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Yorodumi- PDB-8bwn: Crystal structure of human Twisted gastrulation protein homolog 1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bwn | |||||||||||||||
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Title | Crystal structure of human Twisted gastrulation protein homolog 1 (TWSG1) in complex with human Growth Differentiation Factor 5 (GDF5) and calcium, long-wavelength X-ray dataset (4010 eV) | |||||||||||||||
Components |
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Keywords | SIGNALING PROTEIN / Twisted gastrulation protein homolog 1 (TWSG1) / Transforming Growth Factor beta (TGF-beta) signalling pathway / Growth Differentiation Factor 5 (GDF5) / long-wavelength X-rays. | |||||||||||||||
Function / homology | Function and homology information negative regulation of CD4-positive, alpha-beta T cell activation / ossification involved in bone remodeling / forelimb morphogenesis / BMP binding / chondroblast differentiation / hindlimb morphogenesis / negative regulation of mesenchymal cell apoptotic process / positive regulation of chondrocyte differentiation / regulation of BMP signaling pathway / mesenchymal cell apoptotic process ...negative regulation of CD4-positive, alpha-beta T cell activation / ossification involved in bone remodeling / forelimb morphogenesis / BMP binding / chondroblast differentiation / hindlimb morphogenesis / negative regulation of mesenchymal cell apoptotic process / positive regulation of chondrocyte differentiation / regulation of BMP signaling pathway / mesenchymal cell apoptotic process / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of BMP signaling pathway / transforming growth factor beta binding / camera-type eye development / negative regulation of chondrocyte differentiation / embryonic limb morphogenesis / Molecules associated with elastic fibres / negative regulation of BMP signaling pathway / negative regulation of cytokine production / negative regulation of osteoblast differentiation / BMP signaling pathway / salivary gland morphogenesis / positive regulation of transforming growth factor beta receptor signaling pathway / positive regulation of SMAD protein signal transduction / hemopoiesis / mesoderm formation / regulation of multicellular organism growth / chondrocyte differentiation / ossification / response to mechanical stimulus / forebrain development / positive regulation of neuron differentiation / transforming growth factor beta receptor signaling pathway / cytokine activity / growth factor activity / negative regulation of epithelial cell proliferation / cell-cell signaling / heparin binding / negative regulation of neuron apoptotic process / extracellular space / extracellular region / identical protein binding / plasma membrane Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å | |||||||||||||||
Authors | Malinauskas, T. / Rudolf, A.F. / Moore, G. / Eggington, H. / Belnoue-Davis, H. / El Omari, K. / Woolley, R.E. / Griffiths, S.C. / Duman, R. / Wagner, A. ...Malinauskas, T. / Rudolf, A.F. / Moore, G. / Eggington, H. / Belnoue-Davis, H. / El Omari, K. / Woolley, R.E. / Griffiths, S.C. / Duman, R. / Wagner, A. / Leedham, S.J. / Baldock, C. / Ashe, H. / Siebold, C. | |||||||||||||||
Funding support | United Kingdom, European Union, France, 4items
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Citation | Journal: Nat Commun / Year: 2024 Title: Molecular mechanism of BMP signal control by Twisted gastrulation. Authors: Malinauskas, T. / Moore, G. / Rudolf, A.F. / Eggington, H. / Belnoue-Davis, H.L. / El Omari, K. / Griffiths, S.C. / Woolley, R.E. / Duman, R. / Wagner, A. / Leedham, S.J. / Baldock, C. / Ashe, H.L. / Siebold, C. | |||||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bwn.cif.gz | 225.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bwn.ent.gz | 153.1 KB | Display | PDB format |
PDBx/mmJSON format | 8bwn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bwn_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8bwn_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8bwn_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 8bwn_validation.cif.gz | 17.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/8bwn ftp://data.pdbj.org/pub/pdb/validation_reports/bw/8bwn | HTTPS FTP |
-Related structure data
Related structure data | 8bwaC 8bwdC 8bwiC 8bwlC 8bwmC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
#1: Protein | Mass: 13729.833 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: GDF5, BMP14, CDMP1 / Details (production host): pET22b / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLysS / References: UniProt: P43026 #2: Protein | Mass: 7499.739 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TWSG1, TSG, PSEC0250 / Cell line (production host): HEK293T / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: Q9GZX9 #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.35 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 12.5% w/v PEG 1000, 12.5% w/v PEG 3350, 12.5% v/v MPD, 100 mM CaCl2, 0.1 M MOPS/HEPES-Na pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I23 / Wavelength: 3.09187 Å |
Detector | Type: DECTRIS PILATUS 12M / Detector: PIXEL / Date: Feb 17, 2022 |
Radiation | Monochromator: Silicon crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 3.09187 Å / Relative weight: 1 |
Reflection | Resolution: 2.567→65.86 Å / Num. obs: 12005 / % possible obs: 72 % / Redundancy: 10.2 % / Biso Wilson estimate: 83.72 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.029 / Rrim(I) all: 0.097 / Net I/σ(I): 13.5 |
Reflection shell | Resolution: 2.567→2.845 Å / Redundancy: 10.1 % / Rmerge(I) obs: 1.59 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 600 / CC1/2: 0.599 / Rpim(I) all: 0.52 / Rrim(I) all: 1.674 / % possible all: 13.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.57→65.86 Å / SU ML: 0.3705 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 38.6184 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 94.27 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.57→65.86 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION
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