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- PDB-4apc: Crystal Structure of Human NIMA-related Kinase 1 (NEK1) -

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Basic information

Entry
Database: PDB / ID: 4apc
TitleCrystal Structure of Human NIMA-related Kinase 1 (NEK1)
ComponentsSERINE/THREONINE-PROTEIN KINASE NEK1
KeywordsTRANSFERASE
Function / homology
Function and homology information


pericentriolar material / cilium assembly / centriolar satellite / 14-3-3 protein binding / kinase activity / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / cell cycle / cell division ...pericentriolar material / cilium assembly / centriolar satellite / 14-3-3 protein binding / kinase activity / protein tyrosine kinase activity / non-specific serine/threonine protein kinase / protein kinase activity / cell cycle / cell division / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / nucleoplasm / ATP binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
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. ...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
Serine/threonine-protein kinase Nek1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsElkins, J.M. / Hanchuk, T.D.M. / Lovato, D.V. / Basei, F.L. / Meirelles, G.V. / Kobarg, J. / Szklarz, M. / Vollmar, M. / Mahajan, P. / Rellos, P. ...Elkins, J.M. / Hanchuk, T.D.M. / Lovato, D.V. / Basei, F.L. / Meirelles, G.V. / Kobarg, J. / Szklarz, M. / Vollmar, M. / Mahajan, P. / Rellos, P. / Zhang, Y. / Krojer, T. / Pike, A.C.W. / Bountra, C. / Arrowsmith, C. / Edwards, A. / Knapp, S.
CitationJournal: Sci Rep / Year: 2017
Title: NEK1 kinase domain structure and its dynamic protein interactome after exposure to Cisplatin.
Authors: Melo-Hanchuk, T.D. / Slepicka, P.F. / Meirelles, G.V. / Basei, F.L. / Lovato, D.V. / Granato, D.C. / Pauletti, B.A. / Domingues, R.R. / Leme, A.F.P. / Pelegrini, A.L. / Lenz, G. / Knapp, S. ...Authors: Melo-Hanchuk, T.D. / Slepicka, P.F. / Meirelles, G.V. / Basei, F.L. / Lovato, D.V. / Granato, D.C. / Pauletti, B.A. / Domingues, R.R. / Leme, A.F.P. / Pelegrini, A.L. / Lenz, G. / Knapp, S. / Elkins, J.M. / Kobarg, J.
History
DepositionApr 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Other
Revision 1.2Aug 12, 2020Group: Database references / Derived calculations / Other
Category: citation / citation_author ...citation / citation_author / pdbx_database_status / struct_site
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Dec 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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 NEK1
B: SERINE/THREONINE-PROTEIN KINASE NEK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,0729
Polymers79,8242
Non-polymers2487
Water2,972165
1
A: SERINE/THREONINE-PROTEIN KINASE NEK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0545
Polymers39,9121
Non-polymers1424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SERINE/THREONINE-PROTEIN KINASE NEK1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0184
Polymers39,9121
Non-polymers1063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.910, 92.810, 163.940
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: 0 / Auth seq-ID: -20 - 284

Dom-IDAuth asym-IDLabel asym-IDLabel seq-ID
1AA4 - 306
2BB2 - 306

NCS oper: (Code: given
Matrix: (0.04854, 0.99882, 0.00085), (-0.99814, 0.04854, -0.03697), (-0.03697, 0.00095, 0.99932)
Vector: -3.03855, 41.88874, 41.92957)

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Components

#1: Protein SERINE/THREONINE-PROTEIN KINASE NEK1 / NEVER IN MITOSIS A-RELATED KINASE 1 / NIMA-RELATED PROTEIN KINASE 1 / RENAL CARCINOMA ANTIGEN NY-REN-55


Mass: 39912.066 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 1-238 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC28-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q96PY6, non-specific serine/threonine protein kinase
#2: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 165 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 162 TO ALA ENGINEERED RESIDUE IN CHAIN B, THR 162 TO ALA

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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: 2.15 Å3/Da / Density % sol: 42.71 % / Description: NONE
Crystal growpH: 7.5
Details: 0.2 M AMMONIUM CHLORIDE, 20 %(W/V) PEG 3350, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9686
DetectorDate: Feb 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.1→46.41 Å / Num. obs: 40349 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 8.5
Reflection shellResolution: 2.1→2.17 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2JAV

2jav


Resolution: 2.1→81.97 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.909 / SU B: 5.061 / SU ML: 0.133 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.189 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24768 2021 5 %RANDOM
Rwork0.21457 ---
obs0.21625 38286 99.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.487 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2--1.63 Å20 Å2
3----0.64 Å2
Refinement stepCycle: LAST / Resolution: 2.1→81.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4692 0 7 165 4864
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0194835
X-RAY DIFFRACTIONr_bond_other_d0.0030.023343
X-RAY DIFFRACTIONr_angle_refined_deg1.2661.9576529
X-RAY DIFFRACTIONr_angle_other_deg0.97338132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8025597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.56323.7227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.55415874
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4391533
X-RAY DIFFRACTIONr_chiral_restr0.0750.2726
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025337
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021012
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11004 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 143 -
Rwork0.283 2653 -
obs--99.79 %

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