[English] 日本語
Yorodumi
- PDB-1re6: Localisation of Dynein Light Chains 1 and 2 and their Pro-apoptot... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1re6
TitleLocalisation of Dynein Light Chains 1 and 2 and their Pro-apoptotic Ligands
Componentsdynein light chain 2
KeywordsCONTRACTILE PROTEIN / dynein light chain / apoptosis / dimer
Function / homology
Function and homology information


Activation of BMF and translocation to mitochondria / Intraflagellar transport / Macroautophagy / myosin V complex / COPI-independent Golgi-to-ER retrograde traffic / 9+0 non-motile cilium / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / Aggrephagy ...Activation of BMF and translocation to mitochondria / Intraflagellar transport / Macroautophagy / myosin V complex / COPI-independent Golgi-to-ER retrograde traffic / 9+0 non-motile cilium / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / Aggrephagy / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins / Separation of Sister Chromatids / MHC class II antigen presentation / cytoplasmic dynein complex / dynein intermediate chain binding / microtubule-based process / postsynapse / scaffold protein binding / microtubule / postsynaptic density / cytoskeleton / centrosome / glutamatergic synapse / protein-containing complex binding / identical protein binding / cytoplasm
Similarity search - Function
Protein Inhibitor Of Neuronal Nitric Oxide Synthase / Protein Inhibitor Of Neuronal Nitric Oxide Synthase; / 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 / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
: / Dynein light chain 2, cytoplasmic
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsDay, C.L. / Puthalakath, H. / Skea, G. / Strasser, A. / Barsukov, I. / Lian, L.Y. / Huang, D.C. / Hinds, M.G.
CitationJournal: Biochem.J. / Year: 2004
Title: Localization of dynein light chains 1 and 2 and their pro-apoptotic ligands.
Authors: Day, C.L. / Puthalakath, H. / Skea, G. / Strasser, A. / Barsukov, I. / Lian, L.Y. / Huang, D.C. / Hinds, M.G.
History
DepositionNov 6, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: dynein light chain 2
B: dynein light chain 2


Theoretical massNumber of molelcules
Total (without water)21,5532
Polymers21,5532
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 256structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy,target function
RepresentativeModel #1closest to the average

-
Components

#1: Protein dynein light chain 2


Mass: 10776.303 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: DLC2 / Plasmid: PGEX6P-3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: GenBank: 18087731, UniProt: Q9D0M5*PLUS

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-separated NOESY
1333D 13C-separated NOESY
142HNHA
NMR detailsText: THE STRUCTURE WAS DETERMINED USING STANDARD 2D AND 3D HETERONUCLEAR TECHNIQUES

-
Sample preparation

Details
Solution-IDContentsSolvent system
11mM DLC2, 50mM Sodium phosphate buffer pH 6.7, 70mM NaCl, 2mM TCEP, 0.04% Sodium Azide, 95% H2O, 5% D2O95% H2O/5% D2O
21mM U-15N DLC2, 50mM Sodium phosphate buffer pH 6.7, 70mM NaCl, 2mM TCEP, 0.04% Sodium Azide, 95% H2O, 5% D2O95% H2O/5% D2O
31mM U-13C,15N DLC2, 50mM Sodium phosphate buffer pH 6.7, 70mM NaCl, 2mM TCEP, 0.04% Sodium Azide, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1120mM 6.7 ambient 298 K
2120mM 6.7 ambient 298 K
3120mM 6.7 ambient 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6BRUKER AGcollection
XwinNMR2.6BRUKER AGprocessing
XEASY1.3BARTELS, XIA, BILLETER, GUNTERT, WUTHRICHdata analysis
DYANA1.5GUNTERT, MUMENTHALER, WUTHRICHstructure solution
CNS1BRUNGER, ADAMS, CLORE, DELANO, GROS, GROSSE-KUNSTLEVE, JIANG, KUSEWSKI, NILGES, PANNU, READ, RICE, SIMONSON, WARRENrefinement
RefinementMethod: distance geometry, simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: the structures are based on a total of 1602 restraints, 1417 are NOE derived distance constraints,99 are interprotomer distance constraints, 127 are dihedral angle restraints and 29 hydrogen bonds.
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with acceptable covalent geometry,structures with favorable non-bond energy,structures with the least restraint violations,structures with the lowest energy,target function
Conformers calculated total number: 256 / Conformers submitted total number: 20

+
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