+Open data
-Basic information
Entry | Database: PDB / ID: 4g3c | ||||||
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Title | Crystal structure of apo murine Nf-kappaB inducing kinase (NIK) | ||||||
Components | NF-kappa-beta-inducing kinase | ||||||
Keywords | TRANSFERASE / non-RD kinase / protein serine/threonine kinase / NF-kappaB / MAP3K14 | ||||||
Function / homology | Function and homology information CD28 dependent PI3K/Akt signaling / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / mitogen-activated protein kinase kinase kinase / non-canonical NF-kappaB signal transduction / MAP kinase kinase kinase activity / canonical NF-kappaB signal transduction / fibrillar center ...CD28 dependent PI3K/Akt signaling / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / Dectin-1 mediated noncanonical NF-kB signaling / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / mitogen-activated protein kinase kinase kinase / non-canonical NF-kappaB signal transduction / MAP kinase kinase kinase activity / canonical NF-kappaB signal transduction / fibrillar center / cellular response to mechanical stimulus / defense response to virus / protein kinase activity / immune response / phosphorylation / protein serine kinase activity / intracellular membrane-bounded organelle / protein serine/threonine kinase activity / nucleoplasm / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Hymowitz, S.G. / de Leon-Boenig, G. | ||||||
Citation | Journal: Structure / Year: 2012 Title: The crystal structure of the catalytic domain of the NF-kappaB inducing kinase reveals a narrow but flexible active site. Authors: de Leon-Boenig, G. / Bowman, K.K. / Feng, J.A. / Crawford, T. / Everett, C. / Franke, Y. / Oh, A. / Stanley, M. / Staben, S.T. / Starovasnik, M.A. / Wallweber, H.J. / Wu, J. / Wu, L.C. / ...Authors: de Leon-Boenig, G. / Bowman, K.K. / Feng, J.A. / Crawford, T. / Everett, C. / Franke, Y. / Oh, A. / Stanley, M. / Staben, S.T. / Starovasnik, M.A. / Wallweber, H.J. / Wu, J. / Wu, L.C. / Johnson, A.R. / Hymowitz, S.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g3c.cif.gz | 261.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g3c.ent.gz | 213.1 KB | Display | PDB format |
PDBx/mmJSON format | 4g3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g3/4g3c ftp://data.pdbj.org/pub/pdb/validation_reports/g3/4g3c | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 38801.680 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Map3k14, NF-kabbaB inducing kinase, Nik / Plasmid: pAcGP67 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9 References: UniProt: Q9WUL6, mitogen-activated protein kinase kinase kinase #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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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: 2.94 Å3/Da / Density % sol: 58.12 % |
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Crystal grow | Temperature: 276 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 2uL protein with 2uL well solution of 0.5 M ammonium sulfate, 0.9 M lithium sulfate,0.1M sodium citrate tribasic dihydrate , pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 276K |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 10, 2008 |
Radiation | Monochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9774 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→50 Å / Num. all: 49462 / Num. obs: 49462 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rsym value: 0.069 / Net I/σ(I): 19.9 |
Reflection shell | Resolution: 2.15→2.23 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 4920 / Rsym value: 0.584 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: homology model Resolution: 2.15→47.4 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.934 / SU B: 8.892 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.173 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.428 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→47.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.151→2.195 Å / Total num. of bins used: 25
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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