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- PDB-2coy: Solution structure of the CAP-Gly domain in human Dynactin 1 -

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Basic information

Entry
Database: PDB / ID: 2coy
TitleSolution structure of the CAP-Gly domain in human Dynactin 1
ComponentsDynactin-1
KeywordsPROTEIN BINDING / microtubule binding / cytoskeleton associated protein / p150-glued / DAP-150 / structural genomics / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


cell cortex region / centriolar subdistal appendage / centriole-centriole cohesion / positive regulation of neuromuscular junction development / microtubule anchoring at centrosome / lysosome to ER cholesterol transport / maintenance of synapse structure / ventral spinal cord development / dynein complex / microtubule plus-end ...cell cortex region / centriolar subdistal appendage / centriole-centriole cohesion / positive regulation of neuromuscular junction development / microtubule anchoring at centrosome / lysosome to ER cholesterol transport / maintenance of synapse structure / ventral spinal cord development / dynein complex / microtubule plus-end / mitotic nuclear membrane disassembly / XBP1(S) activates chaperone genes / positive regulation of microtubule nucleation / non-motile cilium assembly / motor behavior / neuron cellular homeostasis / retrograde transport, endosome to Golgi / COPI-independent Golgi-to-ER retrograde traffic / neuromuscular process / microtubule associated complex / nuclear migration / intercellular bridge / establishment of mitotic spindle orientation / cell leading edge / neuromuscular junction development / positive regulation of microtubule polymerization / COPI-mediated anterograde transport / cholesterol homeostasis / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / neuron projection maintenance / Recruitment of mitotic centrosome proteins and complexes / centriole / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / AURKA Activation by TPX2 / regulation of mitotic spindle organization / tubulin binding / tau protein binding / spindle / kinetochore / spindle pole / microtubule cytoskeleton / Signaling by ALK fusions and activated point mutants / Regulation of PLK1 Activity at G2/M Transition / nuclear envelope / mitotic cell cycle / nervous system development / ciliary basal body / cell cortex / microtubule binding / microtubule / endosome membrane / neuron projection / axon / cell division / neuronal cell body / centrosome / protein kinase binding / protein-containing complex / membrane / cytosol / cytoplasm
Similarity search - Function
CAP Gly-rich-like domain / : / Domain of unknown function (DUF8221) / Dynein associated protein / Dynein associated protein / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. ...CAP Gly-rich-like domain / : / Domain of unknown function (DUF8221) / Dynein associated protein / Dynein associated protein / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsSaito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Solution structure of the CAP-Gly domain in human Dynactin 1
Authors: Saito, K. / Koshiba, S. / Inoue, M. / Kigawa, T. / Yokoyama, S.
History
DepositionMay 19, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 19, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 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 / 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 / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4May 29, 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: Dynactin-1


Theoretical massNumber of molelcules
Total (without water)11,7951
Polymers11,7951
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)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Dynactin-1 / 150 kDa dynein-associated polypeptide / DP-150 / DAP-150 / p150-glued / p135


Mass: 11795.139 Da / Num. of mol.: 1 / Fragment: CAP-Gly domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Description: Cell-free protein synthesis / Gene: FB1898_A06 / Plasmid: P040816-05 / References: UniProt: Q14203

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1213D 13C-separated NOESY

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Sample preparation

DetailsContents: 1mM protein, 20mM d-Tris-HCl, pH7.0, 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionsIonic strength: 120 / pH: 7 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6Brukercollection
NMRPipe20020425Delaglio, F.processing
NMRView5Johnson, B.A.data analysis
CNS1.1Brunger, A.T.structure solution
CNS1.1Brunger, A.T.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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