[English] 日本語
Yorodumi- EMDB-2857: CryoEM reconstruction of dynactin complex from pig brain at 4.0 A... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2857 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | CryoEM reconstruction of dynactin complex from pig brain at 4.0 Angstrom resolution overall | |||||||||
Map data | CryoEM reconstruction of the Arp filament of dynactin complex from at 3.5 angstrom resolution | |||||||||
Sample |
| |||||||||
Keywords | dynactin / dynein co-factor / actin-like filament / cellular cargo transport | |||||||||
Function / homology | Function and homology information COPI-independent Golgi-to-ER retrograde traffic / retrograde axonal transport of mitochondrion / Gap junction degradation / Formation of annular gap junctions / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs ...COPI-independent Golgi-to-ER retrograde traffic / retrograde axonal transport of mitochondrion / Gap junction degradation / Formation of annular gap junctions / Regulation of actin dynamics for phagocytic cup formation / EPHB-mediated forward signaling / Adherens junctions interactions / VEGFA-VEGFR2 Pathway / Cell-extracellular matrix interactions / RHO GTPases Activate WASPs and WAVEs / MAP2K and MAPK activation / UCH proteinases / Clathrin-mediated endocytosis / RHOF GTPase cycle / dynactin complex / Regulation of PLK1 Activity at G2/M Transition / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / F-actin capping protein complex / negative regulation of filopodium assembly / actin cortical patch / structural constituent of postsynaptic actin cytoskeleton / dense body / dynein complex / Neutrophil degranulation / coronary vasculature development / barbed-end actin filament capping / regulation of lamellipodium assembly / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / aorta development / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / COPI-mediated anterograde transport / ventricular septum development / dynein complex binding / NuA4 histone acetyltransferase complex / axon cytoplasm / mitotic spindle organization / axonogenesis / actin filament / cell motility / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / cell morphogenesis / kinetochore / actin filament binding / actin cytoskeleton / cell cortex / nuclear membrane / actin cytoskeleton organization / cytoskeleton / hydrolase activity / axon / focal adhesion / centrosome / synapse / protein kinase binding / protein-containing complex / nucleoplasm / ATP binding / membrane / nucleus / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Sus scrofa domesticus (domestic pig) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Zhang K / Urnavicius L / Diamant AG / Motz C / Schlager MA / Yu M / Patel NA / Robinson CV / Carter AP | |||||||||
Citation | Journal: Science / Year: 2015 Title: The structure of the dynactin complex and its interaction with dynein. Authors: Linas Urnavicius / Kai Zhang / Aristides G Diamant / Carina Motz / Max A Schlager / Minmin Yu / Nisha A Patel / Carol V Robinson / Andrew P Carter / Abstract: Dynactin is an essential cofactor for the microtubule motor cytoplasmic dynein-1. We report the structure of the 23-subunit dynactin complex by cryo-electron microscopy to 4.0 angstroms. Our ...Dynactin is an essential cofactor for the microtubule motor cytoplasmic dynein-1. We report the structure of the 23-subunit dynactin complex by cryo-electron microscopy to 4.0 angstroms. Our reconstruction reveals how dynactin is built around a filament containing eight copies of the actin-related protein Arp1 and one of β-actin. The filament is capped at each end by distinct protein complexes, and its length is defined by elongated peptides that emerge from the α-helical shoulder domain. A further 8.2 angstrom structure of the complex between dynein, dynactin, and the motility-inducing cargo adaptor Bicaudal-D2 shows how the translational symmetry of the dynein tail matches that of the dynactin filament. The Bicaudal-D2 coiled coil runs between dynein and dynactin to stabilize the mutually dependent interactions between all three components. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2857.map.gz | 1.6 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-2857-v30.xml emd-2857.xml | 18.6 KB 18.6 KB | Display Display | EMDB header |
Images | emd_2857.png | 137.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2857 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2857 | HTTPS FTP |
-Validation report
Summary document | emd_2857_validation.pdf.gz | 199.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_2857_full_validation.pdf.gz | 198.7 KB | Display | |
Data in XML | emd_2857_validation.xml.gz | 4.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2857 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2857 | HTTPS FTP |
-Related structure data
Related structure data | 5adxMC 2854C 2855C 2856C 2860C 2861C 2862C 5afrC 5afuC M: atomic model generated by this map C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|---|
Related items in Molecule of the Month |
-Map
File | Download / File: emd_2857.map.gz / Format: CCP4 / Size: 16.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | CryoEM reconstruction of the Arp filament of dynactin complex from at 3.5 angstrom resolution | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
+Entire : Dynactin complex from pig brain
+Supramolecule #1000: Dynactin complex from pig brain
+Macromolecule #1: Actin related protein 1
+Macromolecule #2: Actin related protein 11
+Macromolecule #3: beta-actin
+Macromolecule #4: Dynactin subunit 1
+Macromolecule #5: Dynactin subunit 2
+Macromolecule #6: Dynactin subunit 3
+Macromolecule #7: Actin capping protein
+Macromolecule #8: Dynactin subunit 4
+Macromolecule #9: Dynactin subunit 5
+Macromolecule #10: Dynactin subunit 6
-Experimental details
-Structure determination
Method | cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.07 mg/mL |
---|---|
Buffer | pH: 6.5 Details: 50mM KCl, 25mM KH2PO4-K2HPO4, 5mM DDT, 1mM MgCl2, 0.1 mM ATP |
Grid | Details: R2/2 400 square mesh copper grid with thin carbon support |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 105 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
---|---|
Temperature | Min: 80 K / Max: 100 K |
Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at 96,000 times nominal magnification Legacy - Electron beam tilt params: 0 |
Date | Sep 12, 2014 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 14423 / Average electron dose: 54 e/Å2 / Bits/pixel: 32 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 102967 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 7.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | The particles were selected using a GPU accelerated automatic program Gautomatch. The CTF parameter were determined and refined using a GPU accelerated program Gctf. |
---|---|
CTF correction | Details: Each particle by Gctf |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: OTHER / Software - Name: Relion Details: Final map were sharpened to 3.5 angstrom from a 4.1 angstrom map in overall This map was only used for analysis of Arp filament of dynactin Number images used: 115044 |