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- EMDB-6074: Negative stain EM structure of the yeast dynein motor domain in t... -

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Basic information

Entry
Database: EMDB / ID: EMD-6074
TitleNegative stain EM structure of the yeast dynein motor domain in the presence of ADP
Map dataReconstruction of yeast dynein motor domain in the presence of 5 mM ADP
Sample
  • Sample: yeast dynein motor domain in the presence of 5 mM ADP
  • Protein or peptide: dynein
Keywordsmotor proteins / power stroke / dynein / AAA protein / ATPase
Function / homology
Function and homology information


karyogamy / astral microtubule / establishment of mitotic spindle localization / nuclear migration along microtubule / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / nuclear migration / spindle pole body / dynein intermediate chain binding ...karyogamy / astral microtubule / establishment of mitotic spindle localization / nuclear migration along microtubule / minus-end-directed microtubule motor activity / cytoplasmic dynein complex / dynein light intermediate chain binding / nuclear migration / spindle pole body / dynein intermediate chain binding / cytoplasmic microtubule / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / cytoplasmic microtubule organization / Neutrophil degranulation / mitotic spindle organization / cell cortex / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
: / DYN1, AAA+ ATPase lid domain / : / Dynein heavy chain, ATPase lid domain / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, linker / Dynein heavy chain, AAA module D4 ...: / DYN1, AAA+ ATPase lid domain / : / Dynein heavy chain, ATPase lid domain / P-loop containing dynein motor region / Dynein heavy chain, tail / Dynein heavy chain, N-terminal region 1 / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, linker / Dynein heavy chain, AAA module D4 / Dynein heavy chain, coiled coil stalk / Dynein heavy chain / Dynein heavy chain, hydrolytic ATP-binding dynein motor region / Dynein heavy chain, ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / Dynein heavy chain AAA lid domain superfamily / Dynein heavy chain, domain 2, N-terminal / Dynein heavy chain, linker, subdomain 3 / Dynein heavy chain, AAA1 domain, small subdomain / Dynein heavy chain region D6 P-loop domain / Dynein heavy chain, N-terminal region 2 / Hydrolytic ATP binding site of dynein motor region / Microtubule-binding stalk of dynein motor / P-loop containing dynein motor region D4 / ATP-binding dynein motor region / Dynein heavy chain AAA lid domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Dynein heavy chain, cytoplasmic
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / negative staining / Resolution: 15.0 Å
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 /
Abstract: Dyneins power microtubule motility using ring-shaped, AAA-containing motor domains. Here, we report X-ray and electron microscopy (EM) structures of yeast dynein bound to different ATP analogs, which ...Dyneins power microtubule motility using ring-shaped, AAA-containing motor domains. Here, we report X-ray and electron microscopy (EM) structures of yeast dynein bound to different ATP analogs, which collectively provide insight into the roles of dynein's two major ATPase sites, AAA1 and AAA3, in the conformational change mechanism. ATP binding to AAA1 triggers a cascade of conformational changes that propagate to all six AAA domains and cause a large movement of the "linker," dynein's mechanical element. In contrast to the role of AAA1 in driving motility, nucleotide transitions in AAA3 gate the transmission of conformational changes between AAA1 and the linker, suggesting that AAA3 acts as a regulatory switch. Further structural and mutational studies also uncover a role for the linker in regulating the catalytic cycle of AAA1. Together, these results reveal how dynein's two major ATP-binding sites initiate and modulate conformational changes in the motor domain during motility.
History
DepositionAug 27, 2014-
Header (metadata) releaseSep 24, 2014-
Map releaseNov 5, 2014-
UpdateDec 17, 2014-
Current statusDec 17, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6074.png

Downloads & links

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Map

FileDownload / File: emd_6074.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of yeast dynein motor domain in the presence of 5 mM ADP
Projections & slices

Image control

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

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.09274308 - 0.17127843
Average (Standard dev.)0.0006653 (±0.01405295)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 272.64 Å
α=β=γ: 90.0 °

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-0.0930.1710.001

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Supplemental data

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Sample components

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Entire : yeast dynein motor domain in the presence of 5 mM ADP

EntireName: yeast dynein motor domain in the presence of 5 mM ADP
Components
  • Sample: yeast dynein motor domain in the presence of 5 mM ADP
  • Protein or peptide: dynein

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Supramolecule #1000: yeast dynein motor domain in the presence of 5 mM ADP

SupramoleculeName: yeast dynein motor domain in the presence of 5 mM ADP / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1
Molecular weightTheoretical: 303 KDa

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Macromolecule #1: dynein

MacromoleculeName: dynein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: VY137 / synonym: yeast
Molecular weightTheoretical: 303 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceUniProtKB: Dynein heavy chain, cytoplasmic

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.02 mg/mL
BufferpH: 8
Details: 50 mM Tris, pH 8.0, 200 mM sodium chloride, 1 mM EGTA, 2 mM magnesium acetate, 1 mM DTT
StainingType: NEGATIVE
Details: Samples 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 ...Details: Samples 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.
GridDetails: Cu 400 mesh
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
DateFeb 26, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 253 / Average electron dose: 50 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 80000
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 11282

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Atomic model buiding 1

Initial modelPDB ID:

4w8f


Chain - Chain ID: A
SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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Atomic model buiding 2

Initial modelPDB ID:

3vkg


Chain - Chain ID: A
SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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