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Yorodumi- PDB-8bwi: Crystal structure of human Twisted gastrulation protein homolog 1... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bwi | |||||||||||||||
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Title | Crystal structure of human Twisted gastrulation protein homolog 1 (TWSG1), crystal form 2 | |||||||||||||||
Components | Twisted gastrulation protein homolog 1 | |||||||||||||||
Keywords | SIGNALING PROTEIN / Twisted gastrulation protein homolog 1 (TWSG1) / Transforming Growth Factor beta (TGF-beta) signalling pathway / extracellular protein / disulfide rich domains. | |||||||||||||||
Function / homology | Function and homology information negative regulation of CD4-positive, alpha-beta T cell activation / regulation of BMP signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of BMP signaling pathway / camera-type eye development / transforming growth factor beta binding / negative regulation of cytokine production / positive regulation of transforming growth factor beta receptor signaling pathway / hemopoiesis / positive regulation of SMAD protein signal transduction ...negative regulation of CD4-positive, alpha-beta T cell activation / regulation of BMP signaling pathway / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of BMP signaling pathway / camera-type eye development / transforming growth factor beta binding / negative regulation of cytokine production / positive regulation of transforming growth factor beta receptor signaling pathway / hemopoiesis / positive regulation of SMAD protein signal transduction / mesoderm formation / negative regulation of BMP signaling pathway / negative regulation of osteoblast differentiation / chondrocyte differentiation / BMP signaling pathway / salivary gland morphogenesis / forebrain development / ossification / heparin binding / extracellular space Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 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 | 8bwi.cif.gz | 125.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bwi.ent.gz | 82.6 KB | Display | PDB format |
PDBx/mmJSON format | 8bwi.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bwi_validation.pdf.gz | 427.4 KB | Display | wwPDB validaton report |
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Full document | 8bwi_full_validation.pdf.gz | 429.9 KB | Display | |
Data in XML | 8bwi_validation.xml.gz | 8 KB | Display | |
Data in CIF | 8bwi_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bw/8bwi ftp://data.pdbj.org/pub/pdb/validation_reports/bw/8bwi | HTTPS FTP |
-Related structure data
Related structure data | 8bwaC 8bwdC 8bwlC 8bwmC 8bwnC 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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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23569.760 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TWSG1, TSG, PSEC0250 / Plasmid: pHLsec / Cell line (production host): HEK293T / Organ (production host): Kidney / Production host: Homo sapiens (human) / References: UniProt: Q9GZX9 |
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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: 2.5 Å3/Da / Density % sol: 50.81 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / Details: 1.0 M K/Na tartrate, 0.1 M MES pH 6.0 / PH range: 6.0-7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96862 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 30, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.96862 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→48.08 Å / Num. obs: 3626 / % possible obs: 99.4 % / Redundancy: 15.6 % / Biso Wilson estimate: 99.38 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.251 / Rpim(I) all: 0.069 / Rrim(I) all: 0.265 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 3.4→3.49 Å / Redundancy: 15.4 % / Rmerge(I) obs: 5.961 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 254 / CC1/2: 0.436 / Rpim(I) all: 1.551 / Rrim(I) all: 6.167 / % possible all: 98.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→46.12 Å / SU ML: 0.6835 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.5408 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: 109.51 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→46.12 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.4→46.12 Å
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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 / Auth asym-ID: A / Label asym-ID: A
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