[English] 日本語
Yorodumi
- PDB-7k3j: Crystal structure of dLC8 in complex with Panoramix TQT+TQ peptide -

+
Open data


ID or keywords:

Loading...

-
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 / 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 / dynein light intermediate chain binding / cytoplasmic dynein complex / 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 / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

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

-
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

-
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

-
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

+
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