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- PDB-2wqm: Structure of apo human Nek7 -

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Basic information

Entry
Database: PDB / ID: 2wqm
TitleStructure of apo human Nek7
ComponentsSERINE/THREONINE-PROTEIN KINASE NEK7
KeywordsTRANSFERASE / ATP-BINDING / POLYMORPHISM / METAL-BINDING / SERINE/THREONINE-PROTEIN KINASE / CELL CYCLE KINASE / MITOSIS / CYTOPLASM / MAGNESIUM / PHOSPHOPROTEIN / PROTEIN KINASE / NUCLEOTIDE-BINDING
Function / homology
Function and homology information


NEK6-subfamily protein kinase / Activation of NIMA Kinases NEK9, NEK6, NEK7 / cellular response to potassium ion / Nuclear Pore Complex (NPC) Disassembly / microtubule organizing center / positive regulation of NLRP3 inflammasome complex assembly / regulation of mitotic cell cycle / positive regulation of telomere capping / spindle assembly / EML4 and NUDC in mitotic spindle formation ...NEK6-subfamily protein kinase / Activation of NIMA Kinases NEK9, NEK6, NEK7 / cellular response to potassium ion / Nuclear Pore Complex (NPC) Disassembly / microtubule organizing center / positive regulation of NLRP3 inflammasome complex assembly / regulation of mitotic cell cycle / positive regulation of telomere capping / spindle assembly / EML4 and NUDC in mitotic spindle formation / positive regulation of telomerase activity / positive regulation of telomere maintenance via telomerase / molecular function activator activity / spindle pole / microtubule / protein phosphorylation / protein serine kinase activity / centrosome / protein serine/threonine kinase activity / nucleoplasm / ATP binding / metal ion binding / nucleus / cytoplasm
Similarity search - Function
Serine-threonine/tyrosine-protein kinase, 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 ...Serine-threonine/tyrosine-protein kinase, 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
NICKEL (II) ION / Serine/threonine-protein kinase Nek7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRichards, M.W. / Bayliss, R.
CitationJournal: Mol.Cell / Year: 2009
Title: An Auto-Inhibitory Tyrosine Motif in the Cell-Cycle Regulated Nek7 Kinase is Released Through Binding of Nek9
Authors: Richards, M.W. / O'Regan, L. / Mas-Droux, C. / Blot, J.M.Y. / Cheung, J. / Hoelder, S. / Fry, A.M. / Bayliss, R.
History
DepositionAug 24, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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.ptnr1_symmetry / _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_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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: SERINE/THREONINE-PROTEIN KINASE NEK7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8253
Polymers35,6701
Non-polymers1552
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.937, 132.322, 133.366
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1302-

NI

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE NEK7 / NEK7 / NIMA-RELATED PROTEIN KINASE 7


Mass: 35670.113 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PET30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS RPIL
References: UniProt: Q8TDX7, non-specific serine/threonine protein kinase
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsADDITION OF C-TERMINAL HIS6 TAG AND LINKER LEHHHHHH

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.89 Å3/Da / Density % sol: 57.4 % / Description: NONE
Crystal growDetails: 100 MM HEPES, PH 7.5, 15% PEG 5000 MME, 400 MM AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9796
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.1→66.2 Å / Num. obs: 23808 / % possible obs: 96.9 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Biso Wilson estimate: 31.08 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.5
Reflection shellResolution: 2.1→2.21 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.8 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2W5B

2w5b


Resolution: 2.1→9.977 Å / SU ML: 0.26 / σ(F): 0.01 / Phase error: 20.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2155 1106 5 %
Rwork0.1735 --
obs0.1755 22221 90.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 67.922 Å2 / ksol: 0.399 e/Å3
Displacement parametersBiso mean: 45.1 Å2
Baniso -1Baniso -2Baniso -3
1--10.4072 Å2-0 Å20 Å2
2---6.517 Å2-0 Å2
3---16.9242 Å2
Refinement stepCycle: LAST / Resolution: 2.1→9.977 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2068 0 6 179 2253
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082151
X-RAY DIFFRACTIONf_angle_d1.0632914
X-RAY DIFFRACTIONf_dihedral_angle_d16.637799
X-RAY DIFFRACTIONf_chiral_restr0.072317
X-RAY DIFFRACTIONf_plane_restr0.004376
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.19460.27161410.21992393X-RAY DIFFRACTION84
2.1946-2.3090.27041290.20812503X-RAY DIFFRACTION87
2.309-2.45160.2151420.18452536X-RAY DIFFRACTION89
2.4516-2.63770.24611520.17672623X-RAY DIFFRACTION91
2.6377-2.89720.19071300.17532705X-RAY DIFFRACTION93
2.8972-3.30310.21481330.16672751X-RAY DIFFRACTION94
3.3031-4.11240.20191560.14542782X-RAY DIFFRACTION95
4.1124-9.9770.19321230.17192822X-RAY DIFFRACTION92
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)
12.90391.40920.2773.27290.78031.64240.03580.51330.1686-0.49120.10640.1416-0.21560.1077-0.12310.25510.032-0.00850.3245-0.0970.2554.196139.784824.7703
24.3165-1.93920.08963.46450.85691.3409-0.0623-0.05860.8535-0.10490.067-0.7715-0.06980.06350.01070.1951-0.03410.01080.1929-0.0520.380710.070818.078724.7235
31.1375-0.10531.04621.001-0.20971.2130.07350.42760.0841-0.4321-0.0451-0.0977-0.0180.1638-0.02120.30320.02610.00180.254-0.02270.14715.003112.202610.5921
42.82960.19920.58642.69180.20461.52140.2212-0.1711-0.52660.0867-0.0770.05650.1283-0.0012-0.13750.2219-0.0298-0.01290.1799-0.02150.13874.25324.561823.5563
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 20:117)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 118:203)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 204:254)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 255:300)

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