[English] 日本語
Yorodumi
- EMDB-6290: Negative stain reconstruction of bovine dynactin complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6290
TitleNegative stain reconstruction of bovine dynactin complex
Map dataNegative stain reconstruction of bovine dynactin complex
Sample
  • Sample: Bovine dynactin complex
  • Protein or peptide: x 11 types
Keywordsdynactin / actin-related proteins / dynein
Biological speciesBos taurus (domestic cattle)
Methodsingle particle reconstruction / negative staining / Resolution: 24.0 Å
AuthorsChowdhury S / Ketcham SA / Schroer TA / Lander GC
CitationJournal: 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
DepositionFeb 27, 2015-
Header (metadata) releaseMar 11, 2015-
Map releaseMar 11, 2015-
UpdateMay 27, 2015-
Current statusMay 27, 2015Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.14
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.14
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6290.png

Downloads & links

-
Map

FileDownload / File: emd_6290.map.gz / Format: CCP4 / Size: 22.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain reconstruction of bovine dynactin complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.1 Å/pix.
x 182 pix.
= 746.2 Å		4.1 Å/pix.
x 182 pix.
= 746.2 Å		4.1 Å/pix.
x 182 pix.
= 746.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.14 / Movie #1: 2.14
Minimum - Maximum-1.95755327 - 40.294017789999998
Average (Standard dev.)0.05338419 (±0.84441221)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions182182182
Spacing182182182
CellA=B=C: 746.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.14.14.1
M x/y/z182182182
origin x/y/z0.0000.0000.000
length x/y/z746.200746.200746.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-72-72-72
NX/NY/NZ145145145
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS182182182
D min/max/mean-1.95840.2940.053

-
Supplemental data

-
Sample components

+
Entire : Bovine dynactin complex

EntireName: Bovine dynactin complex
Components
  • Sample: Bovine dynactin complex
  • Protein or peptide: p150Glued
  • Protein or peptide: p50
  • Protein or peptide: p24
  • Protein or peptide: Arp1
  • Protein or peptide: Actin
  • Protein or peptide: Arp11
  • Protein or peptide: p62
  • Protein or peptide: p25
  • Protein or peptide: p27
  • Protein or peptide: CapZ alpha
  • Protein or peptide: CapZ beta

+
Supramolecule #1000: Bovine dynactin complex

SupramoleculeName: Bovine dynactin complex / type: sample / ID: 1000 / Details: The sample was monodisperse.
Oligomeric state: One CapZ alpha, one capZ beta, two p150Glued, four p50/dynamitin, two p24, eight Arp1, one actin, one Arp11, one p25, one p27, one p62
Number unique components: 11
Molecular weightExperimental: 1 MDa / Theoretical: 1 MDa

+
Macromolecule #1: p150Glued

MacromoleculeName: p150Glued / type: protein_or_peptide / ID: 1 / Name.synonym: dynactin subunit 1 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (domestic cattle) / synonym: bovine / Tissue: Brain / Cell: Neuron / Location in cell: Cytoplasm
Molecular weightTheoretical: 150 KDa

+
Macromolecule #2: p50

MacromoleculeName: p50 / type: protein_or_peptide / ID: 2 / Name.synonym: Dynamitin / Number of copies: 4 / Oligomeric state: Tetramer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (domestic cattle) / synonym: bovine / Tissue: Brain / Cell: Neuron / Location in cell: Cytoplasm
Molecular weightTheoretical: 50 KDa

+
Macromolecule #3: p24

MacromoleculeName: p24 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Oligomeric state: Dimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (domestic cattle) / synonym: bovine / Tissue: Brain / Cell: Neuron / Location in cell: Cytoplasm
Molecular weightTheoretical: 24 KDa

+
Macromolecule #4: Arp1

MacromoleculeName: Arp1 / type: protein_or_peptide / ID: 4 / Number of copies: 8 / Oligomeric state: Octamer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (domestic cattle) / synonym: bovine / Tissue: Brain / Cell: Neuron / Location in cell: Cytoplasm
Molecular weightTheoretical: 42.6 KDa

+
Macromolecule #5: Actin

MacromoleculeName: Actin / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (domestic cattle) / synonym: bovine / Tissue: Brain / Cell: Neuron / Location in cell: Cytoplasm
Molecular weightTheoretical: 42 KDa

+
Macromolecule #6: Arp11

MacromoleculeName: Arp11 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (domestic cattle) / synonym: bovine / Tissue: Brain / Cell: Neuron / Location in cell: Cytoplasm
Molecular weightTheoretical: 42 KDa

+
Macromolecule #7: p62

MacromoleculeName: p62 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (domestic cattle) / synonym: bovine / Tissue: Brain / Cell: Neuron / Location in cell: Cytoplasm
Molecular weightTheoretical: 62 KDa

+
Macromolecule #8: p25

MacromoleculeName: p25 / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (domestic cattle) / synonym: bovine / Tissue: Brain / Cell: Neuron / Location in cell: Cytoplasm
Molecular weightTheoretical: 25 KDa

+
Macromolecule #9: p27

MacromoleculeName: p27 / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (domestic cattle) / synonym: bovine / Tissue: Brain / Cell: Neuron / Location in cell: Cytoplasm
Molecular weightTheoretical: 27 KDa

+
Macromolecule #10: CapZ alpha

MacromoleculeName: CapZ alpha / type: protein_or_peptide / ID: 10 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (domestic cattle) / synonym: bovine / Tissue: Brain / Cell: Neuron / Location in cell: Cytoplasm
Molecular weightTheoretical: 33 KDa

+
Macromolecule #11: CapZ beta

MacromoleculeName: CapZ beta / type: protein_or_peptide / ID: 11 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Bos taurus (domestic cattle) / synonym: bovine / Tissue: Brain / Cell: Neuron / Location in cell: Cytoplasm
Molecular weightTheoretical: 33 KDa

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.05 mg/mL
BufferpH: 7.2 / Details: 35 mM Tris, 5 mM MgSO4, 150 mM KCl, 1mM TCEP
StainingType: 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.
GridDetails: 400 mesh Cu-Rh Maxtaform grid with a thin continuous carbon film on top
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeFEI TECNAI SPIRIT
TemperatureMin: 294 K / Max: 297 K / Average: 295 K
Alignment procedureLegacy - Astigmatism: Objective astigmatism was corrected using a quadrupole stigmator at 52,000 times magnification.
DateMay 1, 2013
Image recordingCategory: 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 beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsCalibrated 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 stageSpecimen holder: Room temperature holder / Specimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

-
Image processing

DetailsProcessing 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.
CTF correctionDetails: Phase flipping of whole micrograph
Final reconstructionAlgorithm: 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 assignmentDetails: EMAN2: az 90 degrees, alt 90 degrees, phi 90 degrees

+
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