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- PDB-4g3f: Crystal structure of murine NF-kappaB inducing kinase (NIK) bound... -

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Basic information

Entry
Database: PDB / ID: 4g3f
TitleCrystal structure of murine NF-kappaB inducing kinase (NIK) bound to a 2-(aminothiazoly)phenol (cmp2)
ComponentsNF-kappa-beta-inducing kinase
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / non-RD kinase / protein serine/threonine kinase / NF-kappaB / structure-based drug design / MAP3K14 / TRANSFERASE / TRANSFERASE-TRANSFERASE INHIBITOR complex
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 / protein serine kinase activity / protein serine/threonine kinase activity / nucleoplasm / ATP binding / cytosol
Similarity search - Function
Mitogen-activated protein (MAP) kinase kinase kinase 14 / M3K14, catalytic domain / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain ...Mitogen-activated protein (MAP) kinase kinase kinase 14 / M3K14, catalytic domain / : / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-0WB / Mitogen-activated protein kinase kinase kinase 14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.642 Å
AuthorsHymowitz, S.G. / de Leon-Boenig, G.
CitationJournal: 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
DepositionJul 13, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NF-kappa-beta-inducing kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2912
Polymers36,9801
Non-polymers3111
Water4,396244
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.789, 135.619, 64.857
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-910-

HOH

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Components

#1: Protein NF-kappa-beta-inducing kinase / Serine/threonine-protein kinase NIK


Mass: 36979.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Map3k14, NF-kappaB inducing kinase (NIK), 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-0WB / 3-{2-[(5-fluoro-2-hydroxyphenyl)amino]-1,3-thiazol-4-yl}benzonitrile


Mass: 311.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H10FN3OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 2 uL plus 2 uL well solution containing 1 mm cmp2, 100 mM bis-TRIS pH 6.5, 100 mM sodium chloride, 20% PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jul 29, 2009
RadiationMonochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 1.64→50 Å / Num. all: 39429 / % possible obs: 96.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Rsym value: 0.053 / Net I/σ(I): 36.4
Reflection shellResolution: 1.64→1.7 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 4.3 / Num. unique all: 3607 / Rsym value: 0.34 / % possible all: 89.4

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.3_928)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.642→33.226 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 18.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2081 3946 10.01 %Random
Rwork0.1773 ---
all0.1804 39407 --
obs0.1804 39407 97.06 %-
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.725 Å2 / ksol: 0.378 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0.0551 Å2-0 Å20 Å2
2---0.1335 Å20 Å2
3---0.0784 Å2
Refinement stepCycle: LAST / Resolution: 1.642→33.226 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2420 0 22 244 2686
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062555
X-RAY DIFFRACTIONf_angle_d1.1233462
X-RAY DIFFRACTIONf_dihedral_angle_d12.345970
X-RAY DIFFRACTIONf_chiral_restr0.076364
X-RAY DIFFRACTIONf_plane_restr0.006449
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6425-1.66250.26111320.24811153X-RAY DIFFRACTION89
1.6625-1.68350.25221510.22331209X-RAY DIFFRACTION95
1.6835-1.70570.21431380.21151205X-RAY DIFFRACTION95
1.7057-1.7290.22611140.19091242X-RAY DIFFRACTION95
1.729-1.75380.24231480.19241230X-RAY DIFFRACTION95
1.7538-1.77990.26481190.19711244X-RAY DIFFRACTION96
1.7799-1.80770.22931630.17771247X-RAY DIFFRACTION97
1.8077-1.83740.21791350.17841233X-RAY DIFFRACTION97
1.8374-1.86910.22681370.16691278X-RAY DIFFRACTION97
1.8691-1.9030.19691490.17291235X-RAY DIFFRACTION97
1.903-1.93960.20481370.16571242X-RAY DIFFRACTION97
1.9396-1.97920.20811460.16211264X-RAY DIFFRACTION98
1.9792-2.02230.21681380.15721259X-RAY DIFFRACTION97
2.0223-2.06930.20311430.1571245X-RAY DIFFRACTION97
2.0693-2.1210.2231300.16411278X-RAY DIFFRACTION97
2.121-2.17840.18271450.16331256X-RAY DIFFRACTION98
2.1784-2.24250.19091500.16551272X-RAY DIFFRACTION98
2.2425-2.31480.20711360.16221260X-RAY DIFFRACTION98
2.3148-2.39750.21521370.17191301X-RAY DIFFRACTION98
2.3975-2.49350.21541300.17651291X-RAY DIFFRACTION98
2.4935-2.60690.1971500.17521268X-RAY DIFFRACTION98
2.6069-2.74430.22061460.18121285X-RAY DIFFRACTION99
2.7443-2.91620.20031350.19341304X-RAY DIFFRACTION99
2.9162-3.14120.23021750.18521266X-RAY DIFFRACTION98
3.1412-3.4570.21440.18011297X-RAY DIFFRACTION99
3.457-3.95650.18281460.17191335X-RAY DIFFRACTION99
3.9565-4.98210.17421310.15311358X-RAY DIFFRACTION99
4.9821-33.23240.23811410.21271404X-RAY DIFFRACTION98
Refinement TLS params.Method: refined / Origin x: 18.7599 Å / Origin y: 17.8369 Å / Origin z: 2.465 Å
111213212223313233
T0.0698 Å20.0021 Å20.0097 Å2-0.0968 Å2-0.0073 Å2--0.0827 Å2
L0.1815 °2-0.1773 °20.1619 °2-1.0653 °2-0.5144 °2--0.9699 °2
S0.0125 Å °-0.0054 Å °-0.0145 Å °0.0111 Å °0.0021 Å °0.0508 Å °0.1007 Å °-0.0081 Å °0.0002 Å °
Refinement TLS groupSelection details: (chain A and resseq 345:676)

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