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- PDB-4dn5: Crystal Structure of NF-kB-inducing Kinase (NIK) -

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Basic information

Entry
Database: PDB / ID: 4dn5
TitleCrystal Structure of NF-kB-inducing Kinase (NIK)
ComponentsMitogen-activated protein kinase kinase kinase 14
KeywordsTRANSFERASE / 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
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
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Mitogen-activated protein kinase kinase kinase 14
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMin, X. / Liu, J. / Sudom, A. / Walker, N.P. / Wang, Z.
CitationJournal: 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
DepositionFeb 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Non-polymer description
Revision 1.2Jul 17, 2013Group: Database references
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_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.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_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_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: Mitogen-activated protein kinase kinase kinase 14
B: Mitogen-activated protein kinase kinase kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,90713
Polymers78,3472
Non-polymers1,56011
Water1,26170
1
A: Mitogen-activated protein kinase kinase kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1249
Polymers39,1741
Non-polymers9508
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Mitogen-activated protein kinase kinase kinase 14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7834
Polymers39,1741
Non-polymers6103
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6350 Å2
ΔGint-27 kcal/mol
Surface area29040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)85.060, 85.060, 115.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Mitogen-activated protein kinase kinase kinase 14 / NF-kappa-beta-inducing kinase / HsNIK / Serine/threonine-protein kinase NIK


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 ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 70 / 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: 2.66 Å3/Da / Density % sol: 53.83 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 1, 2006 / Details: mirrors
RadiationMonochromator: DOUBLE-CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.626
11K, H, -L20.374
ReflectionResolution: 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 shellResolution: 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

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Processing

Software
NameVersionClassification
BOSdata collection
PHASERphasing
REFMAC5.6.0117refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod 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
RfactorNum. reflection% reflectionSelection details
Rfree0.22185 1417 5 %RANDOM
Rwork0.18244 ---
obs0.18435 26957 99.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 55.864 Å2
Baniso -1Baniso -2Baniso -3
1--7.04 Å20 Å20 Å2
2---7.04 Å20 Å2
3---14.09 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5128 0 94 70 5292
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0195337
X-RAY DIFFRACTIONr_angle_refined_deg0.9971.9857225
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7325657
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.68823.19232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.82415893
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.7741544
X-RAY DIFFRACTIONr_chiral_restr0.0660.2774
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214024
LS refinement shellResolution: 2.499→2.563 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 125 -
Rwork0.242 1922 -
obs--97.57 %

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