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- PDB-3zke: Structure of LC8 in complex with Nek9 peptide -

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Basic information

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


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 / ciliary tip / Intraflagellar transport ...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 / ciliary tip / 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 / dynein intermediate chain binding / tertiary granule membrane / ficolin-1-rich granule membrane / protein kinase activator activity / enzyme inhibitor activity / spermatid development / positive regulation of insulin secretion involved in cellular response to glucose stimulus / COPI-mediated anterograde transport / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / axon cytoplasm / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / substantia nigra development / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Resolution of Sister Chromatid Cohesion / AURKA Activation by TPX2 / 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 / centrosome / Neutrophil degranulation / protein kinase binding / protein-containing complex binding / enzyme binding / mitochondrion / ATP binding / metal ion binding / identical protein binding / nucleus / membrane / 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. / Dynein light chain, type 1/2 ...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 / Dynein light chain type 1 / Dynein light chain type 1 / Regulator of chromosome condensation 1/beta-lactamase-inhibitor protein II / 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: 2.2 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 1.3May 22, 2013Group: Derived calculations
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)69,00112
Polymers69,00112
Non-polymers00
Water1,928107
1
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)23,0004
Polymers23,0004
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5050 Å2
ΔGint-23.7 kcal/mol
Surface area8530 Å2
MethodPISA
2
E: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
F: NEK9 PROTEIN
G: DYNEIN LIGHT CHAIN 1, CYTOPLASMIC
H: NEK9 PROTEIN


Theoretical massNumber of molelcules
Total (without water)23,0004
Polymers23,0004
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-22.9 kcal/mol
Surface area8420 Å2
MethodPISA
3
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)23,0004
Polymers23,0004
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5020 Å2
ΔGint-24 kcal/mol
Surface area8550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.984, 105.124, 133.899
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31D
41F
51I
61K
12G
22C
32E
42H
52J
62L

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A5 - 99
2111B940 - 950
3111D940 - 950
4111F941 - 950
5111I5 - 89
6111K5 - 89
1121G5 - 89
2121C5 - 89
3121E5 - 89
4121H940 - 950
5121J940 - 950
6121L940 - 950

NCS ensembles :
ID
1
2

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.904569, -0.426259, 0.007678), (-0.426048, 0.903175, -0.05251), (0.015448, -0.050771, -0.998591)-39.42123, -7.97296, 30.43234
3given(0.896908, 0.368707, -0.244154), (0.437957, -0.817068, 0.374959), (-0.061241, -0.443233, -0.894312)29.64951, -29.61178, 18.42435
4given(-0.998837, 0.015332, 0.045704), (0.00907, -0.871377, 0.49053), (0.047347, 0.490374, 0.870225)-53.24747, -48.57833, 13.82059
5given(-0.568661, 0.822378, 0.017871), (0.738398, 0.519923, -0.429473), (-0.362481, -0.231029, -0.902903)25.14783, 50.00758, 2.60422
6given(0.199244, -0.967465, 0.155926), (0.925825, 0.133691, -0.353519), (0.321171, 0.214797, 0.92234)-83.49152, 26.47094, 25.60437

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Components

#1: Protein
DYNEIN LIGHT CHAIN 1, CYTOPLASMIC / DYNLL-LC8 / 8 KDA DYNEIN LIGHT CHAIN / DLC8 / DYNEIN LIGHT CHAIN LC8-TYPE 1 / PROTEIN INHIBITOR OF ...DYNLL-LC8 / 8 KDA DYNEIN LIGHT CHAIN / DLC8 / DYNEIN LIGHT CHAIN LC8-TYPE 1 / 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 / NEK9


Mass: 1118.264 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: Q6PKF2, UniProt: Q8TD19*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.68 % / 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: 2.2→44.63 Å / Num. obs: 28774 / % possible obs: 97.6 % / Observed criterion σ(I): 2 / Redundancy: 3.2 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.7 / % possible all: 95.4

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→82.69 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.483 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.332 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 1-5 DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.22769 1459 5.1 %RANDOM
Rwork0.19575 ---
obs0.19738 27276 96.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.801 Å2
Baniso -1Baniso -2Baniso -3
1-0.26 Å20 Å20 Å2
2--0.89 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 2.2→82.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4619 0 0 107 4726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.024715
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9241.9246326
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9135563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.32625.135222
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.44415869
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.589156
X-RAY DIFFRACTIONr_chiral_restr0.1050.2676
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.023500
X-RAY DIFFRACTIONr_gen_planes_other
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

Refine-ID: X-RAY DIFFRACTION / Type: tight thermal / Weight position: 0.5

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A6955.57
12B6953.89
13D6954.86
14F6954.53
15I6957.99
16K6958.39
21G694.64
22C693.75
23E695.97
24H694.84
25J693.61
26L699.73
LS refinement shellResolution: 2.197→2.254 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 82 -
Rwork0.265 1710 -
obs--91.01 %

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