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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: 1581
TitleStructure and functional role of dynein's microtubule-binding domain
KeywordsAssembly 1 is a helical 15 protofilaments / component name / tubulin. Assembly 2 is a monomer of the SRS-MTBD construct
SampleSynthetic construct of dynein microtubule-binding domain (85-82) fused to seryl-tRNA synthase-monomer. Abbreviated name is SRS-MTBD-85-82
SourceMus musculus / mammal / House Mouse / ハツカネズミ, はつかねずみ /
Map dataThis is a 3-D map of the SRS-MTBD construct
Methodhelical reconstruction, at 35 A resolution
AuthorsCarter AP / Garbarino JE / Wilson-Kubalek EM / Shipley WE / Cho C / Milligan RA / Vale RD / Gibbons IR
CitationScience, 2008, 322, 1691-1695

Science, 2008, 322, 1691-1695 StrPapers
Structure and functional role of dynein's microtubule-binding domain.
Andrew P Carter / Joan E Garbarino / Elizabeth M Wilson-Kubalek / Wesley E Shipley / Carol Cho / Ronald A Milligan / Ronald D Vale / I R Gibbons

DateDeposition: Nov 5, 2008 / Header (metadata) release: Nov 7, 2008 / Map release: Jun 11, 2009 / Last update: Nov 5, 2008

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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
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1581.map.gz (map file in CCP4 format, 8229 KB)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
103 pix
3.5 A/pix
= 360.5 A
143 pix
3.5 A/pix
= 500.5 A
143 pix
3.5 A/pix
= 500.5 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.5 A
Density
Contour Level:7 (by author), 9 (movie #1):
Minimum - Maximum-30 - 52
Average (Standard dev.)0.367653 (12.0869)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions143143103
Origin000
Limit142142102
Spacing143143103
CellA: 500.5 A / B: 500.5 A / C: 360.5 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
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
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.
Number of components: 2
Oligomeric State: SRS-MTBD-85-82 monomers bound to 15 protofilaments helical microtubules

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Component #1: protein, microtubule

ProteinName: microtubule / a.k.a: microtubule / Oligomeric Details: monomer / Recombinant expression: Yes
SourceSpecies: Mus musculus / mammal / House Mouse / ハツカネズミ, はつかねずみ /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Experimental details

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Sample preparation

Specimen statefilament
Helical parametersHand: RIGHT HANDED
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 4 K / Humidity: 90 % / Method: 1.5 sec blot / Details: Vitrification instrument: Vitrobot

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 10 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 29000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Energy filter: Field Emission Gun
Specimen HolderHolder: eucentric / Model: GATAN LIQUID NITROGEN
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 10 / Sampling size: 3.5 microns / Bit depth: 8

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Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: Fourier methods / Software: phoelix / CTF correction: each image / Resolution: 35 A / Resolution method: phase overplots

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Refinement space: REAL
Details: Protocol: Rigid body. The crystal structure was manually docked into the EM density using the chimera software package.
Input PDB model: 3ERR
Chain ID: 3ERR_A

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