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Yorodumi- PDB-4ym4: Truncated Human TIFA in complex with its Thr9 phosphorylated N-te... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4ym4 | |||||||||
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Title | Truncated Human TIFA in complex with its Thr9 phosphorylated N-terminal peptide 1-15 | |||||||||
Components | (TRAF-interacting protein with FHA domain-containing protein A) x 2 | |||||||||
Keywords | SIGNALING PROTEIN / Complex / FHA domian / adaptor | |||||||||
Function / homology | Function and homology information cytoplasmic pattern recognition receptor signaling pathway / tumor necrosis factor-mediated signaling pathway / Alpha-protein kinase 1 signaling pathway / TAK1-dependent IKK and NF-kappa-B activation / protein homooligomerization / positive regulation of canonical NF-kappaB signal transduction / innate immune response / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.12 Å | |||||||||
Authors | Weng, J.H. / Wei, T.Y.W. / Hsieh, Y.C. / Huang, C.C.F. / Wu, P.Y.G. / Chen, E.S.W. / Huang, K.F. / Chen, C.J. / Tsai, M.D. | |||||||||
Funding support | Taiwan, 2items
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Citation | Journal: Biochemistry / Year: 2015 Title: Uncovering the Mechanism of Forkhead-Associated Domain-Mediated TIFA Oligomerization That Plays a Central Role in Immune Responses. Authors: Weng, J.H. / Hsieh, Y.C. / Huang, C.C. / Wei, T.Y. / Lim, L.H. / Chen, Y.H. / Ho, M.R. / Wang, I. / Huang, K.F. / Chen, C.J. / Tsai, M.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4ym4.cif.gz | 40.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ym4.ent.gz | 31.6 KB | Display | PDB format |
PDBx/mmJSON format | 4ym4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4ym4_validation.pdf.gz | 443.1 KB | Display | wwPDB validaton report |
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Full document | 4ym4_full_validation.pdf.gz | 447.5 KB | Display | |
Data in XML | 4ym4_validation.xml.gz | 8.7 KB | Display | |
Data in CIF | 4ym4_validation.cif.gz | 10.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ym/4ym4 ftp://data.pdbj.org/pub/pdb/validation_reports/ym/4ym4 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 16848.533 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 10-150 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TIFA, T2BP / Plasmid: pET43.1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96CG3 |
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#2: Protein/peptide | Mass: 1455.349 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 1-12 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q96CG3 |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.3 Å3/Da / Density % sol: 62.76 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / Details: 2.1 M DL-malic acid pH7.0 / PH range: 6.5-7.5 |
-Data collection
Diffraction | Mean temperature: 110 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→20 Å / Num. obs: 4922 / % possible obs: 100 % / Redundancy: 21.8 % / Rmerge(I) obs: 0.161 / Rpim(I) all: 0.035 / Rrim(I) all: 0.164 / Χ2: 0.947 / Net I/av σ(I): 23.556 / Net I/σ(I): 6.3 / Num. measured all: 107113 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _ / % possible all: 100
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-Processing
Software |
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Refinement | Resolution: 3.12→20 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.888 / SU B: 0.004 / SU ML: 0 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.354 / ESU R Free: 0.396 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||
Displacement parameters | Biso max: 186.46 Å2 / Biso mean: 44.632 Å2 / Biso min: 16.05 Å2
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Refinement step | Cycle: final / Resolution: 3.12→20 Å
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LS refinement shell | Resolution: 3.121→3.202 Å / Total num. of bins used: 20
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