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- PDB-3dvt: Biochemical and structural characterization of the PAK1- LC8 inte... -

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Basic information

Entry
Database: PDB / ID: 3dvt
TitleBiochemical and structural characterization of the PAK1- LC8 interaction
ComponentsDynein light chain 1, cytoplasmic
KeywordsMOTOR PROTEIN / Dynein / LC8 / light chain / PIN / dlc1 / DYNLL1 / Microtubule
Function / homology
Function and homology information


spermatid nucleus elongation / chaeta morphogenesis / Macroautophagy / Aggrephagy / positive regulation of neuron remodeling / wing disc development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / chaeta development ...spermatid nucleus elongation / chaeta morphogenesis / Macroautophagy / Aggrephagy / positive regulation of neuron remodeling / wing disc development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / chaeta development / sperm individualization / imaginal disc-derived wing morphogenesis / transposable element silencing by piRNA-mediated heterochromatin formation / RNA polymerase II transcription repressor complex / microtubule anchoring at centrosome / Neutrophil degranulation / dynein complex / cytoplasmic dynein complex / dynein light intermediate chain binding / oogenesis / dynein intermediate chain binding / establishment of mitotic spindle orientation / actin filament bundle assembly / centriole / disordered domain specific binding / transcription corepressor activity / spermatogenesis / microtubule / protein homodimerization activity / protein-containing complex / nucleus / cytoplasm / cytosol
Similarity search - Function
Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / 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 / Dynein light chain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Dynein light chain 1, cytoplasmic
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsLIghtcap, C.M. / Williams, J.C.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Biochemical and structural characterization of the Pak1-LC8 interaction.
Authors: Lightcap, C.M. / Sun, S. / Lear, J.D. / Rodeck, U. / Polenova, T. / Williams, J.C.
History
DepositionJul 20, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dynein light chain 1, cytoplasmic
B: Dynein light chain 1, cytoplasmic
C: Dynein light chain 1, cytoplasmic
D: Dynein light chain 1, cytoplasmic
E: Dynein light chain 1, cytoplasmic
F: Dynein light chain 1, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)63,8116
Polymers63,8116
Non-polymers00
Water2,828157
1
E: Dynein light chain 1, cytoplasmic
F: Dynein light chain 1, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)21,2702
Polymers21,2702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-11 kcal/mol
Surface area8820 Å2
MethodPISA
2
C: Dynein light chain 1, cytoplasmic
D: Dynein light chain 1, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)21,2702
Polymers21,2702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-9 kcal/mol
Surface area8550 Å2
MethodPISA
3
A: Dynein light chain 1, cytoplasmic
B: Dynein light chain 1, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)21,2702
Polymers21,2702
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-9 kcal/mol
Surface area8720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.482, 44.871, 84.825
Angle α, β, γ (deg.)79.62, 77.54, 88.03
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Dynein light chain 1, cytoplasmic / 8 kDa dynein light chain / Cut up protein


Mass: 10635.133 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: ctp, Cdlc1, ddlc1, CG6998 / Plasmid: pet21D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3* / References: UniProt: Q24117
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / Source method: isolated from a natural source / Formula: H2O

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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: 2.09 Å3/Da / Density % sol: 41.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 50 mM MgCl2, 100 mM MES, 32% (w/v) PEG 4000, and 20% xylitol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.9793 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.3→30 Å / Num. obs: 22187 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0

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Processing

Software
NameVersionClassification
REFMAC5.4.0034refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→27.78 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.891 / SU B: 16.335 / SU ML: 0.196 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.487 / ESU R Free: 0.277 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2577 1149 5.2 %RANDOM
Rwork0.18905 ---
obs0.19263 20970 96.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 8.359 Å2
Baniso -1Baniso -2Baniso -3
1--0.63 Å20.15 Å2-0.93 Å2
2---0.74 Å2-0.04 Å2
3---1.78 Å2
Refinement stepCycle: LAST / Resolution: 2.3→27.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4169 0 0 157 4326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0224265
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5011.9295749
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4045506
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.20624.791215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.59915749
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0841511
X-RAY DIFFRACTIONr_chiral_restr0.0050.02607
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023249
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_it0.6981.52541
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.34124075
X-RAY DIFFRACTIONr_scbond_it2.431724
X-RAY DIFFRACTIONr_scangle_it3.9384.51674
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 52 -
Rwork0.208 1339 -
obs--81.3 %
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)
12.43650.53370.43622.57150.91234.1835-0.16160.13750.0921-0.5341-0.10010.26-0.3429-0.20820.26170.030.006-0.0415-0.03010.0001-0.1584-13.37541.733-9.1565
22.79660.3520.41923.16330.66091.15150.0066-0.1809-0.05670.2059-0.03820.24370.0763-0.0790.0316-0.096-0.0030.079-0.0766-0.013-0.1567-10.4762-2.647410.4927
32.01060.76680.46212.695-0.00893.8091-0.145-0.23460.1050.39720.0083-0.0739-0.0913-0.22160.1367-0.00560.03860.0486-0.0164-0.0274-0.19934.903716.657326.2887
42.9244-0.8412-0.84413.3252-0.35531.93460.06150.20950.2459-0.2197-0.0625-0.1028-0.0208-0.05950.001-0.0914-0.02760.0638-0.07680.0141-0.1717.933720.78196.9454
52.2350.5605-0.76614.3537-0.91343.81960.1629-0.0286-0.13260.176-0.008-0.24040.49440.4548-0.15490.09570.0387-0.0580.03-0.0397-0.12744.405819.9936-22.4554
63.7799-0.18051.63033.0404-1.45356.11940.17890.29990.0247-0.2061-0.1446-0.148-0.0520.5963-0.03440.07180.01270.02440.0835-0.0471-0.1624.497127.8586-41.184
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 89
2X-RAY DIFFRACTION2B5 - 89
3X-RAY DIFFRACTION3C5 - 89
4X-RAY DIFFRACTION4D5 - 89
5X-RAY DIFFRACTION5E5 - 89
6X-RAY DIFFRACTION6F5 - 89

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