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- PDB-2wqn: Structure of ADP-bound human Nek7 -

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Basic information

Entry
Database: PDB / ID: 2wqn
TitleStructure of ADP-bound human Nek7
ComponentsSERINE/THREONINE-PROTEIN KINASE NEK7
KeywordsTRANSFERASE / ATP-BINDING / POLYMORPHISM / METAL-BINDING / SERINE/THREONINE-PROTEIN KINASE / MITOSIS / CYTOPLASM / 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 / positive regulation of telomere capping / spindle assembly / EML4 and NUDC in mitotic spindle formation / positive regulation of telomerase activity ...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 / 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 / regulation of mitotic cell cycle / molecular function activator activity / spindle pole / microtubule / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / nucleoplasm / ATP binding / nucleus / metal ion binding / 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
ADENOSINE-5'-DIPHOSPHATE / NICKEL (II) ION / Serine/threonine-protein kinase Nek7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRichards, M.W. / Bayliss, R.
CitationJournal: Mol.Cell / Year: 2009
Title: An Autoinhibitory 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. / 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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)36,2765
Polymers35,6701
Non-polymers6064
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.835, 133.108, 131.851
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

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Protein , 1 types, 1 molecules A

#1: Protein SERINE/THREONINE-PROTEIN KINASE 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

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Non-polymers , 5 types, 123 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.88 Å3/Da / Density % sol: 57.39 % / Description: NONE
Crystal growDetails: 100MM HEPES 7.5, 15% PEG 5000MME, 400MM AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9721
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9721 Å / Relative weight: 1
ReflectionResolution: 2.3→66.2 Å / Num. obs: 18761 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Biso Wilson estimate: 35.81 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 10.7
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 3.3 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WQM

2wqm


Resolution: 2.3→44.18 Å / SU ML: 0.29 / σ(F): 0.03 / Phase error: 21.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2205 900 4.9 %
Rwork0.1906 --
obs0.192 18172 96.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.329 Å2 / ksol: 0.367 e/Å3
Displacement parametersBiso mean: 52.25 Å2
Baniso -1Baniso -2Baniso -3
1--11.8151 Å20 Å20 Å2
2---5.5089 Å2-0 Å2
3---17.324 Å2
Refinement stepCycle: LAST / Resolution: 2.3→44.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 34 119 2219
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072170
X-RAY DIFFRACTIONf_angle_d1.0352946
X-RAY DIFFRACTIONf_dihedral_angle_d17.121805
X-RAY DIFFRACTIONf_chiral_restr0.065320
X-RAY DIFFRACTIONf_plane_restr0.004375
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3001-2.44420.2621540.21562676X-RAY DIFFRACTION92
2.4442-2.63290.23391610.19972755X-RAY DIFFRACTION95
2.6329-2.89780.23411470.18872814X-RAY DIFFRACTION96
2.8978-3.3170.21921450.19142941X-RAY DIFFRACTION99
3.317-4.17850.20211550.16622977X-RAY DIFFRACTION99
4.1785-44.1880.21571380.19583109X-RAY DIFFRACTION99
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)
13.66592.43250.26354.04370.43132.03370.0060.8845-0.3008-0.97290.0488-0.10170.2824-0.02890.00830.23480.06640.03490.30010.11990.2243-4.3849-40.0095-41.8678
25.4096-0.56340.84985.3496-1.12522.32190.17560.1177-0.9442-0.3945-0.07331.06080.1076-0.1542-0.23010.0728-0.0238-0.04290.05190.08390.2264-10.114-18.1355-41.5396
31.38450.1355-0.9761.59650.17352.03680.16190.6662-0.1432-0.69120.06270.19020.1888-0.080.00260.34050.0211-0.03160.1960.03460.0524-4.9935-12.0427-55.3071
44.549-0.13710.56484.138-0.07652.11590.3352-0.23960.76730.0332-0.1240.0956-0.34410.05110.22710.11-0.0730.01790.03010.02830.0464-4.4304-4.5341-42.1234
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 21:117)
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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