathway / ventricular trabecula myocardium morphogenesis / response to cholesterol / I-SMAD binding / transforming growth factor beta binding / collagen fibril organization / negative regulation of chondrocyte differentiation / lens development in camera-type eye / endothelial cell activation / positive regulation of filopodium assembly / anterior/posterior pattern specification / artery morphogenesis / skeletal system morphogenesis / ventricular septum morphogenesis / SMAD binding / negative regulation of endothelial cell proliferation / TGF-beta receptor signaling activates SMADs / roof of mouth development / positive regulation of SMAD protein signal transduction / blastocyst development / epithelial to mesenchymal transition / regulation of protein ubiquitination / bicellular tight junction / endothelial cell migration / cellular response to transforming growth factor beta stimulus / positive regulation of epithelial to mesenchymal transition / positive regulation of stress fiber assembly / Downregulation of TGF-beta receptor signaling / positive regulation of endothelial cell proliferation / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / transforming growth factor beta receptor signaling pathway / negative regulation of cell migration / thymus development / positive regulation of apoptotic signaling pathway / skeletal system development / post-embryonic development / negative regulation of extrinsic apoptotic signaling pathway / cell motility / kidney development / wound healing / cellular response to growth factor stimulus / UCH proteinases / male gonad development / peptidyl-serine phosphorylation / nervous system development / regulation of gene expression / heart development / positive regulation of cell growth / in utero embryonic development / receptor complex / Ub-specific processing proteases / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein kinase activity / regulation of cell cycle / endosome / intracellular signal transduction / cilium / positive regulation of cell migration / membrane raft / protein serine/threonine kinase activity / apoptotic process / positive regulation of cell population proliferation / ubiquitin protein ligase binding
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 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. ...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 / 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
Similarity search - Domain/homology
: / TGF-beta receptor type-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsWang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Xu, Y.
Funding support China, 1items
OrganizationGrant numberCountry
Not funded China
CitationJournal: To Be Published
Title: The Crystal Structure of the Type I TGF beta receptor from Biortus.
Authors: Wang, F. / Cheng, W. / Lv, Z. / Meng, Q. / Xu, Y.
History
DepositionFeb 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2024Group: Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_contact_author / pdbx_entity_nonpoly / pdbx_entry_details
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_contact_author.email / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TGF-beta receptor type-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3772
Polymers38,9781
Non-polymers3991
Water6,323351
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.196, 76.764, 89.707
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein TGF-beta receptor type-1 / TGFR-1 / Activin A receptor type II-like protein kinase of 53kD / Activin receptor-like kinase 5 / ...TGFR-1 / Activin A receptor type II-like protein kinase of 53kD / Activin receptor-like kinase 5 / ALK-5 / ALK5 / Serine/threonine-protein kinase receptor R4 / SKR4 / TGF-beta type I receptor / Transforming growth factor-beta receptor type I / TGF-beta receptor type I / TbetaR-I


Mass: 38977.691 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBR1, ALK5, SKR4 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: P36897, receptor protein serine/threonine kinase
#2: Chemical ChemComp-A1D6I / Vactosertib


Mass: 399.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18FN7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.86 Å3/Da / Density % sol: 34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.02M K/Na PO4, 0.1M Bis-Tris propane pH6.5, 20% PEG3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 4, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→44.85 Å / Num. obs: 56084 / % possible obs: 96.4 % / Redundancy: 13.1 % / CC1/2: 0.999 / Net I/σ(I): 22
Reflection shellResolution: 1.4→1.42 Å / Num. unique obs: 2705 / CC1/2: 0.866

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→38.757 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.962 / SU B: 1.028 / SU ML: 0.041 / Cross valid method: FREE R-VALUE / ESU R: 0.062 / ESU R Free: 0.064
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1924 2711 4.839 %
Rwork0.1661 53314 -
all0.167 --
obs-56025 96.251 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.27 Å2
Baniso -1Baniso -2Baniso -3
1--0.403 Å2-0 Å2-0 Å2
2--1.147 Å2-0 Å2
3----0.744 Å2
Refinement stepCycle: LAST / Resolution: 1.4→38.757 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2397 0 30 351 2778
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0122565
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162453
X-RAY DIFFRACTIONr_angle_refined_deg1.2251.6563487
X-RAY DIFFRACTIONr_angle_other_deg0.4291.5845643
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4055325
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.525.53628
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85210468
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.56910121
X-RAY DIFFRACTIONr_chiral_restr0.0640.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023105
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02633
X-RAY DIFFRACTIONr_nbd_refined0.2150.2468
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1780.22188
X-RAY DIFFRACTIONr_nbtor_refined0.1790.21231
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0760.21214
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1470.2216
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0950.27
X-RAY DIFFRACTIONr_nbd_other0.1650.258
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1180.220
X-RAY DIFFRACTIONr_mcbond_it1.3081.8371219
X-RAY DIFFRACTIONr_mcbond_other1.3071.8371219
X-RAY DIFFRACTIONr_mcangle_it2.0833.2991529
X-RAY DIFFRACTIONr_mcangle_other2.0823.3031530
X-RAY DIFFRACTIONr_scbond_it1.9782.0761346
X-RAY DIFFRACTIONr_scbond_other1.9772.0751347
X-RAY DIFFRACTIONr_scangle_it3.213.6981944
X-RAY DIFFRACTIONr_scangle_other3.2093.6971945
X-RAY DIFFRACTIONr_lrange_it4.96821.1613025
X-RAY DIFFRACTIONr_lrange_other4.72618.7192931
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.4-1.4360.2551930.24738170.24742600.9550.9694.13150.213
1.436-1.4760.2651800.22737180.22841170.9530.96594.68060.192
1.476-1.5180.2341810.20735970.20840280.9590.9793.79340.17
1.518-1.5650.2081700.19635450.19739280.9710.97494.57740.164
1.565-1.6160.2191690.1834560.18137820.9670.97895.84880.151
1.616-1.6730.2051930.17533160.17736730.9740.9895.5350.147
1.673-1.7360.2021790.16532070.16735420.9730.98295.59570.143
1.736-1.8070.1981730.17331170.17434250.9740.98196.05840.152
1.807-1.8870.1771460.1630090.16132710.9780.98496.45370.143
1.887-1.9790.1871480.16729010.16831540.9770.98396.67090.155
1.979-2.0850.191430.15827850.1630200.9790.98596.95360.15
2.085-2.2110.1641250.15326340.15328440.9830.98797.01130.149
2.211-2.3640.1771110.15825210.15826950.9790.98497.66230.157
2.364-2.5520.1941220.1523340.15224950.9790.98598.43690.155
2.552-2.7950.1961120.16421680.16623250.9760.98298.06450.175
2.795-3.1220.221990.16619690.16920990.9690.98298.52310.182
3.122-3.6020.171850.14817770.14918870.9820.98798.67510.17
3.602-4.4010.177790.14815130.14916080.9810.98699.0050.176
4.401-6.1850.181670.17512000.17512780.9810.98699.13930.212
6.185-38.7570.206360.2047300.2047740.9660.97798.96640.242

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more