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- PDB-5e0l: LC8 - Chica (415-424) Complex -

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Basic information

Entry
Database: PDB / ID: 5e0l
TitleLC8 - Chica (415-424) Complex
Components
  • Dynein light chain 1, cytoplasmic
  • Protein Chica peptide
KeywordsTRANSPORT PROTEIN / Complex / Dynein
Function / homology
Function and homology information


spermatid nucleus elongation / positive regulation of neuron remodeling / chaeta morphogenesis / Macroautophagy / Aggrephagy / wing disc development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport / protein localization to mitotic spindle / COPI-independent Golgi-to-ER retrograde traffic ...spermatid nucleus elongation / positive regulation of neuron remodeling / chaeta morphogenesis / Macroautophagy / Aggrephagy / wing disc development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport / protein localization to mitotic spindle / COPI-independent Golgi-to-ER retrograde traffic / microtubule anchoring at centrosome / transposable element silencing by piRNA-mediated heterochromatin formation / chaeta development / sperm individualization / metaphase chromosome alignment / imaginal disc-derived wing morphogenesis / RNA polymerase II transcription repressor complex / Neutrophil degranulation / positive regulation of cell cycle G1/S phase transition / regulation of TOR signaling / dynein complex / cytoplasmic dynein complex / dynein light intermediate chain binding / dynein intermediate chain binding / intercellular bridge / oogenesis / Signaling by EGFR / regulation of protein catabolic process / mitotic spindle pole / establishment of mitotic spindle orientation / kinesin binding / actin filament bundle assembly / epithelial to mesenchymal transition / centriole / regulation of ERK1 and ERK2 cascade / mitotic spindle / spindle / transcription corepressor activity / microtubule cytoskeleton / disordered domain specific binding / cell migration / microtubule binding / spermatogenesis / microtubule / cell population proliferation / cell division / protein kinase binding / signal transduction / protein homodimerization activity / protein-containing complex / nucleus / cytosol / cytoplasm
Similarity search - Function
FAM83, N-terminal / : / FAM83 A-H / 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 1/2 / Dynein light chain type 1 / Dynein light chain type 1 ...FAM83, N-terminal / : / FAM83 A-H / 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 1/2 / Dynein light chain type 1 / Dynein light chain type 1 / Dynein light chain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Dynein light chain 1, cytoplasmic / Protein FAM83D
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.31 Å
AuthorsClark, S.A. / Barbar, E.B. / Karplus, P.A.
CitationJournal: Biochemistry / Year: 2016
Title: The Anchored Flexibility Model in LC8 Motif Recognition: Insights from the Chica Complex.
Authors: Clark, S. / Nyarko, A. / Lohr, F. / Karplus, P.A. / Barbar, E.
History
DepositionSep 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2015Provider: repository / Type: Initial release
Revision 1.1Jan 20, 2016Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations / Refinement description
Category: citation / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Sep 27, 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 1, cytoplasmic
C: Protein Chica peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0703
Polymers11,9742
Non-polymers961
Water1,06359
1
A: Dynein light chain 1, cytoplasmic
C: Protein Chica peptide
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)24,1396
Polymers23,9474
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area5500 Å2
ΔGint-49 kcal/mol
Surface area8820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.695, 44.695, 204.096
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-237-

HOH

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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 Protein Chica peptide


Mass: 1584.684 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H4H8*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.56 % / Description: Long hexagonal rods
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 M calcium acetate, 0.1 M sodium cacodylate, 15% polyethylene glycol 8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.31→38.7 Å / Num. obs: 30438 / % possible obs: 100 % / Redundancy: 30.8 % / Rmerge(I) obs: 0.081 / Net I/σ(I): 20.6
Reflection shellResolution: 1.31→1.33 Å / Redundancy: 8 % / Rmerge(I) obs: 4.45 / Mean I/σ(I) obs: 0.4 / % possible all: 99.1

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
PHENIX(dev_2006: ???)refinement
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BRI

3bri


Resolution: 1.31→38.7 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2015 1495 4.96 %
Rwork0.1964 --
obs0.1967 30142 99.37 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.31→38.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms798 0 5 59 862
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.014847
X-RAY DIFFRACTIONf_angle_d1.3461151
X-RAY DIFFRACTIONf_dihedral_angle_d13.367321
X-RAY DIFFRACTIONf_chiral_restr0.09125
X-RAY DIFFRACTIONf_plane_restr0.007148
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.35230.49061300.47912461X-RAY DIFFRACTION97
1.3523-1.40060.39861260.39172550X-RAY DIFFRACTION99
1.4006-1.45670.33441340.31832519X-RAY DIFFRACTION100
1.4567-1.5230.29831160.26672576X-RAY DIFFRACTION100
1.523-1.60330.23771350.22892575X-RAY DIFFRACTION100
1.6033-1.70380.20251470.19822544X-RAY DIFFRACTION100
1.7038-1.83530.22151270.1932588X-RAY DIFFRACTION100
1.8353-2.020.22181470.18582610X-RAY DIFFRACTION100
2.02-2.31230.17071340.17382633X-RAY DIFFRACTION100
2.3123-2.91310.1681380.18212683X-RAY DIFFRACTION99
2.9131-38.72380.18821610.18042908X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -17.0657 Å / Origin y: 15.4526 Å / Origin z: -8.4479 Å
111213212223313233
T0.4899 Å2-0.0226 Å20.02 Å2-0.2192 Å2-0.0067 Å2--0.1011 Å2
L2.5847 °20.3706 °20.2905 °2-3.9864 °2-0.1615 °2--3.6615 °2
S-0.0486 Å °-0.1845 Å °0.2234 Å °0.8457 Å °0.0546 Å °0.1032 Å °-0.4977 Å °-0.0427 Å °-0.0402 Å °
Refinement TLS groupSelection details: all

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