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- EMDB-1581: Structure and functional role of dynein's microtubule-binding domain -

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Basic information

Entry
Database: EMDB / ID: EMD-1581
TitleStructure and functional role of dynein's microtubule-binding domain
Map dataThis is a 3-D map of the SRS-MTBD construct
Sample
  • Sample: Synthetic construct of dynein microtubule-binding domain (85-82) fused to seryl-tRNA synthase-monomer. Abbreviated name is SRS-MTBD-85-82
  • Protein or peptide: microtubule
KeywordsAssembly 1 is a helical 15 protofilaments / component name / tubulin. Assembly 2 is a monomer of the SRS-MTBD construct
Biological speciesMus musculus (house mouse)
Methodhelical reconstruction / cryo EM / Resolution: 35.0 Å
AuthorsCarter AP / Garbarino JE / Wilson-Kubalek EM / Shipley WE / Cho C / Milligan RA / Vale RD / Gibbons IR
CitationJournal: Science / Year: 2008
Title: Structure and functional role of dynein's microtubule-binding domain.
Authors: Andrew P Carter / Joan E Garbarino / Elizabeth M Wilson-Kubalek / Wesley E Shipley / Carol Cho / Ronald A Milligan / Ronald D Vale / I R Gibbons /
Abstract: Dynein motors move various cargos along microtubules within the cytoplasm and power the beating of cilia and flagella. An unusual feature of dynein is that its microtubule-binding domain (MTBD) is ...Dynein motors move various cargos along microtubules within the cytoplasm and power the beating of cilia and flagella. An unusual feature of dynein is that its microtubule-binding domain (MTBD) is separated from its ring-shaped AAA+ adenosine triphosphatase (ATPase) domain by a 15-nanometer coiled-coil stalk. We report the crystal structure of the mouse cytoplasmic dynein MTBD and a portion of the coiled coil, which supports a mechanism by which the ATPase domain and MTBD may communicate through a shift in the heptad registry of the coiled coil. Surprisingly, functional data suggest that the MTBD, and not the ATPase domain, is the main determinant of the direction of dynein motility.
History
DepositionNov 5, 2008-
Header (metadata) releaseNov 7, 2008-
Map releaseJun 11, 2009-
UpdateNov 7, 2012-
Current statusNov 7, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 9
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 9
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1581.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a 3-D map of the SRS-MTBD construct
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.5 Å/pix.
x 103 pix.
= 360.5 Å
3.5 Å/pix.
x 143 pix.
= 500.5 Å
3.5 Å/pix.
x 143 pix.
= 500.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 3.5 Å
Density
Contour LevelBy AUTHOR: 7.0 / Movie #1: 9
Minimum - Maximum-30.0 - 52.0
Average (Standard dev.)0.367653 (±12.0869)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions143143103
Spacing143143103
CellA: 500.5 Å / B: 500.5 Å / C: 360.5 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.53.53.5
M x/y/z143143103
origin x/y/z0.0000.0000.000
length x/y/z500.500500.500360.500
α/β/γ90.00090.00090.000
start NX/NY/NZ-100-100-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS143143103
D min/max/mean-30.00052.0000.368

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Supplemental data

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Sample components

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Entire : Synthetic construct of dynein microtubule-binding domain (85-82) ...

EntireName: Synthetic construct of dynein microtubule-binding domain (85-82) fused to seryl-tRNA synthase-monomer. Abbreviated name is SRS-MTBD-85-82
Components
  • Sample: Synthetic construct of dynein microtubule-binding domain (85-82) fused to seryl-tRNA synthase-monomer. Abbreviated name is SRS-MTBD-85-82
  • Protein or peptide: microtubule

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Supramolecule #1000: Synthetic construct of dynein microtubule-binding domain (85-82) ...

SupramoleculeName: Synthetic construct of dynein microtubule-binding domain (85-82) fused to seryl-tRNA synthase-monomer. Abbreviated name is SRS-MTBD-85-82
type: sample / ID: 1000
Details: The SRS-MTBD-85-82 construct has a 12 heptad long stalk, only the first 3 heptad repeats were visible in this map. No density was observed for the SRS.
Oligomeric state: SRS-MTBD-85-82 monomers bound to 15 protofilaments helical microtubules
Number unique components: 2

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Macromolecule #1: microtubule

MacromoleculeName: microtubule / type: protein_or_peptide / ID: 1 / Name.synonym: microtubule / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Mus musculus (house mouse) / synonym: House Mouse
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 4 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: 1.5 sec blot

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal magnification: 29000
Specialist opticsEnergy filter - Name: Field Emission Gun
Sample stageSpecimen holder: eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 3.5 µm / Number real images: 10 / Average electron dose: 10 e/Å2 / Bits/pixel: 8
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each image
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 35.0 Å / Resolution method: OTHER / Software - Name: phoelix

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Atomic model buiding 1

Initial modelPDB ID:

Chain - Chain ID: A
DetailsPDBEntryID_givenInChain. Protocol: Rigid body. The crystal structure was manually docked into the EM density using the chimera software package.
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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