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- PDB-4qh8: LC8 - Ana2 (237-246) Complex -

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Basic information

Entry
Database: PDB / ID: 4qh8
TitleLC8 - Ana2 (237-246) Complex
Components
  • (Anastral spindle 2) x 2
  • Dynein light chain 1, cytoplasmic
KeywordsMOTOR PROTEIN / LC8 fold Dimer / Target dimerization / Ana2 / Cellular
Function / homology
Function and homology information


ciliary basal body organization / spermatid nucleus elongation / chaeta morphogenesis / Macroautophagy / Aggrephagy / wing disc development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of neuron remodeling / COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic ...ciliary basal body organization / spermatid nucleus elongation / chaeta morphogenesis / Macroautophagy / Aggrephagy / wing disc development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of neuron remodeling / COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / centriole assembly / chaeta development / sperm individualization / imaginal disc-derived wing morphogenesis / centriole-centriole cohesion / RNA polymerase II transcription repressor complex / transposable element silencing by piRNA-mediated heterochromatin formation / microtubule anchoring at centrosome / asymmetric neuroblast division / Neutrophil degranulation / dynein complex / dynein light intermediate chain binding / cytoplasmic dynein complex / oogenesis / centriole replication / dynein intermediate chain binding / actin filament bundle assembly / establishment of mitotic spindle orientation / centriole / disordered domain specific binding / transcription corepressor activity / spermatogenesis / microtubule / ciliary basal body / centrosome / 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 / Anastral spindle 2, isoform A
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSlevin, L.K. / Romes, E.R. / Dandulakis, M.G. / Slep, K.C.
CitationJournal: J.Biol.Chem. / Year: 2014
Title: The Mechanism of Dynein Light Chain LC8-mediated Oligomerization of the Ana2 Centriole Duplication Factor.
Authors: Slevin, L.K. / Romes, E.M. / Dandulakis, M.G. / Slep, K.C.
History
DepositionMay 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 20, 2014Group: Database references
Revision 1.2Sep 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_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: Anastral spindle 2
D: Anastral spindle 2
E: Dynein light chain 1, cytoplasmic
F: Dynein light chain 1, cytoplasmic
G: Dynein light chain 1, cytoplasmic
H: Dynein light chain 1, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)67,4528
Polymers67,4528
Non-polymers00
Water4,684260
1
A: Dynein light chain 1, cytoplasmic
B: Dynein light chain 1, cytoplasmic
C: Anastral spindle 2
D: Anastral spindle 2


Theoretical massNumber of molelcules
Total (without water)24,2504
Polymers24,2504
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5000 Å2
ΔGint-22 kcal/mol
Surface area8750 Å2
MethodPISA
2
E: Dynein light chain 1, cytoplasmic
F: Dynein light chain 1, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)21,6012
Polymers21,6012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1900 Å2
ΔGint-7 kcal/mol
Surface area8640 Å2
MethodPISA
3
G: Dynein light chain 1, cytoplasmic
H: Dynein light chain 1, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)21,6012
Polymers21,6012
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-10 kcal/mol
Surface area8620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.627, 44.802, 85.895
Angle α, β, γ (deg.)99.33, 103.04, 91.79
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: 10800.304 Da / Num. of mol.: 6 / Fragment: LC8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: ctp, Cdlc1, ddlc1, CG6998 / Plasmid: pGEX-6P-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q24117
#2: Protein/peptide Anastral spindle 2


Mass: 1360.406 Da / Num. of mol.: 1 / Fragment: Ana2 S237-I246 / Source method: obtained synthetically
Details: Sequence S237-I246 occurs naturally in Drosophila melanogaster. Peptide synthesized is NYSSTTGTQCDI with C-terminal amide.
Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: Q9XZ31
#3: Protein/peptide Anastral spindle 2


Mass: 1289.328 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: Sequence S237-I246 occurs naturally in Drosophila melanogaster. Peptide synthesized is NYSSTTGTQCDI with C-terminal amide.
Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: Q9XZ31
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / 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 Å3/Da / Density % sol: 38.62 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.19M ammonium acetate, 0.1M sodium acetate, 0.1% beta-mercaptoethanol, and 27% PEG 4000, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.07426 / Wavelength: 1.07426 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 19, 2013
RadiationMonochromator: Double crystal - liquid nitrogen-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07426 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 70555 / Num. obs: 36096 / % possible obs: 87.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.04 / Net I/σ(I): 19.5
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 7 / Rsym value: 0.12 / % possible all: 47.3

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Processing

Software
NameVersionClassification
SERGUIdata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PG1

2pg1


Resolution: 1.9→35.594 Å / SU ML: 0.23 / σ(F): 0.14 / Phase error: 25.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2358 1991 5.58 %Random
Rwork0.1852 ---
obs0.188 35664 86.44 %-
all-36096 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→35.594 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4311 0 0 260 4571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084415
X-RAY DIFFRACTIONf_angle_d1.0515945
X-RAY DIFFRACTIONf_dihedral_angle_d15.3911602
X-RAY DIFFRACTIONf_chiral_restr0.074634
X-RAY DIFFRACTIONf_plane_restr0.004753
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.94760.3114690.20141221X-RAY DIFFRACTION43
1.9476-2.00030.2482920.21041441X-RAY DIFFRACTION53
2.0003-2.05910.25531010.20941855X-RAY DIFFRACTION66
2.0591-2.12560.27681440.19522462X-RAY DIFFRACTION88
2.1256-2.20160.26371600.19952595X-RAY DIFFRACTION94
2.2016-2.28970.2511500.19442694X-RAY DIFFRACTION95
2.2897-2.39390.27831530.19672631X-RAY DIFFRACTION96
2.3939-2.520.26631570.19632663X-RAY DIFFRACTION96
2.52-2.67790.25241600.20692685X-RAY DIFFRACTION96
2.6779-2.88460.2721570.21782649X-RAY DIFFRACTION96
2.8846-3.17470.29041570.20542709X-RAY DIFFRACTION96
3.1747-3.63370.22261590.18032674X-RAY DIFFRACTION96
3.6337-4.57650.18521630.15012696X-RAY DIFFRACTION97
4.5765-35.59980.17841690.15592698X-RAY DIFFRACTION98

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