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- PDB-3zkf: Structure of LC8 in complex with Nek9 phosphopeptide -

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Basic information

Entry
Database: PDB / ID: 3zkf
TitleStructure of LC8 in complex with Nek9 phosphopeptide
Components
  • DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
  • NEK9 PROTEIN
KeywordsCONTRACTILE PROTEIN/PEPTIDE / CONTRACTILE PROTEIN-PEPTIDE COMPLEX
Function / homology
Function and homology information


NEK9 subfamily protein kinase / nitric-oxide synthase inhibitor activity / deoxyribonuclease inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / negative regulation of phosphorylation / intraciliary retrograde transport / Activation of BIM and translocation to mitochondria / motile cilium assembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Intraflagellar transport ...NEK9 subfamily protein kinase / nitric-oxide synthase inhibitor activity / deoxyribonuclease inhibitor activity / negative regulation of DNA strand resection involved in replication fork processing / negative regulation of phosphorylation / intraciliary retrograde transport / Activation of BIM and translocation to mitochondria / motile cilium assembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / Intraflagellar transport / Nuclear Pore Complex (NPC) Disassembly / negative regulation of nitric oxide biosynthetic process / dynein complex / COPI-independent Golgi-to-ER retrograde traffic / cytoplasmic dynein complex / Macroautophagy / ciliary tip / dynein intermediate chain binding / tertiary granule membrane / ficolin-1-rich granule membrane / spermatid development / protein kinase activator activity / positive regulation of insulin secretion involved in cellular response to glucose stimulus / COPI-mediated anterograde transport / axon cytoplasm / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / enzyme inhibitor activity / substantia nigra development / Mitotic Prometaphase / Anchoring of the basal body to the plasma membrane / EML4 and NUDC in mitotic spindle formation / regulation of mitotic cell cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / AURKA Activation by TPX2 / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins / kinetochore / HCMV Early Events / Aggrephagy / mitotic spindle / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / site of double-strand break / scaffold protein binding / microtubule / cytoskeleton / non-specific serine/threonine protein kinase / cilium / cell division / protein serine kinase activity / protein serine/threonine kinase activity / apoptotic process / DNA damage response / Neutrophil degranulation / centrosome / protein kinase binding / protein-containing complex binding / enzyme binding / mitochondrion / ATP binding / metal ion binding / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Serine/threonine-protein kinase Nek9, catalytic domain / : / : / Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / RCC1-like domain / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. ...Serine/threonine-protein kinase Nek9, catalytic domain / : / : / Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / RCC1-like domain / Regulator of chromosome condensation, RCC1 / Regulator of chromosome condensation (RCC1) repeat profile. / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. / Dynein light chain, type 1/2 / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Dynein light chain 1, cytoplasmic / non-specific serine/threonine protein kinase / Serine/threonine-protein kinase Nek9
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGallego, P. / Velazquez-Campoy, A. / Regue, L. / Roig, J. / Reverter, D.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Structural Analysis of the Regulation of the Dynll/Lc8 Binding to Nek9 by Phosphorylation
Authors: Gallego, P. / Velazquez-Campoy, A. / Regue, L. / Roig, J. / Reverter, D.
History
DepositionJan 22, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 20, 2013Provider: repository / Type: Initial release
Revision 1.1Apr 3, 2013Group: Database references
Revision 1.2May 15, 2013Group: Database references
Revision 1.3Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
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.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
B: NEK9 PROTEIN
C: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
D: NEK9 PROTEIN
E: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
F: NEK9 PROTEIN
G: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
H: NEK9 PROTEIN
I: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
J: NEK9 PROTEIN
K: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
L: NEK9 PROTEIN


Theoretical massNumber of molelcules
Total (without water)69,48112
Polymers69,48112
Non-polymers00
Water34219
1
E: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
F: NEK9 PROTEIN
K: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
L: NEK9 PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,1604
Polymers23,1604
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-28.4 kcal/mol
Surface area8780 Å2
MethodPISA
2
A: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
B: NEK9 PROTEIN
C: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
D: NEK9 PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,1604
Polymers23,1604
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5090 Å2
ΔGint-27.7 kcal/mol
Surface area8650 Å2
MethodPISA
3
G: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
H: NEK9 PROTEIN
I: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
J: NEK9 PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,1604
Polymers23,1604
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-27.2 kcal/mol
Surface area8710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.868, 154.868, 47.729
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

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Components

#1: Protein
DYNEIN LIGHT CHAIN 1, CYTOPLASMIC / 8 KDA DYNEIN LIGHT CHAIN / DLC8 / DYNEIN LIGHT CHAIN LC8-TYPE 1 / DYNLL-LC8 / PROTEIN INHIBITOR OF ...8 KDA DYNEIN LIGHT CHAIN / DLC8 / DYNEIN LIGHT CHAIN LC8-TYPE 1 / DYNLL-LC8 / PROTEIN INHIBITOR OF NEURONAL NITRIC OXIDE SYNTHASE / PIN


Mass: 10381.899 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63167
#2: Protein/peptide
NEK9 PROTEIN


Mass: 1198.243 Da / Num. of mol.: 6 / Source method: obtained synthetically / Details: PHOSPHORYLATION AT SER944 / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q6PKF2, UniProt: Q8TD19*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.28 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979494
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979494 Å / Relative weight: 1
ReflectionResolution: 2.49→47.73 Å / Num. obs: 22982 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 49.17 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.6
Reflection shellResolution: 2.49→2.63 Å / Redundancy: 3.3 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.5 / % possible all: 95.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→44.967 Å / SU ML: 0.41 / σ(F): 0.01 / Phase error: 28 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2686 993 5.1 %
Rwork0.2196 --
obs0.2222 19327 94.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.636 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--1.7433 Å20 Å20 Å2
2---1.7433 Å20 Å2
3---3.4867 Å2
Refinement stepCycle: LAST / Resolution: 2.6→44.967 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4639 0 0 19 4658
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0094735
X-RAY DIFFRACTIONf_angle_d1.1966361
X-RAY DIFFRACTIONf_dihedral_angle_d20.1691701
X-RAY DIFFRACTIONf_chiral_restr0.078674
X-RAY DIFFRACTIONf_plane_restr0.004796
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.73710.34991070.27822354X-RAY DIFFRACTION85
2.7371-2.90850.33381420.2582463X-RAY DIFFRACTION90
2.9085-3.13310.30551380.24352576X-RAY DIFFRACTION93
3.1331-3.44830.27691540.22212657X-RAY DIFFRACTION96
3.4483-3.9470.28411480.21792705X-RAY DIFFRACTION98
3.947-4.97180.24931520.19812740X-RAY DIFFRACTION99
4.9718-44.97320.22671520.20812839X-RAY DIFFRACTION99

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