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- PDB-3e2b: Crystal structure of Dynein Light chain LC8 in complex with a pep... -

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Basic information

Entry
Database: PDB / ID: 3e2b
TitleCrystal structure of Dynein Light chain LC8 in complex with a peptide derived from Swallow
Components
  • Dynein light chain 1, cytoplasmic
  • Protein swallow 16-residue peptide
KeywordsTRANSPORT PROTEIN / protein-peptide complex / Cytoplasm / Dynein / Microtubule / Motor protein
Function / homology
Function and homology information


pole plasm mRNA localization / bicoid mRNA localization / spermatid nucleus elongation / chaeta morphogenesis / regulation of pole plasm oskar mRNA localization / positive regulation of neuron remodeling / Macroautophagy / Aggrephagy / wing disc development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand ...pole plasm mRNA localization / bicoid mRNA localization / spermatid nucleus elongation / chaeta morphogenesis / regulation of pole plasm oskar mRNA localization / 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 / anterior/posterior axis specification, embryo / Neutrophil degranulation / dynein complex / dynein light intermediate chain binding / cytoplasmic dynein complex / dynein intermediate chain binding / dynein complex binding / oogenesis / establishment of mitotic spindle orientation / actin filament bundle assembly / centriole / actin filament organization / disordered domain specific binding / spermatogenesis / microtubule / cell cycle / cell division / mRNA binding / protein homodimerization activity / protein-containing complex / nucleus / 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
ACETATE ION / Protein swallow / Dynein light chain 1, cytoplasmic
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsBenison, G. / Barbar, E. / Karplus, P.A.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: The interplay of ligand binding and quaternary structure in the diverse interactions of dynein light chain LC8.
Authors: Benison, G. / Karplus, P.A. / Barbar, E.
#1: Journal: 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
DepositionAug 5, 2008Deposition site: RCSB / Processing site: RCSB
SupersessionAug 12, 2008ID: 2P1K
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Downloads & links

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Assembly

Deposited unit
A: Dynein light chain 1, cytoplasmic
C: Protein swallow 16-residue peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,2323
Polymers12,1732
Non-polymers591
Water1,09961
1
A: Dynein light chain 1, cytoplasmic
C: Protein swallow 16-residue peptide
hetero molecules

A: Dynein light chain 1, cytoplasmic
C: Protein swallow 16-residue peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4646
Polymers24,3464
Non-polymers1182
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area4780 Å2
ΔGint-20 kcal/mol
Surface area8600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.158, 44.158, 203.718
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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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) / Strain (production host): BL21(DE3) / References: UniProt: Q24117
#2: Protein/peptide Protein swallow 16-residue peptide


Mass: 1783.980 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: P40688
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 61 / 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: 2.36 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2M sodium potassium tartrate, 0.1M sodium citrate, 2.0M ammonium sulfate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 0.979 Å
DetectorDetector: AREA DETECTOR / Date: Feb 27, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.9→40.7 Å / Num. all: 10184 / Num. obs: 10184 / % possible obs: 100 % / Redundancy: 13.7 % / Biso Wilson estimate: 28.4 Å2 / Rsym value: 0.07 / Net I/σ(I): 23.5
Reflection shellResolution: 1.9→2 Å / Redundancy: 14.3 % / Mean I/σ(I) obs: 5.1 / Num. unique all: 1436 / Rsym value: 0.63 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2p1k

2p1k
PDB Unreleased entry


Resolution: 2→35.81 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.925 / SU B: 11.277 / SU ML: 0.154 / Cross valid method: THROUGHOUT / ESU R: 0.2 / ESU R Free: 0.183 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26599 869 10 %RANDOM
Rwork0.21591 ---
obs0.22084 7844 99.94 %-
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: 34.422 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å20 Å2
2--0.08 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2→35.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms804 0 4 61 869
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022826
X-RAY DIFFRACTIONr_angle_refined_deg0.881.9341116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1815102
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.9082542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43315151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.856153
X-RAY DIFFRACTIONr_chiral_restr0.0630.2120
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02630
X-RAY DIFFRACTIONr_nbd_refined0.2080.3365
X-RAY DIFFRACTIONr_nbtor_refined0.3170.5558
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1880.572
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.343
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1350.510
X-RAY DIFFRACTIONr_mcbond_it2.2422508
X-RAY DIFFRACTIONr_mcangle_it3.0563797
X-RAY DIFFRACTIONr_scbond_it2.5392360
X-RAY DIFFRACTIONr_scangle_it3.573315
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.347 53 -
Rwork0.263 552 -
obs--100 %

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