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- PDB-4g3d: Crystal structure of human NF-kappaB inducing kinase (NIK) -

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Basic information

Entry
Database: PDB / ID: 4g3d
TitleCrystal structure of human NF-kappaB inducing kinase (NIK)
ComponentsNF-kappa-beta-inducing kinase
KeywordsTRANSFERASE / non-RD kinase / protein serine/threonine kinase / NF-kappaB / MAP3K14
Function / homology
Function and homology information


TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / mitogen-activated protein kinase kinase kinase / JUN kinase kinase kinase activity / non-canonical NF-kappaB signal transduction / CD28 dependent PI3K/Akt signaling / 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 ...TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / mitogen-activated protein kinase kinase kinase / JUN kinase kinase kinase activity / non-canonical NF-kappaB signal transduction / CD28 dependent PI3K/Akt signaling / 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 / MAPK cascade / defense response to virus / protein kinase activity / immune response / intracellular membrane-bounded organelle / 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 / : / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase domain ...Mitogen-activated protein (MAP) kinase kinase kinase 14 / M3K14, catalytic domain / : / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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
Mitogen-activated protein kinase kinase kinase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _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
B: NF-kappa-beta-inducing kinase
D: NF-kappa-beta-inducing kinase
E: NF-kappa-beta-inducing kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,9227
Polymers162,8504
Non-polymers733
Water32418
1
A: NF-kappa-beta-inducing kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7372
Polymers40,7121
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: NF-kappa-beta-inducing kinase


Theoretical massNumber of molelcules
Total (without water)40,7121
Polymers40,7121
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
D: NF-kappa-beta-inducing kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7372
Polymers40,7121
Non-polymers241
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
E: NF-kappa-beta-inducing kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7372
Polymers40,7121
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.746, 145.851, 230.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.998665, 0.04522, 0.024954), (-0.017572, 0.751816, -0.659138), (-0.048567, 0.65782, 0.751608)-8.16074, 5.4088, -23.18439
3given(-0.988703, 0.130267, -0.074143), (-0.065251, 0.071258, 0.995321), (0.134941, 0.988915, -0.061953)43.4327, -78.60721, 38.17986
4given(-0.993738, 0.07328, 0.084353), (-0.007207, 0.711314, -0.702838), (-0.111505, -0.699044, -0.706331)37.34609, 40.64146, 160.30974

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Components

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


Mass: 40712.395 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MAP3K14, NF-kappaB inducing kinase (NIK), NIK / Plasmid: pAcGP67 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: Q99558, mitogen-activated protein kinase kinase kinase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.36 Å3/Da / Density % sol: 47.97 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1:1 protein and well solution of 100 mM imidazole (pH 6.5), 1 M sodium acetate tri-hydrate, 7.5% 1,6-hexanediol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 28, 2008
RadiationMonochromator: 0.97945 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 35489 / Num. obs: 35489 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Net I/σ(I): 21.8
Reflection shellResolution: 2.9→3 Å / Redundancy: 7.4 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.611 / % 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 / Resolution: 2.9→47.57 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.887 / SU B: 35.575 / SU ML: 0.314 / Cross valid method: THROUGHOUT / ESU R Free: 0.443 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26646 2687 8 %RANDOM
Rwork0.20071 ---
obs0.20601 31030 95.22 %-
all-33717 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 80.574 Å2
Baniso -1Baniso -2Baniso -3
1-4.77 Å2-0 Å2-0 Å2
2---3.53 Å20 Å2
3----1.24 Å2
Refinement stepCycle: LAST / Resolution: 2.9→47.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9325 0 3 18 9346
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0199527
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0391.96512889
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.15451199
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.89423.698411
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.73151601
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.031565
X-RAY DIFFRACTIONr_chiral_restr0.0640.21413
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0217193
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.96 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rwork0.256 1625 -
Rfree-0 -
obs--85.8 %
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)
10.98390.59040.07092.7521-0.78550.32040.1485-0.16350.0389-0.2912-0.10380.00390.0720.0364-0.04480.375-0.02980.00050.3781-0.00980.456910.137330.503439.3384
21.04520.0519-0.06521.9936-0.870.91460.14260.10080.10430.1758-0.17170.020.02090.07920.0290.2848-0.03080.00240.47450.06890.41458.71486.234953.3823
30.94250.648-0.19571.0184-0.43112.76630.00350.0218-0.0901-0.22150.0532-0.0359-0.2037-0.0375-0.05670.4410.02040.04710.3374-0.04580.418514.683560.78630.8365
42.46570.47820.0050.56550.3291.23140.2758-0.1189-0.24760.1237-0.1548-0.02690.00480.0175-0.1210.2782-0.0095-0.05140.43670.01290.473412.576252.149357.3259
50.62690.4678-1.50492.3124-0.93033.86640.1784-0.0067-0.00730.3785-0.22960.2159-0.2890.25110.05120.70450.00360.1020.3211-0.03340.188425.09124.204110.331
61.15490.0605-0.49831.5099-1.05313.19460.13060.16850.0637-0.03990.1295-0.131-0.8046-0.1557-0.26020.8244-0.09310.1240.15080.04620.259931.220216.808885.9221
71.61130.2929-0.55062.5195-0.18362.44380.04930.13370.08270.21690.0141-0.00330.33870.0196-0.06340.64840-0.10670.26540.01190.24340.714875.508890.2764
82.45580.5521-1.11534.2014-1.07150.7401-0.12560.152-0.16760.41730.0531-0.04260.2472-0.03410.07251.26970.0573-0.08780.0684-0.01140.103838.87347.853395.7349
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A332 - 470
2X-RAY DIFFRACTION2A471 - 671
3X-RAY DIFFRACTION3B332 - 470
4X-RAY DIFFRACTION4B471 - 666
5X-RAY DIFFRACTION5D338 - 470
6X-RAY DIFFRACTION6D471 - 657
7X-RAY DIFFRACTION7E332 - 470
8X-RAY DIFFRACTION8E471 - 663

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