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- PDB-7k3l: Crystal structure of dLC8 in complex with Panoramix TQ peptide -

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Basic information

Entry
Database: PDB / ID: 7k3l
TitleCrystal structure of dLC8 in complex with Panoramix TQ peptide
Components
  • Dynein light chain 1, cytoplasmic
  • Protein panoramix
KeywordsMOTOR PROTEIN / Piwi / transposon siliencing / heterochromatin formation / piRNA pathway / transcriptional silencing
Function / homology
Function and homology information


piRNA-mediated heterochromatin formation / 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 / COPI-independent Golgi-to-ER retrograde traffic ...piRNA-mediated heterochromatin formation / 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 / COPI-independent Golgi-to-ER retrograde traffic / piRNA binding / microtubule anchoring at centrosome / transposable element silencing by heterochromatin formation / transposable element silencing by piRNA-mediated heterochromatin formation / chaeta development / sperm individualization / imaginal disc-derived wing morphogenesis / : / RNA polymerase II transcription repressor complex / Neutrophil degranulation / dynein complex / cytoplasmic dynein complex / dynein light intermediate chain binding / dynein intermediate chain binding / oogenesis / establishment of mitotic spindle orientation / actin filament bundle assembly / transcription repressor complex / centriole / transcription corepressor activity / disordered domain specific binding / spermatogenesis / microtubule / protein homodimerization activity / protein-containing complex / nucleus / cytosol / cytoplasm
Similarity search - Function
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
Similarity search - Domain/homology
Dynein light chain 1, cytoplasmic / Protein panoramix
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsWang, J. / Patel, D.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Center for Advancing Translational Sciences (NIH/NCATS)P30 GM124165 United States
Department of Energy (DOE, United States)DE-AC02-06CH11357 United States
CitationJournal: Genes Dev. / Year: 2021
Title: Molecular principles of Piwi-mediated cotranscriptional silencing through the dimeric SFiNX complex.
Authors: Schnabl, J. / Wang, J. / Hohmann, U. / Gehre, M. / Batki, J. / Andreev, V.I. / Purkhauser, K. / Fasching, N. / Duchek, P. / Novatchkova, M. / Mechtler, K. / Plaschka, C. / Patel, D.J. / Brennecke, J.
History
DepositionSep 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 10, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 18, 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
B: Protein panoramix
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,0825
Polymers11,8952
Non-polymers1863
Water1,29772
1
A: Dynein light chain 1, cytoplasmic
B: Protein panoramix
hetero molecules

A: Dynein light chain 1, cytoplasmic
B: Protein panoramix
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,16310
Polymers23,7914
Non-polymers3726
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-x,-y,z1
Buried area5140 Å2
ΔGint-11 kcal/mol
Surface area9640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.900, 62.900, 120.400
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11B-614-

HOH

21B-616-

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 BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q24117
#2: Protein/peptide Protein panoramix / Protein silencio


Mass: 1506.618 Da / Num. of mol.: 1 / Fragment: residues 468-480
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Panx, CG9754 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / Variant (production host): RIL / References: UniProt: Q9W2H9
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.5 Å3/Da / Density % sol: 50.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M KSCN, 30% (w/v) PEG 2000 MME

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9792 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.79→60.2 Å / Num. obs: 11305 / % possible obs: 96.1 % / Redundancy: 8.6 % / Biso Wilson estimate: 19.92 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Net I/σ(I): 14.2
Reflection shellResolution: 1.79→1.89 Å / Rmerge(I) obs: 0.415 / Num. unique obs: 1281 / CC1/2: 0.8

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PHENIX1.16_3549refinement
iMOSFLMdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZKE

3zke


Resolution: 1.79→55.75 Å / SU ML: 0.1555 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.3632
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2095 552 4.89 %
Rwork0.1762 10734 -
obs0.178 11286 95.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 24.1 Å2
Refinement stepCycle: LAST / Resolution: 1.79→55.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms780 0 12 72 864
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068804
X-RAY DIFFRACTIONf_angle_d0.85661078
X-RAY DIFFRACTIONf_chiral_restr0.057118
X-RAY DIFFRACTIONf_plane_restr0.0042136
X-RAY DIFFRACTIONf_dihedral_angle_d15.5247472
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.79-1.970.29591130.21452298X-RAY DIFFRACTION83.63
1.97-2.260.1961390.15922731X-RAY DIFFRACTION99.69
2.26-2.840.23631360.17942789X-RAY DIFFRACTION99.9
2.84-55.750.19091640.17362916X-RAY DIFFRACTION99.87

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