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- PDB-2mpx: Three-dimensional structure of CAP-GLY DOMAIN ASSEMBLED ON MICROT... -

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Basic information

Entry
Database: PDB / ID: 2mpx
TitleThree-dimensional structure of CAP-GLY DOMAIN ASSEMBLED ON MICROTUBULES DETERMINED BY MAS NMR SPECTROSCOPY
ComponentsDynactin subunit 1
KeywordsMOTOR PROTEIN / structure of CAP-Gly domain assembled on microtubules
Function / homology
Function and homology information


COPI-independent Golgi-to-ER retrograde traffic / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / positive regulation of neuromuscular junction development / centriolar subdistal appendage ...COPI-independent Golgi-to-ER retrograde traffic / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / positive regulation of neuromuscular junction development / centriolar subdistal appendage / COPI-mediated anterograde transport / cell cortex region / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / centriole-centriole cohesion / ventral spinal cord development / microtubule anchoring at centrosome / MHC class II antigen presentation / melanosome transport / retromer complex / nuclear membrane disassembly / microtubule plus-end / positive regulation of microtubule nucleation / positive regulation of intracellular protein transport / cytoplasmic dynein complex / non-motile cilium assembly / retrograde transport, endosome to Golgi / nuclear migration / microtubule associated complex / motor behavior / neuromuscular process / neuromuscular junction development / cell leading edge / establishment of mitotic spindle orientation / cytoplasmic microtubule organization / regulation of mitotic spindle organization / positive regulation of microtubule polymerization / neuron projection maintenance / centriole / tubulin binding / ciliary basal body / spindle / kinetochore / spindle pole / neuron cellular homeostasis / nuclear envelope / cell cortex / microtubule binding / microtubule / molecular adaptor activity / neuron projection / cell division / axon / centrosome / neuronal cell body / protein kinase binding / protein-containing complex / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Dynein associated protein / Dynein associated protein / CAP Gly-rich-like domain / 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. ...Dynein associated protein / Dynein associated protein / CAP Gly-rich-like domain / 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 speciesRattus norvegicus (Norway rat)
MethodSOLID-STATE NMR / simulated annealing, torsion angle dynamics
Model detailslowest energy, model 1
AuthorsYan, S. / Hou, G. / Zhang, H. / Polenova, T. / Williams, J.C.
CitationJournal: To be Published
Title: THREE-DIMENSIONAL STRUCTURE of CAP-GLY DOMAIN ASSEMBLED ON MICROTUBULES DETERMINED BY MAS NMR SPECTROSCOPY
Authors: Yan, S. / Polenova, T. / Williams, J. / Zhang, H. / Hou, G. / Ahmed, S.
History
DepositionJun 8, 2014Deposition site: BMRB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Dynactin subunit 1


Theoretical massNumber of molelcules
Total (without water)7,5731
Polymers7,5731
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 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 7572.622 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dctn1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P28023

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Experimental details

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Experiment

ExperimentMethod: SOLID-STATE NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D CORD
1212D CORD
1312D CORD
1412D NCACX
1532D NCACX
1622D PAIN-CP
1712D NCOCX
1813D NCACX
1913D NCOCX

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Sample preparation

Details
Solution-IDContentsSolvent system
11.4-2.0 mg [U-100% 13C; U-100% 15N] CAP-Gly, 5 mg Bovine Alpha Tubulin, 5 mg Bovine Beta Tubulin, 5 uM Taxol, 1 mM GTP, <1 mM GDP-6, 100% H2O100% H2O
21.4-2.0 mg [2-13C]-glucose; U-100% 15N CAP-Gly, 5 mg Bovine Alpha Tubulin, 5 mg Bovine Beta Tubulin, 5 uM Taxol, 1 mM GTP-11, <1 mM GDP, 100% H2O100% H2O
31.4-2.0 mg [1,3-13C]-glucose; U-100% 15N CAP-Gly, 5 mg Bovine Alpha Tubulin, 5 mg Bovine Beta Tubulin, 5 uM Taxol, 1 mM GTP, <1 mM GDP, 100% H2O100% H2O
Sample
Conc. (mg/ml)UnitsComponentIsotopic labelingConc. range (mg/ml)Solution-ID
mg/mLCAP-Gly-1[U-100% 13C; U-100% 15N]1.4-2.01
5 mg/mLBovine Alpha Tubulin-21
5 mg/mLBovine Beta Tubulin-31
5 uMTaxol-41
1 mMGTP-51
1 mMGDP-61
mg/mLCAP-Gly-7[2-13C]-glucose; U-100% 15N1.4-2.02
5 mg/mLBovine Alpha Tubulin-82
5 mg/mLBovine Beta Tubulin-92
5 uMTaxol-102
1 mMGTP-112
1 mMGDP-122
mg/mLCAP-Gly-13[1,3-13C]-glucose; U-100% 15N1.4-2.03
5 mg/mLBovine Alpha Tubulin-143
5 mg/mLBovine Beta Tubulin-153
5 uMTaxol-163
1 mMGTP-173
1 mMGDP-183
Sample conditionsIonic strength: 0.0737 / pH: 6.0 / Pressure: ambient / Temperature: 244 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 850 MHz

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
SparkyGoddardpeak picking
TALOSTALOS+Yang Shen, Frank Delaglio, Gabriel Cornilescu, and Ad Baxtorsion angle prediction
X-PLOR NIH2.35Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH2.35Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, torsion angle dynamics / Software ordinal: 1
NMR constraintsProtein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 56 / Protein psi angle constraints total count: 56
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / Conformers submitted total number: 10

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