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- PDB-4qh7: LC8 - Ana2 (159-168) Complex -

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Basic information

Entry
Database: PDB / ID: 4qh7
TitleLC8 - Ana2 (159-168) Complex
Components
  • Anastral spindle 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 / positive regulation of neuron remodeling / Macroautophagy / Aggrephagy / 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 ...ciliary basal body organization / spermatid nucleus elongation / chaeta morphogenesis / positive regulation of neuron remodeling / Macroautophagy / Aggrephagy / 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 / centriole assembly / centriole-centriole cohesion / : / chaeta development / sperm individualization / microtubule anchoring at centrosome / imaginal disc-derived wing morphogenesis / asymmetric neuroblast division / Neutrophil degranulation / dynein complex / cytoplasmic dynein complex / dynein light intermediate chain binding / dynein intermediate chain binding / oogenesis / establishment of mitotic spindle orientation / centriole replication / actin filament bundle assembly / centriole / ciliary basal body / autophagy / disordered domain specific binding / spermatogenesis / microtubule / centrosome / protein homodimerization activity / protein-containing complex / cytoplasm
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 / Dynein light chain, type 1/2 / Dynein light chain superfamily / Dynein light chain type 1 / 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: 1.829 Å
AuthorsSlevin, L.K. / Romes, E.R. / 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: Anastral spindle 2
H: Anastral spindle 2


Theoretical massNumber of molelcules
Total (without water)48,3358
Polymers48,3358
Non-polymers00
Water5,585310
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)24,1674
Polymers24,1674
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4720 Å2
ΔGint-24 kcal/mol
Surface area8720 Å2
MethodPISA
2
E: Dynein light chain 1, cytoplasmic
F: Dynein light chain 1, cytoplasmic
G: Anastral spindle 2
H: Anastral spindle 2


Theoretical massNumber of molelcules
Total (without water)24,1674
Polymers24,1674
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-25 kcal/mol
Surface area8640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.453, 77.913, 108.891
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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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.: 4 / 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: 1283.365 Da / Num. of mol.: 4 / Fragment: Ana2 T159-P168 / Source method: obtained synthetically
Details: Sequence T159-P168 occurs naturally in Drosophila melanogaster. Peptide synthesized is NYTICAGTQTDP with C-terminal amide.
Source: (synth.) Drosophila melanogaster (fruit fly) / References: UniProt: Q9XZ31
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 310 / 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: 2.26 Å3/Da / Density % sol: 45.52 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.3M magnesium acetate, 0.1M sodium cacodylate, 26% PEG 8000, pH 6.5, 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 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Sep 14, 2012
RadiationMonochromator: Double crystal - liquid nitrogen-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. all: 108273 / Num. obs: 37488 / % possible obs: 95.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rsym value: 0.08 / Net I/σ(I): 13.7
Reflection shellResolution: 1.83→1.9 Å / Mean I/σ(I) obs: 2.4 / Rsym value: 0.37 / % possible all: 95.2

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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: 1.829→44.629 Å / SU ML: 0.15 / σ(F): 0 / Phase error: 19.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2073 1953 5.37 %Random
Rwork0.176 ---
obs0.1777 36371 92.23 %-
all-37488 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.829→44.629 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3046 0 0 310 3356
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073112
X-RAY DIFFRACTIONf_angle_d0.9854201
X-RAY DIFFRACTIONf_dihedral_angle_d13.9921113
X-RAY DIFFRACTIONf_chiral_restr0.075456
X-RAY DIFFRACTIONf_plane_restr0.003531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8291-1.87480.24141200.22112092X-RAY DIFFRACTION80
1.8748-1.92550.24941370.19492347X-RAY DIFFRACTION90
1.9255-1.98220.23551380.18972406X-RAY DIFFRACTION91
1.9822-2.04610.20451400.18132450X-RAY DIFFRACTION93
2.0461-2.11930.23671350.17632440X-RAY DIFFRACTION93
2.1193-2.20410.19531390.17062459X-RAY DIFFRACTION94
2.2041-2.30440.18311440.16772515X-RAY DIFFRACTION95
2.3044-2.42590.20381430.17122505X-RAY DIFFRACTION95
2.4259-2.57790.22351450.18332538X-RAY DIFFRACTION95
2.5779-2.77690.22831410.18752523X-RAY DIFFRACTION95
2.7769-3.05630.22151440.19552554X-RAY DIFFRACTION95
3.0563-3.49840.19521420.17122529X-RAY DIFFRACTION94
3.4984-4.4070.16111410.15032509X-RAY DIFFRACTION92
4.407-44.64190.22891440.17932551X-RAY DIFFRACTION89

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