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- PDB-2m02: 3D structure of cap-gly domain of mammalian dynactin determined b... -

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Basic information

Entry
Database: PDB / ID: 2m02
Title3D structure of cap-gly domain of mammalian dynactin determined by magic angle spinning NMR spectroscopy
ComponentsDynactin subunit 1
KeywordsMOTOR PROTEIN
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, molecular dynamics
AuthorsYan, S. / Hou, G. / Schwieters, C.D. / Ahmed, S. / Williams, J.C. / Polenova, T.
Citation
Journal: J.Mol.Biol. / Year: 2013
Title: Three-Dimensional Structure of CAP-Gly Domain of Mammalian Dynactin Determined by Magic Angle Spinning NMR Spectroscopy: Conformational Plasticity and Interactions with End-Binding Protein EB1.
Authors: Yan, S. / Hou, G. / Schwieters, C.D. / Ahmed, S. / Williams, J.C. / Polenova, T.
#1: Journal: J.Am.Chem.Soc. / Year: 2009
Title: Solid-state and solution NMR studies of the CAP-Gly domain of mammalian dynactin and its interaction with microtubules.
Authors: Sun, S. / Siglin, A. / Williams, J.C. / Polenova, T.
History
DepositionOct 15, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 8, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Jun 26, 2013Group: Database references
Revision 1.3Nov 13, 2013Group: Database references
Revision 1.4Jun 25, 2014Group: Structure summary
Revision 1.5Nov 3, 2021Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Refinement description
Category: database_2 / pdbx_nmr_exptl_sample ...database_2 / pdbx_nmr_exptl_sample / pdbx_nmr_refine / 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_nmr_exptl_sample.component / _pdbx_nmr_refine.software_ordinal / _pdbx_nmr_software.name / _pdbx_nmr_software.version / _pdbx_nmr_spectrometer.model / _pdbx_nmr_spectrometer.type
Revision 1.6Jun 14, 2023Group: Other / Category: pdbx_database_status / Item: _pdbx_database_status.status_code_nmr_data

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Dynactin subunit 1


Theoretical massNumber of molelcules
Total (without water)9,5261
Polymers9,5261
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: 9525.583 Da / Num. of mol.: 1 / Fragment: CAP-Gly domain of P150Glued subunit of dynactin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dctn1 / Plasmid: pET28b-His6-SMT3 / 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
211DARR
121NCA
131NCO
141NCACB
151NCACX
161CTUC-COCA
171CTUC-CACB
181CTUC-NCOCA
191NCOCX
1101DARR
2112RDSD
3123RDSD
4134NCACX
4144NCOCX
4154DARR
4164CANCX

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Sample preparation

Details
Solution-IDContentsSolvent system
14.2 mM [U-100% 13C; U-100% 15N] CAP-Gly, 100% H2O100% H2O
24.2 mM [2-13C]-glycerol; U-100% 15N CAP-Gly, 100% H2O100% H2O
34.2 mM [1,3-13C]-glycerol; U-100% 15N CAP-Gly, 100% H2O100% H2O
44.2 mM [U-13C; U-15N] CAP-Gly, 100% H2O100% H2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
4.2 mMCAP-Gly[U-100% 13C; U-100% 15N]1
4.2 mMCAP-Gly[2-13C]-glycerol; U-100% 15N2
4.2 mMCAP-Gly[1,3-13C]-glycerol; U-100% 15N3
4.2 mMCAP-Gly[U-13C; U-15N]4
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
130 6.0 ambient 256.3 K
230 6.0 ambient 271 K
330 6.0 ambient 271 K
430 6.0 ambient 276 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian InfinityPlusVarianInfinityPlus6001
Varian INOVAVarianINOVA9002
Bruker AVANCE IIIBrukerAVANCE III8503

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
SparkyGoddardchemical shift assignment
Roland_NMR_Toolkit(RNMRTK)-Hoch, Stern, Li, Mobli, Maciejewski, Grykprocessing
X-PLOR NIH2.29Schwieters, Kuszewski, Tjandra and Clorestructure calculation
TALOS+3.70F1Cornilescu, Delaglio and Baxtorsion angle prediction
X-PLOR NIH2.29Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing, torsion angle dynamics, molecular dynamics
Software ordinal: 6
NMR constraintsProtein phi angle constraints total count: 69 / Protein psi angle constraints total count: 69
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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