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- EMDB-2156: Cryo-EM structure of axonemal dynein-c in the ADP.Vi state -

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Basic information

Entry
Database: EMDB / ID: EMD-2156
TitleCryo-EM structure of axonemal dynein-c in the ADP.Vi state
Map dataReconstruction of axonemal dynein-c prepared in the ADP.Vi state
Sample
  • Sample: Axonemal dynein-c prepared in the ADP.Vi state
  • Protein or peptide: Dynein-c
KeywordsDynein / motor protein / microtubule / cytoskeleton / cilia / flagella / axoneme / AAA+ ATPase / cryo-electron microscopy
Biological speciesChlamydomonas reinhardtii (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 22.0 Å
AuthorsRoberts AJ / Malkova B / Walker ML / Sakakibara H / Numata N / Kon T / Ohkura R / Edwards TA / Knight PJ / Sutoh K ...Roberts AJ / Malkova B / Walker ML / Sakakibara H / Numata N / Kon T / Ohkura R / Edwards TA / Knight PJ / Sutoh K / Oiwa K / Burgess SA
CitationJournal: Structure / Year: 2012
Title: ATP-driven remodeling of the linker domain in the dynein motor.
Authors: Anthony J Roberts / Bara Malkova / Matt L Walker / Hitoshi Sakakibara / Naoki Numata / Takahide Kon / Reiko Ohkura / Thomas A Edwards / Peter J Knight / Kazuo Sutoh / Kazuhiro Oiwa / Stan A Burgess /
Abstract: Dynein ATPases are the largest known cytoskeletal motors and perform critical functions in cells: carrying cargo along microtubules in the cytoplasm and powering flagellar beating. Dyneins are ...Dynein ATPases are the largest known cytoskeletal motors and perform critical functions in cells: carrying cargo along microtubules in the cytoplasm and powering flagellar beating. Dyneins are members of the AAA+ superfamily of ring-shaped enzymes, but how they harness this architecture to produce movement is poorly understood. Here, we have used cryo-EM to determine 3D maps of native flagellar dynein-c and a cytoplasmic dynein motor domain in different nucleotide states. The structures show key sites of conformational change within the AAA+ ring and a large rearrangement of the "linker" domain, involving a hinge near its middle. Analysis of a mutant in which the linker "undocks" from the ring indicates that linker remodeling requires energy that is supplied by interactions with the AAA+ modules. Fitting the dynein-c structures into flagellar tomograms suggests how this mechanism could drive sliding between microtubules, and also has implications for cytoplasmic cargo transport.
History
DepositionJul 2, 2012-
Header (metadata) releaseAug 15, 2012-
Map releaseAug 15, 2012-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2156.png

emd_2156.png

Downloads & links

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Map

FileDownload / File: emd_2156.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of axonemal dynein-c prepared in the ADP.Vi state
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.16 Å/pix.
x 128 pix.
= 276.48 Å		2.16 Å/pix.
x 128 pix.
= 276.48 Å		2.16 Å/pix.
x 128 pix.
= 276.48 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-9.66834164 - 12.65163231
Average (Standard dev.)0.0 (±0.99999994)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin646464
Dimensions128128128
Spacing128128128
CellA=B=C: 276.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.162.162.16
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z276.480276.480276.480
α/β/γ90.00090.00090.000
start NX/NY/NZ-32-32-32
NX/NY/NZ646464
MAP C/R/S123
start NC/NR/NS646464
NC/NR/NS128128128
D min/max/mean-9.66812.652-0.000

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Supplemental data

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Sample components

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Entire : Axonemal dynein-c prepared in the ADP.Vi state

EntireName: Axonemal dynein-c prepared in the ADP.Vi state
Components
  • Sample: Axonemal dynein-c prepared in the ADP.Vi state
  • Protein or peptide: Dynein-c

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Supramolecule #1000: Axonemal dynein-c prepared in the ADP.Vi state

SupramoleculeName: Axonemal dynein-c prepared in the ADP.Vi state / type: sample / ID: 1000 / Number unique components: 1

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Macromolecule #1: Dynein-c

MacromoleculeName: Dynein-c / type: protein_or_peptide / ID: 1 / Recombinant expression: No
Source (natural)Organism: Chlamydomonas reinhardtii (plant) / Organelle: Axoneme

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.19 mg/mL
BufferpH: 7.5 / Details: 10 mM MOPS, 3 mM MgCl2, 1 mM EGTA
GridDetails: Quantifoil or lacey carbon film, glow discharged
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TECNAI F20
DateMay 1, 2006
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 228 / Average electron dose: 25 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 69444 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Phase flipping
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 22.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider / Number images used: 22667
Final two d classificationNumber classes: 799

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