+Open data
-Basic information
Entry | Database: PDB / ID: 4dn5 | ||||||
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Title | Crystal Structure of NF-kB-inducing Kinase (NIK) | ||||||
Components | Mitogen-activated protein kinase kinase kinase 14 | ||||||
Keywords | TRANSFERASE / non-RD kinase / protein serine/threonine kinase / ATP binding | ||||||
Function / homology | Function and homology information : / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / mitogen-activated protein kinase kinase kinase / non-canonical NF-kappaB signal transduction / CD28 dependent PI3K/Akt signaling / MAP kinase kinase kinase activity / canonical NF-kappaB signal transduction / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / Dectin-1 mediated noncanonical NF-kB signaling ...: / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / mitogen-activated protein kinase kinase kinase / non-canonical NF-kappaB signal transduction / CD28 dependent PI3K/Akt signaling / MAP kinase kinase kinase activity / canonical NF-kappaB signal transduction / NIK-->noncanonical NF-kB signaling / TNFR2 non-canonical NF-kB pathway / Dectin-1 mediated noncanonical NF-kB signaling / fibrillar center / cellular response to mechanical stimulus / defense response to virus / protein kinase activity / immune response / phosphorylation / intracellular membrane-bounded organelle / protein serine kinase activity / protein serine/threonine kinase activity / nucleoplasm / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | ||||||
Authors | Min, X. / Liu, J. / Sudom, A. / Walker, N.P. / Wang, Z. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2012 Title: Structure of Nuclear Factor Kappa B-inducing kinase domain reveals a constitutively active conformation Authors: Liu, J. / Sudom, A. / Min, X. / Cao, Z. / Gao, X. / Ayres, M. / Lee, F. / Cao, P. / Johnstone, S. / Plotnikova, O. / Walker, N. / Chen, G. / Wang, Z. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dn5.cif.gz | 144.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dn5.ent.gz | 112.4 KB | Display | PDB format |
PDBx/mmJSON format | 4dn5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dn/4dn5 ftp://data.pdbj.org/pub/pdb/validation_reports/dn/4dn5 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 39173.715 Da / Num. of mol.: 2 / Fragment: unp residues 330-680 / Mutation: S549D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K14, NF-kB-inducing Kinase, NIK / Plasmid: pFASTBacHT / Cell line (production host): sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q99558, mitogen-activated protein kinase kinase kinase |
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-Non-polymers , 5 types, 81 molecules
#2: Chemical | #3: Chemical | ChemComp-GOL / | #4: Chemical | ChemComp-EDO / #5: Chemical | #6: 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: 2.66 Å3/Da / Density % sol: 53.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.4 Details: 12.5% polyethylene glycol 3350, 200 mM ammonium sulfate and 0.1 M sodium citrate, pH 5.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å | |||||||||||||||
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2006 / Details: mirrors | |||||||||||||||
Radiation | Monochromator: DOUBLE-CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.5→47.75 Å / Num. all: 28420 / Num. obs: 137194 / % possible obs: 99.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Biso Wilson estimate: 60.4 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 15.8 | |||||||||||||||
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 3.4 / Num. unique all: 4101 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.915 / SU B: 10.213 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.094 / ESU R Free: 0.053 / 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: 1.2 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 55.864 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.499→2.563 Å / Total num. of bins used: 20
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