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- PDB-8ws0: Crystal structure of human NEK7 S195D mutant -

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Basic information

Entry
Database: PDB / ID: 8ws0
TitleCrystal structure of human NEK7 S195D mutant
ComponentsSerine/threonine-protein kinase Nek7
KeywordsCELL CYCLE / Kinase / Complex / autoinhibitory / human / inflammasomes
Function / homology
Function and homology information


NEK6-subfamily protein kinase / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Nuclear Pore Complex (NPC) Disassembly / cellular response to potassium ion / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of telomere maintenance / microtubule organizing center / spindle assembly / EML4 and NUDC in mitotic spindle formation / regulation of mitotic cell cycle ...NEK6-subfamily protein kinase / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Nuclear Pore Complex (NPC) Disassembly / cellular response to potassium ion / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of telomere maintenance / microtubule organizing center / spindle assembly / EML4 and NUDC in mitotic spindle formation / regulation of mitotic cell cycle / molecular function activator activity / spindle pole / microtubule / eukaryotic translation initiation factor 2alpha kinase activity / 3-phosphoinositide-dependent protein kinase activity / DNA-dependent protein kinase activity / ribosomal protein S6 kinase activity / histone H3S10 kinase activity / histone H2AXS139 kinase activity / histone H3S28 kinase activity / histone H4S1 kinase activity / histone H2BS14 kinase activity / histone H3T3 kinase activity / histone H2AS121 kinase activity / Rho-dependent protein serine/threonine kinase activity / histone H2BS36 kinase activity / histone H3S57 kinase activity / histone H2AT120 kinase activity / AMP-activated protein kinase activity / histone H2AS1 kinase activity / histone H3T6 kinase activity / histone H3T11 kinase activity / histone H3T45 kinase activity / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Serine-threonine/tyrosine-protein kinase, catalytic domain / 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
Similarity search - Domain/homology
Serine/threonine-protein kinase Nek7
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsBijpuria, S. / Athresh, S. / Subbiah, R. / Mollard, A. / Bearss, D.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: Crystal structure of human NEK7 S195D mutant
Authors: Bijpuria, S. / Athresh, S. / Subbiah, R. / Mollard, A. / Bearss, D.
History
DepositionOct 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Serine/threonine-protein kinase Nek7
B: Serine/threonine-protein kinase Nek7


Theoretical massNumber of molelcules
Total (without water)71,3962
Polymers71,3962
Non-polymers00
Water3,423190
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.601, 88.601, 156.088
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Serine/threonine-protein kinase Nek7 / Never in mitosis A-related kinase 7 / NimA-related protein kinase 7


Mass: 35698.121 Da / Num. of mol.: 2 / Mutation: S195D
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEK7 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TDX7, NEK6-subfamily protein kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 190 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationN

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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: 2.84 Å3/Da / Density % sol: 56.72 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris pH 8.5, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953643918037 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 28, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.953643918037 Å / Relative weight: 1
ReflectionResolution: 2.117→44.34 Å / Num. obs: 41004 / % possible obs: 99.5 % / Redundancy: 20 % / CC1/2: 1 / Rmerge(I) obs: 0.058 / Net I/σ(I): 28.5
Reflection shellResolution: 2.117→2.18 Å / Rmerge(I) obs: 1.149 / Num. unique obs: 3084 / CC1/2: 0.81 / % possible all: 93.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→44.34 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.942 / SU B: 10.265 / SU ML: 0.132 / Cross valid method: THROUGHOUT / ESU R: 0.192 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24176 1948 4.8 %RANDOM
Rwork0.19117 ---
obs0.1936 39008 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 57.613 Å2
Baniso -1Baniso -2Baniso -3
1-0.56 Å20.28 Å20 Å2
2--0.56 Å2-0 Å2
3----1.82 Å2
Refinement stepCycle: 1 / Resolution: 2.12→44.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4324 0 0 190 4514
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0134449
X-RAY DIFFRACTIONr_bond_other_d0.0040.0154241
X-RAY DIFFRACTIONr_angle_refined_deg1.9171.6446016
X-RAY DIFFRACTIONr_angle_other_deg1.4191.5839782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8315543
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.82922.076236
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.0215795
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.0381529
X-RAY DIFFRACTIONr_chiral_restr0.0940.2563
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.024986
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021020
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_it3.8714.5962160
X-RAY DIFFRACTIONr_mcbond_other3.8714.5952159
X-RAY DIFFRACTIONr_mcangle_it5.2716.8662698
X-RAY DIFFRACTIONr_mcangle_other5.276.8682699
X-RAY DIFFRACTIONr_scbond_it4.6715.1262289
X-RAY DIFFRACTIONr_scbond_other4.675.1272290
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.9917.4633316
X-RAY DIFFRACTIONr_long_range_B_refined9.01253.5464953
X-RAY DIFFRACTIONr_long_range_B_other9.01353.4154933
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.12→2.172 Å
RfactorNum. reflection% reflection
Rfree0.289 125 -
Rwork0.268 2704 -
obs--94.81 %
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)
11.0393-0.12850.0220.20680.17410.3181-0.07730.0277-0.0958-0.10690.0110.0368-0.06390.02110.06630.0979-0.00360.00370.00590.00980.089122.952125.2949-24.3789
20.3230.206-0.2924.2342-1.44910.8971-0.01060.003-0.0291-0.05980.03110.57840.0638-0.0428-0.02050.04630.05470.01370.0949-0.01430.165232.50516.00350.1178
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A20 - 300
2X-RAY DIFFRACTION2B19 - 299

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