+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-6290 | |||||||||
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Title | Negative stain reconstruction of bovine dynactin complex | |||||||||
Map data | Negative stain reconstruction of bovine dynactin complex | |||||||||
Sample |
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Keywords | dynactin / actin-related proteins / dynein | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 24.0 Å | |||||||||
Authors | Chowdhury S / Ketcham SA / Schroer TA / Lander GC | |||||||||
Citation | Journal: Nat Struct Mol Biol / Year: 2015 Title: Structural organization of the dynein-dynactin complex bound to microtubules. Authors: Saikat Chowdhury / Stephanie A Ketcham / Trina A Schroer / Gabriel C Lander / Abstract: Cytoplasmic dynein associates with dynactin to drive cargo movement on microtubules, but the structure of the dynein-dynactin complex is unknown. Using electron microscopy, we determined the ...Cytoplasmic dynein associates with dynactin to drive cargo movement on microtubules, but the structure of the dynein-dynactin complex is unknown. Using electron microscopy, we determined the organization of native bovine dynein, dynactin and the dynein-dynactin-microtubule quaternary complex. In the microtubule-bound complex, the dynein motor domains are positioned for processive unidirectional movement, and the cargo-binding domains of both dynein and dynactin are accessible. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_6290.map.gz | 576 KB | EMDB map data format | |
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Header (meta data) | emd-6290-v30.xml emd-6290.xml | 20 KB 20 KB | Display Display | EMDB header |
Images | emd_6290.png | 270.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-6290 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-6290 | HTTPS FTP |
-Validation report
Summary document | emd_6290_validation.pdf.gz | 78.1 KB | Display | EMDB validaton report |
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Full document | emd_6290_full_validation.pdf.gz | 77.2 KB | Display | |
Data in XML | emd_6290_validation.xml.gz | 494 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6290 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-6290 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_6290.map.gz / Format: CCP4 / Size: 22.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Negative stain reconstruction of bovine dynactin complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 4.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Bovine dynactin complex
+Supramolecule #1000: Bovine dynactin complex
+Macromolecule #1: p150Glued
+Macromolecule #2: p50
+Macromolecule #3: p24
+Macromolecule #4: Arp1
+Macromolecule #5: Actin
+Macromolecule #6: Arp11
+Macromolecule #7: p62
+Macromolecule #8: p25
+Macromolecule #9: p27
+Macromolecule #10: CapZ alpha
+Macromolecule #11: CapZ beta
-Experimental details
-Structure determination
Method | negative staining |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.05 mg/mL |
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Buffer | pH: 7.2 / Details: 35 mM Tris, 5 mM MgSO4, 150 mM KCl, 1mM TCEP |
Staining | Type: NEGATIVE Details: 4 uL of sample was applied to a freshly plasma-cleaned thin carbon surface that was pre-treated with 0.1% w/v poly-L-lysine hydrobromide. After removing excess protein, negative staining was ...Details: 4 uL of sample was applied to a freshly plasma-cleaned thin carbon surface that was pre-treated with 0.1% w/v poly-L-lysine hydrobromide. After removing excess protein, negative staining was performed with 2% w/v uranyl formate solution. |
Grid | Details: 400 mesh Cu-Rh Maxtaform grid with a thin continuous carbon film on top |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI SPIRIT |
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Temperature | Min: 294 K / Max: 297 K / Average: 295 K |
Alignment procedure | Legacy - Astigmatism: Objective astigmatism was corrected using a quadrupole stigmator at 52,000 times magnification. |
Date | May 1, 2013 |
Image recording | Category: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 1978 / Average electron dose: 20 e/Å2 Details: Data were collected using Leginon automated image acquisition software. |
Electron beam | Acceleration voltage: 120 kV / Electron source: LAB6 |
Electron optics | Calibrated magnification: 52000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.20 mm / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 52000 |
Sample stage | Specimen holder: Room temperature holder / Specimen holder model: SIDE ENTRY, EUCENTRIC |
Experimental equipment | Model: Tecnai Spirit / Image courtesy: FEI Company |
-Image processing
Details | Processing leading up to 3D reconstruction was performed using the Appion package. Particles were selected from micrographs using an automated template-based particle picker. The stack was subjected to five iterations of iterative 2D alignment and classification using multivariate statistical analysis (MSA) and multi-reference alignment (MRA). The clean particle stack was subsequently subjected to 3D refinement by iterative projection matching using EMAN2 and SPARX libraries. |
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CTF correction | Details: Phase flipping of whole micrograph |
Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 24.0 Å / Resolution method: OTHER / Software - Name: EMAN2, SPARX Details: Processing leading up to 3D reconstruction was performed using the Appion package. Particles were selected from micrographs using an automated template-based particle picker. The stack was ...Details: Processing leading up to 3D reconstruction was performed using the Appion package. Particles were selected from micrographs using an automated template-based particle picker. The stack was subjected to five iterations of iterative 2D alignment and classification using multivariate statistical analysis (MSA) and multi-reference alignment (MRA). The clean particle stack was subsequently subjected to 3D refinement by iterative projection matching using EMAN2 and SPARX libraries. Number images used: 46734 |
Final angle assignment | Details: EMAN2: az 90 degrees, alt 90 degrees, phi 90 degrees |