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- EMDB-6067: Negative stain EM structure of the yeast dynein motor domain with... -

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Basic information

Entry
Database: EMDB / ID: 6067
TitleNegative stain EM structure of the yeast dynein motor domain with stalk and MTBD in the presence of ATP
Map dataReconstruction of yeast dynein motor domain with full stalk and MTBD in the presence of 5 mM ATP
Sampleyeast dynein motor domain with full stalk and MTBD in the presence of 5 mM ATP:
dynein
Keywordsmotor proteins / power stroke / dynein / AAA protein / ATPase
Function / homologyDynein heavy chain, N-terminal region 1 / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, domain-1 / Dynein heavy chain, domain-2 / Dynein heavy chain, AAA module D4 / Dynein heavy chain, N-terminal region 2 / Dynein heavy chain, coiled coil stalk / Dynein heavy chain / P-loop containing nucleoside triphosphate hydrolase / Dynein heavy chain, hydrolytic ATP-binding dynein motor region ...Dynein heavy chain, N-terminal region 1 / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, domain-1 / Dynein heavy chain, domain-2 / Dynein heavy chain, AAA module D4 / Dynein heavy chain, N-terminal region 2 / Dynein heavy chain, coiled coil stalk / Dynein heavy chain / P-loop containing nucleoside triphosphate hydrolase / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / Hydrolytic ATP binding site of dynein motor region / Microtubule-binding stalk of dynein motor / P-loop containing dynein motor region D4 / Dynein heavy chain, ATP-binding dynein motor region / Dynein heavy chain region D6 P-loop domain / ATP-binding dynein motor region / AAA+ ATPase domain / karyogamy / astral microtubule / nuclear migration along microtubule / minus-end-directed vesicle transport along microtubule / establishment of mitotic spindle localization / dynein light chain binding / ATP-dependent microtubule motor activity, minus-end-directed / dynein light intermediate chain binding / cytoplasmic dynein complex / dynein complex / dynein intermediate chain binding / spindle pole body / establishment of mitotic spindle orientation / cytoplasmic microtubule organization / mitotic sister chromatid segregation / cytoplasmic microtubule / microtubule-based movement / cell cortex / ATP binding / Dynein heavy chain, cytoplasmic
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / negative staining / 23 Å resolution
AuthorsBhabha G / Moeller A / Liao M / Speir JA / Vale RD / Cheng Y
CitationJournal: Cell / Year: 2014
Title: Allosteric communication in the dynein motor domain.
Authors: Gira Bhabha / Hui-Chun Cheng / Nan Zhang / Arne Moeller / Maofu Liao / Jeffrey A Speir / Yifan Cheng / Ronald D Vale
DateDeposition: Aug 27, 2014 / Header (metadata) release: Sep 24, 2014 / Map release: Nov 5, 2014 / Last update: Dec 17, 2014

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6067.map.gz (map file in CCP4 format, 1025 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
64 pix
4.26 Å/pix.
= 272.64 Å
64 pix
4.26 Å/pix.
= 272.64 Å
64 pix
4.26 Å/pix.
= 272.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.26 Å
Density
Contour Level:0.045 (by emdb), 0.04 (movie #1):
Minimum - Maximum-0.10076381 - 0.18827015
Average (Standard dev.)0.00075879 (0.01285355)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions646464
Origin000
Limit636363
Spacing646464
CellA=B=C: 272.64 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.264.264.26
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z272.640272.640272.640
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ969680
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-0.1010.1880.001

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Supplemental data

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Sample components

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Entire yeast dynein motor domain with full stalk and MTBD in the presenc...

EntireName: yeast dynein motor domain with full stalk and MTBD in the presence of 5 mM ATP
Number of components: 1 / Oligomeric State: monomer
MassTheoretical: 303 kDa

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Component #1: protein, dynein

ProteinName: dynein / Oligomeric Details: monomer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 303 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: VY137
Source (engineered)Expression System: Saccharomyces cerevisiae (baker's yeast)
External referencesUniProt: Dynein heavy chain, cytoplasmic

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: negative staining
Sample solutionSpecimen conc.: 0.02 mg/ml
Buffer solution: 50 mM Tris, pH 8.0, 200 mM sodium chloride, 1 mM EGTA, 2 mM magnesium acetate, 1 mM DTT
pH: 8
Support filmCu 400 mesh
StainingSamples were applied to freshly glow discharged carbon coated grids and blotted off. Immediately after blotting, a 2% uranyl formate solution was applied for staining and blotted off. The stain was applied five times per sample. Samples were allowed to air dry before imaging.
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Date: Feb 27, 2013
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 80000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 3500 nm
Specimen HolderModel: SIDE ENTRY, EUCENTRIC
CameraDetector: TVIPS TEMCAM-F416 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 168

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 1827
3D reconstructionSoftware: Relion / Resolution: 23 Å / Resolution method: FSC 0.143, gold-standard

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