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- PDB-1z09: Solution structure of km23 -

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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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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
Water00
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

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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

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Experimental details

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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

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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 / Pressure: ambient / Temperature: 315 K

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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

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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

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