[English] 日本語
Yorodumi
- PDB-7k3l: Crystal structure of dLC8 in complex with Panoramix TQ peptide -

+
Open data


ID or keywords:

Loading...

-
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


spermatid nucleus elongation / chaeta morphogenesis / Macroautophagy / Aggrephagy / positive regulation of neuron remodeling / 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 / chaeta development ...spermatid nucleus elongation / chaeta morphogenesis / Macroautophagy / Aggrephagy / positive regulation of neuron remodeling / 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 / chaeta development / sperm individualization / piRNA binding / imaginal disc-derived wing morphogenesis / transposable element silencing by piRNA-mediated heterochromatin formation / RNA polymerase II transcription repressor complex / microtubule anchoring at centrosome / Neutrophil degranulation / transposable element silencing by heterochromatin formation / dynein complex / cytoplasmic dynein complex / dynein light intermediate chain binding / oogenesis / dynein intermediate chain binding / establishment of mitotic spindle orientation / actin filament bundle assembly / transcription repressor complex / centriole / disordered domain specific binding / transcription corepressor activity / spermatogenesis / microtubule / protein homodimerization activity / protein-containing complex / nucleus / cytoplasm / cytosol
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more