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- PDB-5e0m: LC8 - Chica (468-476) Complex -

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Basic information

Entry
Database: PDB / ID: 5e0m
TitleLC8 - Chica (468-476) Complex
Components
  • Dynein light chain 1, cytoplasmic
  • Protein Chica peptide
KeywordsTRANSPORT PROTEIN / Complex / Dynein
Function / homology
Function and homology information


protein localization to mitotic spindle / 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 ...protein localization to mitotic spindle / 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 / metaphase chromosome alignment / Neutrophil degranulation / positive regulation of cell cycle G1/S phase transition / regulation of TOR signaling / dynein complex / dynein light intermediate chain binding / cytoplasmic dynein complex / dynein intermediate chain binding / intercellular bridge / oogenesis / 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 / microtubule cytoskeleton / disordered domain specific binding / cell migration / spermatogenesis / microtubule binding / microtubule / cell population proliferation / cell division / protein kinase binding / signal transduction / protein homodimerization activity / protein-containing complex / cytoplasm / cytosol
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 / Dynein light chain, type 1/2 / Dynein light chain superfamily / 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 / 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 / Protein FAM83D
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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
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

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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)12,0503
Polymers11,9542
Non-polymers961
Water1,08160
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)24,0996
Polymers23,9074
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area5140 Å2
ΔGint-35 kcal/mol
Surface area8380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.540, 44.540, 205.016
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) / References: UniProt: Q24117
#2: Protein/peptide Protein Chica peptide


Mass: 1564.654 Da / Num. of mol.: 1 / Fragment: unp residues 464-476
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.: 60 / 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: 2.46 Å3/Da / Density % sol: 49.91 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.2 M lithium sulfate, 0.1 M Bis-Tris, 25% polyethylene glycol 3350

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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: 1.65→38.6 Å / Num. obs: 15900 / % possible obs: 100 % / Redundancy: 33.4 % / Rmerge(I) obs: 0.37 / Net I/σ(I): 9.8
Reflection shellResolution: 1.64→1.67 Å / Redundancy: 24.7 % / Rmerge(I) obs: 9.11 / Mean I/σ(I) obs: 0.5 / % possible all: 100

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Processing

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

3bri


Resolution: 1.65→38.573 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.85 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2318 763 4.93 %
Rwork0.2069 --
obs0.2082 15462 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→38.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms787 0 5 60 852
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007839
X-RAY DIFFRACTIONf_angle_d1.0761139
X-RAY DIFFRACTIONf_dihedral_angle_d14.781318
X-RAY DIFFRACTIONf_chiral_restr0.045123
X-RAY DIFFRACTIONf_plane_restr0.004146
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6501-1.77750.47381400.44882832X-RAY DIFFRACTION99
1.7775-1.95630.34941540.30132843X-RAY DIFFRACTION100
1.9563-2.23940.24791500.21132891X-RAY DIFFRACTION100
2.2394-2.82130.24561580.20462944X-RAY DIFFRACTION100
2.8213-38.58320.19321610.17543189X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -16.9453 Å / Origin y: 15.4852 Å / Origin z: -8.3955 Å
111213212223313233
T0.4158 Å2-0.0179 Å20.0217 Å2-0.1774 Å20.0069 Å2--0.256 Å2
L0.9762 °20.3104 °20.4188 °2-1.2153 °20.4213 °2--0.6765 °2
S-0.065 Å °-0.1259 Å °0.0984 Å °0.6435 Å °0.0724 Å °0.0612 Å °-0.2585 Å °0.0079 Å °0.031 Å °
Refinement TLS groupSelection details: all

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