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- PDB-7k3k: Crystal structure of dLC8 in complex with Panoramix TQT peptide -

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Basic information

Entry
Database: PDB / ID: 7k3k
TitleCrystal structure of dLC8 in complex with Panoramix TQT peptide
Components
  • Dynein light chain 1, cytoplasmic
  • Protein panoramix
KeywordsMOTOR PROTEIN / Piwi / transposon silencing / heterochromatin formation / piRNA pathway / transcriptional silencing / RNA BINDING PROTEIN
Function / homology
Function and homology information


piRNA-mediated heterochromatin formation / spermatid nucleus elongation / chaeta morphogenesis / positive regulation of neuron remodeling / Macroautophagy / piRNA-mediated retrotransposon silencing by heterochromatin formation / Aggrephagy / wing disc development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport ...piRNA-mediated heterochromatin formation / spermatid nucleus elongation / chaeta morphogenesis / positive regulation of neuron remodeling / Macroautophagy / piRNA-mediated retrotransposon silencing by heterochromatin formation / 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 / chaeta development / sperm individualization / imaginal disc-derived wing morphogenesis / positive regulation of DNA methylation-dependent heterochromatin formation / Neutrophil degranulation / dynein complex / dynein light intermediate chain binding / cytoplasmic dynein complex / dynein intermediate chain binding / oogenesis / establishment of mitotic spindle orientation / actin filament bundle assembly / transcription repressor complex / centriole / disordered domain specific binding / spermatogenesis / microtubule / negative regulation of gene expression / protein homodimerization activity / protein-containing complex / nucleus / cytoplasm
Similarity search - Function
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
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: 1.415 Å
AuthorsWang, J. / Patel, D.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)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


Theoretical massNumber of molelcules
Total (without water)12,0312
Polymers12,0312
Non-polymers00
Water2,612145
1
A: Dynein light chain 1, cytoplasmic
B: Protein panoramix

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


Theoretical massNumber of molelcules
Total (without water)24,0614
Polymers24,0614
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
Buried area5100 Å2
ΔGint-14 kcal/mol
Surface area9860 Å2
Unit cell
Length a, b, c (Å)45.639, 45.639, 202.717
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-174-

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: 1641.804 Da / Num. of mol.: 1 / Fragment: residues 445-467
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.53 Å3/Da / Density % sol: 51.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M NH4Ac, 0.1 M Bis-Tris pH 5.5, 17% (w/v) PEG 10000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.415→101.36 Å / Num. obs: 24954 / % possible obs: 99.1 % / Redundancy: 15.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.069 / Net I/σ(I): 33.6
Reflection shellResolution: 1.42→1.44 Å / Num. unique obs: 999 / CC1/2: 0.946

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZKE

3zke


Resolution: 1.415→38.794 Å / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2006 2000 8.05 %
Rwork0.1827 22845 -
obs0.1842 24845 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 70.88 Å2 / Biso mean: 18.5887 Å2 / Biso min: 8.36 Å2
Refinement stepCycle: final / Resolution: 1.415→38.794 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms835 0 1 146 982
Biso mean--36.17 29.32 -
Num. residues----102
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.005859
X-RAY DIFFRACTIONf_angle_d0.8061152
X-RAY DIFFRACTIONf_dihedral_angle_d2.875490
X-RAY DIFFRACTIONf_chiral_restr0.078123
X-RAY DIFFRACTIONf_plane_restr0.004146
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4152-1.45060.2691210.23139387
1.4506-1.48980.20961410.19641596100
1.4898-1.53370.20171410.18591612100
1.5337-1.58320.20511410.18211606100
1.5832-1.63980.18361380.17761591100
1.6398-1.70540.21161420.17151607100
1.7054-1.7830.21461410.19321615100
1.783-1.8770.22731430.18421637100
1.877-1.99460.20971430.18121633100
1.9946-2.14860.17851420.17791633100
2.1486-2.36480.21591460.18361662100
2.3648-2.7070.20381480.18561676100
2.707-3.41020.19971490.19091713100
3.4102-38.7940.18531640.1731871100

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