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- PDB-3glw: Quaternary Structure of Drosophila melanogaster IC/Tctex-1/LC8; A... -

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Basic information

Entry
Database: PDB / ID: 3glw
TitleQuaternary Structure of Drosophila melanogaster IC/Tctex-1/LC8; Allosteric Interactions of Dynein Light Chains with Dynein Intermediate Chain
Components
  • Dynein intermediate Chain
  • Dynein light chain 1, cytoplasmic
KeywordsCONTRACTILE PROTEIN / LC8 / Tctex / Tctex-1 / Intermediate Chain / IC / Dynein / Dynein Light Chain / Entropy / Allostery / Chelate Effect / Multivalent. / Microtubule / Motor protein
Function / homology
Function and homology information


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 / microtubule anchoring at centrosome ...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 / microtubule anchoring at centrosome / chaeta development / sperm individualization / imaginal disc-derived wing morphogenesis / Neutrophil degranulation / dynein complex / dynein light intermediate chain binding / cytoplasmic dynein complex / dynein intermediate chain binding / oogenesis / establishment of mitotic spindle orientation / actin filament bundle assembly / centriole / disordered domain specific binding / spermatogenesis / microtubule / 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
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsHall, J.D. / Karplus, P.A. / Barbar, E.J.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Multivalency in the assembly of intrinsically disordered Dynein intermediate chain.
Authors: Hall, J. / Karplus, P.A. / Barbar, E.
History
DepositionMar 12, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance

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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
Z: Dynein intermediate Chain


Theoretical massNumber of molelcules
Total (without water)13,5932
Polymers13,5932
Non-polymers00
Water543
1
A: Dynein light chain 1, cytoplasmic
Z: Dynein intermediate Chain

A: Dynein light chain 1, cytoplasmic
Z: Dynein intermediate Chain

A: Dynein light chain 1, cytoplasmic
Z: Dynein intermediate Chain

A: Dynein light chain 1, cytoplasmic
Z: Dynein intermediate Chain


Theoretical massNumber of molelcules
Total (without water)54,3748
Polymers54,3748
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
crystal symmetry operation8_555x-y,-y,-z1
crystal symmetry operation8_455x-y-1,-y,-z1
Unit cell
Length a, b, c (Å)44.645, 44.645, 219.376
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Noncrystallographic symmetry (NCS)NCS domain: (Details: Z) / NCS domain segments: (Refine code: 1 )

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Components

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


Mass: 10388.849 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: ctp, Cdlc1, ddlc1, CG6998 / Production host: Escherichia coli (E. coli) / References: UniProt: Q24117
#2: Protein/peptide Dynein intermediate Chain


Mass: 3204.556 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 10

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.01 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 400, 100 mM Hepes, 200 mM magnesium chloride at pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 1, 2009
RadiationMonochromator: osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.15→38.66 Å / Num. all: 2695 / Num. obs: 2695 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 25.8 % / Rmerge(I) obs: 0.103 / Rsym value: 0.101 / Net I/σ(I): 6.5
Reflection shellResolution: 3.15→3.32 Å / Redundancy: 28.8 % / Rmerge(I) obs: 0.462 / Mean I/σ(I) obs: 19.5 / Rsym value: 0.454 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.5.0046refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.15→38.66 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.88 / SU B: 60.771 / SU ML: 0.447 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.516 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2708 118 4.5 %RANDOM
Rwork0.20329 ---
obs0.2063 2520 99.85 %-
all-2695 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.399 Å2
Baniso -1Baniso -2Baniso -3
1-3.28 Å21.64 Å20 Å2
2--3.28 Å20 Å2
3----4.92 Å2
Refinement stepCycle: LAST / Resolution: 3.15→38.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms844 0 0 3 847
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d00.022914
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.0531.9511244
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg13.4145115
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.87324.54544
X-RAY DIFFRACTIONr_dihedral_angle_3_deg27.40315172
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.767154
X-RAY DIFFRACTIONr_chiral_restr0.0020.2138
X-RAY DIFFRACTIONr_gen_planes_refined00.021691
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_it9.0661.5542
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it14.0332887
X-RAY DIFFRACTIONr_scbond_it19.6483372
X-RAY DIFFRACTIONr_scangle_it24.7774.5351
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: Z / Ens-ID: 1 / Number: 15 / Refine-ID: X-RAY DIFFRACTION / Rms dev position: 0 Å

TypeWeight position
tight positional0.05
tight thermal0.5
LS refinement shellResolution: 3.15→3.231 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 8 -
Rwork0.323 184 -
obs--100 %
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)
12.8126-1.1265-0.44351.02660.31863.436-0.1441-0.2613-0.15270.16180.1985-0.08480.468-0.0984-0.05440.2990.026-0.01510.0486-0.00680.046211.8642-7.26847.2905
20.06420.3565-0.10912.019-0.62940.20270.05930.00550.01030.1416-0.00720.1168-0.03160.0421-0.05210.41880.028-0.07330.1956-0.16380.153.8635-8.8587-5.0599
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 89
2X-RAY DIFFRACTION2Z126 - 142

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