[English] 日本語
Yorodumi
- PDB-2m02: 3D structure of cap-gly domain of mammalian dynactin determined b... -

+
Open data


ID or keywords:

Loading...

-
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 / centriolar subdistal appendage / positive regulation of neuromuscular junction development / Regulation of PLK1 Activity at G2/M Transition ...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 / centriolar subdistal appendage / positive regulation of neuromuscular junction development / Regulation of PLK1 Activity at G2/M Transition / centriole-centriole cohesion / COPI-mediated anterograde transport / cell cortex region / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / microtubule anchoring at centrosome / ventral spinal cord development / melanosome transport / MHC class II antigen presentation / retromer complex / nuclear membrane disassembly / microtubule plus-end / positive regulation of microtubule nucleation / positive regulation of intracellular protein transport / non-motile cilium assembly / cytoplasmic dynein complex / retrograde transport, endosome to Golgi / nuclear migration / motor behavior / microtubule associated complex / 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 / kinetochore / spindle pole / spindle / 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
Revision 1.7May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Dynactin subunit 1


Theoretical massNumber of molelcules
Total (without water)9,5261
Polymers9,5261
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 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

-
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

-
Experimental details

-
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

-
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)
1306ambient 256.3 K
2306ambient 271 K
3306ambient 271 K
4306ambient 276 K

-
NMR measurement

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

-
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

+
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