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- PDB-3fm7: Quaternary Structure of Drosophila melanogaster IC/Tctex-1/LC8; A... -

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Basic information

Entry
Database: PDB / ID: 3fm7
TitleQuaternary Structure of Drosophila melanogaster IC/Tctex-1/LC8; Allosteric Interactions of Dynein Light Chains with Dynein Intermediate Chain
Components
  • Dynein intermediate chain, cytosolic
  • Dynein light chain 1, cytoplasmic
  • Dynein light chain Tctex-type
KeywordsCONTRACTILE PROTEIN / Cytoplasmic Dynein / Light Chain Tctex-1 / Tctex / Light Chain 8 / LC8 / Intermediate Chain / IC / Dynein Cargo Attachment Complex / Dynein Light Chain / Quaternary Structure / Dynein / Microtubule / Motor protein / Lysosome / Membrane / Nucleus / WD repeat
Function / homology
Function and homology information


cellularization / spermatid nucleus elongation / eye photoreceptor cell differentiation / 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 ...cellularization / spermatid nucleus elongation / eye photoreceptor cell differentiation / 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 / transport along microtubule / RNA polymerase II transcription repressor complex / microtubule anchoring at centrosome / dynein light chain binding / dynein heavy chain binding / Neutrophil degranulation / protein localization to kinetochore / axo-dendritic transport / dynein complex / retrograde axonal transport / spindle organization / cytoplasmic dynein complex / dynein light intermediate chain binding / centrosome localization / oogenesis / microtubule-based movement / dynein intermediate chain binding / establishment of mitotic spindle orientation / dynactin binding / actin filament bundle assembly / spermatid development / axon cytoplasm / centriole / determination of adult lifespan / microtubule cytoskeleton organization / disordered domain specific binding / transcription corepressor activity / mitotic cell cycle / spermatogenesis / nuclear membrane / molecular adaptor activity / microtubule / neuron projection / lysosomal membrane / protein homodimerization activity / protein-containing complex / identical protein binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Tctex-1 / Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / Dynein light chain, type 1/2, conserved site / Dynein light chain type 1 signature. ...Tctex-1 / Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / Dynein light chain Tctex-1 like / Tctex-1-like superfamily / Tctex-1 family / Cytoplasmic dynein 1 intermediate chain 1/2 / Cytoplasmic dynein 1 intermediate chain 2 / 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 / Ribosomal protein S3 C-terminal domain / WD domain, G-beta repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Dynein light chain 1, cytoplasmic / Cytoplasmic dynein 1 intermediate chain / Dynein light chain Tctex-type
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 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
DepositionDec 19, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 15, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dynein light chain Tctex-type
B: Dynein light chain Tctex-type
C: Dynein intermediate chain, cytosolic
D: Dynein intermediate chain, cytosolic
E: Dynein light chain 1, cytoplasmic
F: Dynein light chain 1, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)51,8696
Polymers51,8696
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12860 Å2
ΔGint-54 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.790, 115.790, 90.500
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Protein Dynein light chain Tctex-type / TCTEX-1 protein homolog


Mass: 12491.021 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dlc90F, Tctex, CG12363 / Plasmid: pET15(Da) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q94524
#2: Protein/peptide Dynein intermediate chain, cytosolic / DH IC / Cytoplasmic dynein intermediate chain / Protein short wing


Mass: 3054.404 Da / Num. of mol.: 2 / Fragment: IC, Residues 109-135
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: sw, Cdic, Dic19B, CG18000 / Plasmid: pET15(Da) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q24246
#3: Protein Dynein light chain 1, cytoplasmic / 8 kDa dynein light chain / Cut up protein


Mass: 10388.849 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: ctp, Cdlc1, ddlc1, CG6998 / Plasmid: pET15(Da) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(DE3) / References: UniProt: Q24117

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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: 3.36 Å3/Da / Density % sol: 63.44 %
Crystal growTemperature: 277.15 K / Method: hanging drop / pH: 6.5
Details: 16% PEG 8K, 100 mM sodium cacodylate, 200 mM calcium acetate, pH 6.5, Hanging Drop, temperature 277.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2008
RadiationMonochromator: KOHZU: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.5→100 Å / Num. all: 8756 / Num. obs: 8745 / % possible obs: 98.84 % / Observed criterion σ(F): 8.2 / Observed criterion σ(I): 6.6 / Redundancy: 7.1 % / Rmerge(I) obs: 0.088 / Rsym value: 0.06 / Net I/σ(I): 15.9
Reflection shellResolution: 3.5→3.64 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 6.2 / Rsym value: 0.53 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
DENZOdata reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: chains A and F in pdb structure 2PG1

2pg1


Resolution: 3.5→100 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.877 / SU B: 63.772 / SU ML: 0.446 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.659 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2747 870 10 %RANDOM
Rwork0.16975 ---
obs0.18001 7873 99.39 %-
all-7884 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 94.445 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å2-0 Å2
2--0 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 3.5→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3436 0 0 0 3436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d00.0223504
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.0471.9284750
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg12.1685425
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.53625.652161
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.72515612
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.513156
X-RAY DIFFRACTIONr_chiral_restr0.0010.2538
X-RAY DIFFRACTIONr_gen_planes_refined00.022612
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2250.21719
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.22355
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2123
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2040.220
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it70.8381.52138
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it64.60323472
X-RAY DIFFRACTIONr_scbond_it31366
X-RAY DIFFRACTIONr_scangle_it4.51278
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.501→3.592 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.399 76 -
Rwork0.234 569 -
obs--98.93 %
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)
13.7734-0.118-1.27830.73820.26312.5320.0717-0.8954-0.12570.4253-0.14740.70060.22-0.22260.07570.3137-0.13560.36510.3587-0.0830.692-40.0423-30.4297-23.0169
24.36450.6101-0.62424.99111.05422.7671-0.1150.17560.3279-0.1344-0.02920.4617-0.3007-0.30910.14410.18470.0728-0.12380.24830.06980.2915-36.7222-25.85-40.2563
32.12786.88191.056723.99383.2970.68890.2367-0.21250.39410.5521-0.56180.8160.0131-0.01870.32510.2219-0.00640.03940.2148-0.01060.2597-33.7853-49.921-35.1236
41.3261.8021.0062.80791.22490.9245-0.2011-0.06760.93270.1711-0.28381.5426-0.1798-0.16150.48490.2187-0.03380.15620.196-0.11270.8677-53.1914-43.5205-35.0054
53.97520.2708-0.01982.73120.73572.840.0283-0.2797-0.12550.403-0.0871-0.08490.1628-0.06040.05880.3006-0.01590.09240.2203-0.02280.1825-48.7318-73.6662-29.6696
63.3699-0.0177-0.03932.43110.12173.14710.05630.57330.0889-0.41650.03710.1077-0.0951-0.1706-0.09340.2016-0.00010.05070.32-0.03030.1877-52.7204-71.2546-49.7982
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 111
2X-RAY DIFFRACTION2B8 - 111
3X-RAY DIFFRACTION3C109 - 135
4X-RAY DIFFRACTION4D109 - 135
5X-RAY DIFFRACTION5E5 - 89
6X-RAY DIFFRACTION6F5 - 89

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