[English] 日本語
Yorodumi
- PDB-1z09: Solution structure of km23 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1z09
TitleSolution structure of km23
ComponentsDynein light chain 2A, cytoplasmic
KeywordsTRANSPORT PROTEIN / homodimer / protein-protein complex / km23 / LC7 / dynein light chain
Function / homology
Function and homology information


visual behavior / ciliary tip / Intraflagellar transport / dynein complex / cytoplasmic dynein complex / microtubule motor activity / dynein intermediate chain binding / microtubule-based movement / cilium / microtubule ...visual behavior / ciliary tip / Intraflagellar transport / dynein complex / cytoplasmic dynein complex / microtubule motor activity / dynein intermediate chain binding / microtubule-based movement / cilium / microtubule / centrosome / membrane / cytoplasm
Similarity search - Function
Dynein light chain roadblock-type 1/2 / Dynein light chain 2a, cytoplasmic / Roadblock/LAMTOR2 domain / Roadblock/LC7 domain / Roadblock/LC7 domain / Beta-Lactamase / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Dynein light chain roadblock-type 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / distance geometry simulated annealing
AuthorsIlangovan, U. / Ding, W. / Mulder, K. / Hinck, A.P. / Zuniga, J. / Trbovich, J.A. / Demeler, B. / Groppe, J.C.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structure and Dynamics of the Homodimeric Dynein Light Chain km23.
Authors: Ilangovan, U. / Ding, W. / Zhong, Y. / Wilson, C.L. / Groppe, J.C. / Trbovich, J.T. / Zuniga, J. / Demeler, B. / Tang, Q. / Gao, G. / Mulder, K.M. / Hinck, A.P.
History
DepositionMar 1, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dynein light chain 2A, cytoplasmic
B: Dynein light chain 2A, cytoplasmic


Theoretical massNumber of molelcules
Total (without water)21,8692
Polymers21,8692
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)10 / 100structures with the least restraint violations, structures with the lowest energy
RepresentativeModel #10fewest violations, lowest energy

-
Components

#1: Protein Dynein light chain 2A, cytoplasmic / Dynein-associated protein Km23 / Bithoraxoid-like protein / BLP / HSPC162


Mass: 10934.576 Da / Num. of mol.: 2 / Fragment: LC7 Dynein Light Chain KM23
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DNCL2A, BITH, DNLC2A / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NP97

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1223D 13C-separated NOESY
131HNHA
NMR detailsText: Filtered experiments were used to get intermolecular NOEs

-
Sample preparation

Details
Solution-IDContentsSolvent system
11 mM 15N_Km23; 25 mM Sodium Acetate; pH 6.0; 95 % H2O; 5 % D2O95% H2O/5% D2O
21 mM 13C,15N_Km23; 25 mM Sodium Acetate; pH 6.0; 95 % H2O; 5 % D2O95% H2O/5% D2O
Sample conditionsIonic strength: 0 M NaCl / pH: 6.0 / Pressure: ambient / Temperature: 315 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCEBrukerAVANCE7001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE5003

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR3.5Brukercollection
NMRPipe2.2Delaglio, F.processing
NMRView5.0.4Johnson, B. A. & Blevins, R. A.data analysis
XPLOR-NIH1.0.6Clore, M.refinement
RefinementMethod: distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: fewest violations, lowest energy
NMR ensembleConformer selection criteria: structures with the least restraint violations, structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

+
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