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- PDB-4g3e: Crystal structure of murine NF-kappaB inducing kinase (NIK) bound... -

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Basic information

Entry
Database: PDB / ID: 4g3e
TitleCrystal structure of murine NF-kappaB inducing kinase (NIK) bound to a 6-alkynylindoline (cmp1)
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 / phosphorylation / protein serine kinase activity / intracellular membrane-bounded organelle / 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 / Serine/Threonine protein kinases, catalytic 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-0WC / Mitogen-activated protein kinase kinase kinase 14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 15, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Jan 24, 2018Group: Refinement description / Structure summary / Category: audit_author / software / Item: _audit_author.name / _software.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
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)78,6877
Polymers77,6032
Non-polymers1,0845
Water1,09961
1
A: NF-kappa-beta-inducing kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,3924
Polymers38,8021
Non-polymers5903
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NF-kappa-beta-inducing kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,2963
Polymers38,8021
Non-polymers4942
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.145, 143.145, 45.151
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.732896, -0.680151, -0.01605), (0.680038, 0.73307, -0.012527), (0.020286, -0.001733, 0.999793)69.10763, -30.25893, -6.31223

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Components

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


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-kappaB 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 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-0WC / (2R)-4-[1-(2-amino-5-chloropyrimidin-4-yl)-2,3-dihydro-1H-indol-6-yl]-2-(1,3-thiazol-2-yl)but-3-yn-2-ol


Mass: 397.881 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H16ClN5OS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.98 Å3/Da / Density % sol: 58.73 %
Crystal growTemperature: 277 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 then soaked in well solution with 1 mM cmp1, pH 6.2, VAPOR ...Details: 2uL protein with 2uL well solution of 0.5 M ammonium sulfate, 0.9 M lithium sulfate,0.1M sodium citrate tribasic dihydrate then soaked in well solution with 1 mM cmp1, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97946 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 12, 2012
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 32116 / Num. obs: 32116 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rsym value: 0.068 / Net I/σ(I): 18.6
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2 / Num. unique all: 3153 / Rsym value: 0.598 / % possible all: 100

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Processing

Software
NameVersionClassification
Web-Icedata collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo murine NIK kinase domain

Resolution: 2.5→47.73 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.913 / SU B: 17.602 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.381 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24047 3259 10.1 %RANDOM
Rwork0.18931 ---
all0.19446 32110 --
obs0.19446 32110 99.54 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.801 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å2-0 Å2
2---0.28 Å20 Å2
3---0.57 Å2
Refinement stepCycle: LAST / Resolution: 2.5→47.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4956 0 69 61 5086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0195150
X-RAY DIFFRACTIONr_angle_refined_deg1.2241.9926969
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6975634
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.3723.443212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33115892
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4661537
X-RAY DIFFRACTIONr_chiral_restr0.080.2748
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213858
LS refinement shellResolution: 2.5→2.552 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.365 163 -
Rwork0.295 1574 -
obs--99.14 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0346-0.7101-1.60155.41370.10591.63670.0670.09150.2536-0.0639-0.0858-0.21120.0415-0.03610.01880.05760.06790.01360.09150.02080.210246.399940.0639-3.037
22.73960.4319-0.17514.3899-0.35963.9335-0.09180.1618-0.1261-0.26070.0187-0.20230.12440.23470.07310.18870.0560.03780.04260.00310.01753.059912.4309-4.2842
33.58531.3026-1.14795.49040.672.30370.10.01620.02810.0406-0.0803-0.2389-0.04320.0091-0.01970.00890.0202-0.02290.0927-0.030.1831.303667.04082.6789
43.41090.16930.50934.13070.44864.75590.21210.0146-0.1720.0469-0.0633-0.01960.48160.0103-0.14880.081-0.0391-0.0290.11240.04350.054617.324442.93711.0622
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A334 - 472
2X-RAY DIFFRACTION2A473 - 671
3X-RAY DIFFRACTION3B334 - 472
4X-RAY DIFFRACTION4B473 - 674

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