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- PDB-7k3j: Crystal structure of dLC8 in complex with Panoramix TQT+TQ peptide -

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Basic information

Entry
Database: PDB / ID: 7k3j
TitleCrystal structure of dLC8 in complex with Panoramix TQT+TQ 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


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 ...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 / chaeta development / sperm individualization / imaginal disc-derived wing morphogenesis / microtubule anchoring at centrosome / transposable element silencing by piRNA-mediated heterochromatin formation / RNA polymerase II transcription repressor complex / transposable element silencing by 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 / 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: 2.5 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 / Derived calculations
Category: citation / pdbx_struct_assembly ...citation / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
C: Dynein light chain 1, cytoplasmic
D: Protein panoramix
E: Dynein light chain 1, cytoplasmic
F: Protein panoramix
G: Dynein light chain 1, cytoplasmic
H: Protein panoramix
I: Dynein light chain 1, cytoplasmic
K: Dynein light chain 1, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,79513
Polymers74,50610
Non-polymers2883
Water00
1
A: Dynein light chain 1, cytoplasmic
B: Protein panoramix
G: Dynein light chain 1, cytoplasmic
H: Protein panoramix
I: Dynein light chain 1, cytoplasmic
K: Dynein light chain 1, cytoplasmic
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8348
Polymers47,6426
Non-polymers1922
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10460 Å2
ΔGint-59 kcal/mol
Surface area17090 Å2
MethodPISA
2
C: Dynein light chain 1, cytoplasmic
D: Protein panoramix
hetero molecules

E: Dynein light chain 1, cytoplasmic
F: Protein panoramix


Theoretical massNumber of molelcules
Total (without water)26,9605
Polymers26,8644
Non-polymers961
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area4650 Å2
ΔGint-34 kcal/mol
Surface area8510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.100, 175.230, 51.020
Angle α, β, γ (deg.)90.000, 105.480, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 5 through 8 or (resid 9...
21(chain C and (resid 5 through 8 or (resid 9...
31(chain E and ((resid 5 through 6 and (name N...
41(chain G and (resid 5 through 8 or (resid 9...
51(chain I and (resid 5 through 8 or (resid 9...
61(chain K and (resid 5 through 9 or (resid 10...
12(chain B and ((resid 456 through 458 and (name N...
22(chain H and (resid 456 through 470 or (resid 471...
13chain D
23chain F

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LYSLYSILEILE(chain A and (resid 5 through 8 or (resid 9...AA5 - 85 - 8
121LYSLYSALAALA(chain A and (resid 5 through 8 or (resid 9...AA9 - 119 - 11
131LYSLYSGLYGLY(chain A and (resid 5 through 8 or (resid 9...AA5 - 895 - 89
211LYSLYSILEILE(chain C and (resid 5 through 8 or (resid 9...CC5 - 85 - 8
221LYSLYSALAALA(chain C and (resid 5 through 8 or (resid 9...CC9 - 119 - 11
231LYSLYSGLYGLY(chain C and (resid 5 through 8 or (resid 9...CC5 - 895 - 89
311LYSLYSALAALA(chain E and ((resid 5 through 6 and (name N...EE5 - 65 - 6
321LYSLYSGLYGLY(chain E and ((resid 5 through 6 and (name N...EE5 - 895 - 89
331LYSLYSGLYGLY(chain E and ((resid 5 through 6 and (name N...EE5 - 895 - 89
341LYSLYSGLYGLY(chain E and ((resid 5 through 6 and (name N...EE5 - 895 - 89
351LYSLYSGLYGLY(chain E and ((resid 5 through 6 and (name N...EE5 - 895 - 89
411LYSLYSILEILE(chain G and (resid 5 through 8 or (resid 9...GG5 - 85 - 8
421LYSLYSALAALA(chain G and (resid 5 through 8 or (resid 9...GG9 - 119 - 11
431LYSLYSGLYGLY(chain G and (resid 5 through 8 or (resid 9...GG5 - 895 - 89
511LYSLYSILEILE(chain I and (resid 5 through 8 or (resid 9...II5 - 85 - 8
521LYSLYSALAALA(chain I and (resid 5 through 8 or (resid 9...II9 - 119 - 11
531LYSLYSGLYGLY(chain I and (resid 5 through 8 or (resid 9...II5 - 895 - 89
541LYSLYSGLYGLY(chain I and (resid 5 through 8 or (resid 9...II5 - 895 - 89
551LYSLYSGLYGLY(chain I and (resid 5 through 8 or (resid 9...II5 - 895 - 89
561LYSLYSGLYGLY(chain I and (resid 5 through 8 or (resid 9...II5 - 895 - 89
611LYSLYSLYSLYS(chain K and (resid 5 through 9 or (resid 10...KJ5 - 95 - 9
621ASNASNALAALA(chain K and (resid 5 through 9 or (resid 10...KJ10 - 1110 - 11
631LYSLYSSERSER(chain K and (resid 5 through 9 or (resid 10...KJ5 - 885 - 88
641LYSLYSSERSER(chain K and (resid 5 through 9 or (resid 10...KJ5 - 885 - 88
651LYSLYSSERSER(chain K and (resid 5 through 9 or (resid 10...KJ5 - 885 - 88
661LYSLYSSERSER(chain K and (resid 5 through 9 or (resid 10...KJ5 - 885 - 88
112LEULEULYSLYS(chain B and ((resid 456 through 458 and (name N...BB456 - 4583 - 5
122SERSERARGARG(chain B and ((resid 456 through 458 and (name N...BB454 - 4781 - 25
132SERSERARGARG(chain B and ((resid 456 through 458 and (name N...BB454 - 4781 - 25
142SERSERARGARG(chain B and ((resid 456 through 458 and (name N...BB454 - 4781 - 25
212LEULEUTHRTHR(chain H and (resid 456 through 470 or (resid 471...HH456 - 4703 - 17
222ARGARGARGARG(chain H and (resid 456 through 470 or (resid 471...HH47118
232LEULEUGLUGLU(chain H and (resid 456 through 470 or (resid 471...HH456 - 4803 - 27
242LEULEUGLUGLU(chain H and (resid 456 through 470 or (resid 471...HH456 - 4803 - 27
252LEULEUGLUGLU(chain H and (resid 456 through 470 or (resid 471...HH456 - 4803 - 27
262LEULEUGLUGLU(chain H and (resid 456 through 470 or (resid 471...HH456 - 4803 - 27
113THRTHRARGARGchain DDD468 - 47815 - 25
213THRTHRARGARGchain FFF468 - 47815 - 25

NCS ensembles :
ID
1
2
3

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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.: 6
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: 3043.330 Da / Num. of mol.: 4 / Fragment: residues 455-480
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
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: 2.2 Å3/Da / Density % sol: 44.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 0.2 M Li2SO4, 0.1 M Tris pH 8.5, 40% (v/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.5→87.615 Å / Num. all: 21856 / Num. obs: 21856 / % possible obs: 98.2 % / Redundancy: 6.3 % / Rpim(I) all: 0.032 / Rrim(I) all: 0.081 / Rsym value: 0.074 / Net I/av σ(I): 4.7 / Net I/σ(I): 12.8 / Num. measured all: 137634
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique obsRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.5-2.646.30.4431.62000531840.190.4840.4433.598.4
2.64-2.86.40.3232.21947030290.1370.3520.3234.998.8
2.8-2.996.20.213.41746328380.0910.230.216.598.1
2.99-3.2360.1235.41585626420.0540.1350.1239.998.2
3.23-3.546.60.0896.81589624200.0380.0970.08914.998.8
3.54-3.956.10.0767.71342421990.0330.0830.07618.297.8
3.95-4.566.40.0618.91246219370.0260.0660.06122.998.3
4.56-5.596.50.0668.11079816620.0270.0710.06624.698.6
5.59-7.916.30.0629.1788712530.0270.0680.06222.997.3
7.91-49.1696.30.0598.343736920.0260.0650.05926.995.6

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Processing

Software
NameVersionClassification
SCALA3.3.22data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZKE

3zke


Resolution: 2.5→49.169 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 35.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.272 1079 4.95 %
Rwork0.2494 20702 -
obs0.2505 21781 97.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 136.23 Å2 / Biso mean: 79.1242 Å2 / Biso min: 48.22 Å2
Refinement stepCycle: final / Resolution: 2.5→49.169 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4504 0 15 0 4519
Biso mean--104.85 --
Num. residues----581
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034604
X-RAY DIFFRACTIONf_angle_d0.6866231
X-RAY DIFFRACTIONf_dihedral_angle_d15.0882701
X-RAY DIFFRACTIONf_chiral_restr0.048693
X-RAY DIFFRACTIONf_plane_restr0.003795
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2027X-RAY DIFFRACTION15.281TORSIONAL
12C2027X-RAY DIFFRACTION15.281TORSIONAL
13E2027X-RAY DIFFRACTION15.281TORSIONAL
14G2027X-RAY DIFFRACTION15.281TORSIONAL
15I2027X-RAY DIFFRACTION15.281TORSIONAL
16K2027X-RAY DIFFRACTION15.281TORSIONAL
21B174X-RAY DIFFRACTION15.281TORSIONAL
22H174X-RAY DIFFRACTION15.281TORSIONAL
31D74X-RAY DIFFRACTION15.281TORSIONAL
32F74X-RAY DIFFRACTION15.281TORSIONAL
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.61380.42311450.3883256598
2.6138-2.75160.38371420.371261799
2.7516-2.9240.39211350.3522258098
2.924-3.14970.38151240.3239255097
3.1497-3.46660.32811290.2949263499
3.4666-3.96810.23531420.2557255197
3.9681-4.99860.23721340.2019260299
4.9986-49.1690.21921280.205260397

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