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- PDB-2p2t: Crystal structure of dynein light chain LC8 bound to residues 123... -

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Basic information

Entry
Database: PDB / ID: 2p2t
TitleCrystal structure of dynein light chain LC8 bound to residues 123-138 of intermediate chain IC74
Components
  • Dynein intermediate chain peptide
  • Dynein light chain 1, cytoplasmic
KeywordsTRANSPORT PROTEIN / protein - peptide complex
Function / homology
Function and homology information


cellularization / spermatid nucleus elongation / eye photoreceptor cell differentiation / 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 ...cellularization / spermatid nucleus elongation / eye photoreceptor cell differentiation / 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 / transport along microtubule / : / chaeta development / sperm individualization / dynein light chain binding / microtubule anchoring at centrosome / imaginal disc-derived wing morphogenesis / dynein heavy chain binding / Neutrophil degranulation / dynein complex / cytoplasmic dynein complex / dynein light intermediate chain binding / protein localization to kinetochore / axo-dendritic transport / centrosome localization / spindle organization / dynein intermediate chain binding / oogenesis / microtubule-based movement / dynactin binding / establishment of mitotic spindle orientation / actin filament bundle assembly / centriole / microtubule cytoskeleton organization / autophagy / disordered domain specific binding / spermatogenesis / nuclear membrane / microtubule / molecular adaptor activity / neuron projection / lysosomal membrane / protein homodimerization activity / protein-containing complex / cytoplasm
Similarity search - Function
Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / 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 / Dynein light chain, type 1/2 / Dynein light chain superfamily / Dynein light chain type 1 ...Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / 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 / Dynein light chain, type 1/2 / Dynein light chain superfamily / Dynein light chain type 1 / WD domain, G-beta repeat / WD40 repeats / WD40 repeat / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Dynein light chain 1, cytoplasmic / Cytoplasmic dynein 1 intermediate chain
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBenison, G. / Karplus, P.A. / Barbar, E.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structure and dynamics of LC8 complexes with KXTQT-motif peptides: swallow and dynein intermediate chain compete for a common site.
Authors: Benison, G. / Karplus, P.A. / Barbar, E.
History
DepositionMar 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dynein light chain 1, cytoplasmic
C: Dynein intermediate chain peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2594
Polymers12,1772
Non-polymers822
Water90150
1
A: Dynein light chain 1, cytoplasmic
C: Dynein intermediate chain peptide
hetero molecules

A: Dynein light chain 1, cytoplasmic
C: Dynein intermediate chain peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,5188
Polymers24,3544
Non-polymers1644
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area5490 Å2
ΔGint-39 kcal/mol
Surface area8790 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)44.356, 44.356, 204.466
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
DetailsThe biological assembly is a dimer generated from the monomer in the asymmetric unit by the operation: -y, -x, -z + 1/6

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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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q24117
#2: Protein/peptide Dynein intermediate chain peptide / DH IC / Cytoplasmic dynein intermediate chain / Protein short wing


Mass: 1787.961 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide can be naturally found in Drosophila melanogaster (Fruit fly).
References: UniProt: Q24246
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 50 / 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: 2.38 Å3/Da / Density % sol: 48.41 %

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Data collection

DiffractionMean temperature: 130 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 13, 2006
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3→40 Å / Num. all: 2856 / Num. obs: 2817 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rsym value: 0.069 / Net I/σ(I): 30
Reflection shellResolution: 3→3.05 Å / Mean I/σ(I) obs: 12.5 / Num. unique all: 166 / Rsym value: 0.245 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→22.18 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.842 / SU B: 42.419 / SU ML: 0.404 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.534 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29634 259 9.4 %RANDOM
Rwork0.20974 ---
obs0.21797 2501 99.03 %-
all-2501 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.159 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 3→22.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms780 0 5 50 835
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.022803
X-RAY DIFFRACTIONr_angle_refined_deg1.0771.931083
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.009596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.41724.87239
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.00715142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.396152
X-RAY DIFFRACTIONr_chiral_restr0.0690.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02605
X-RAY DIFFRACTIONr_nbd_refined0.2750.3423
X-RAY DIFFRACTIONr_nbtor_refined0.3330.5543
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2480.552
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1990.347
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2670.59
X-RAY DIFFRACTIONr_mcbond_it0.6872482
X-RAY DIFFRACTIONr_mcangle_it1.2313774
X-RAY DIFFRACTIONr_scbond_it0.472333
X-RAY DIFFRACTIONr_scangle_it0.7463308
LS refinement shellResolution: 3→3.077 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 19 -
Rwork0.201 166 -
obs--94.87 %

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