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

by helical reconstruction, at 35 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 9, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 9, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1581
TitleStructure and functional role of dynein's microtubule-binding domain
MapThis is a 3-D map 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
KeywordsAssembly 1 is a helical 15 protofilaments, component name, tubulin. Assembly 2 is a monomer of the SRS-MTBD construct
AuthorsCarter AP, Garbarino JE, Wilson-Kubalek EM, Shipley WE, Cho C, Milligan RA, Vale RD, Gibbons IR
DateDeposition: 2008-11-05, Header release: 2008-11-07, Map release: 2009-06-11, Last update: 2012-11-07
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 9, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 9, Image by UCSF CHIMERA

Supplemental images
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List of similar structure data about Omokage system
Article
Citation - Primary
ArticleScience, Vol. 322, Issue 5908, Page 1691-5, Year 2008
TitleStructure and functional role of dynein's microtubule-binding domain.
AuthorsAndrew P Carter, Joan E Garbarino, Elizabeth M Wilson-Kubalek, Wesley E Shipley, Carol Cho, Ronald A Milligan, Ronald D Vale, I R Gibbons
Howard Hughes Medical Institute and Department of Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA.
KeywordsAdenosine Triphosphate (metabolism), Amino Acid Sequence, Animals, Binding Sites, Crystallization, Crystallography, X-Ray, Dimerization, Dyneins (chemistry, 3.6.4.2), Hydrophobic and Hydrophilic Interactions, Image Processing, Computer-Assisted, Mice, Microscopy, Electron, Microtubules (metabolism), Models, Molecular, Molecular Sequence Data, Movement, Protein Structure, Secondary, Protein Structure, Tertiary, Recombinant Fusion Proteins (chemistry)
LinksDOI: 10.1126/science.1164424, PubMed: 19074350, PMC: PMC2663340
Map
Fileemd_1581.map.gz ( map file in CCP4 format, 8229 KB )
Projections & SlicesSize of images:
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.

Density
Contour Level:7 (by author), 9 (movie #1):
Minimum - Maximum: -30 - 52
Average (Standard dev.): 0.367653 (12.0869)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions143143103
Origin000
Limit142142102
Spacing143143103
Unit CellA: 500.5 A, B: 500.5 A, C: 360.5 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 3.5 A
CCP4 map header info
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
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-30.00052.0000.368
Annotation DetailsThis is a 3-D map of the SRS-MTBD construct
Supplement
Images
Images
Sample
NameSynthetic construct of dynein microtubule-binding domain (85-82) fused to seryl-tRNA synthase-monomer. Abbreviated name is SRS-MTBD-85-82
Number of Components2
Oligomeric StateSRS-MTBD-85-82 monomers bound to 15 protofilaments helical microtubules
DetailsThe 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.
Component #1: protein - microtubule
Scientific namemicrotubule
Oligomeric Detailsmonomer
Scientific Name of SpeciesMus musculus

Common Name of SpeciesHouse Mouse
NCBI taxonomy10090
Recombinant expressionYes
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Experiment
Sample Preparation
Helical ParametersHand: RIGHT HANDED
Specimen Statefilament
Vitrification
Method1.5 sec blot
Cryogen NameETHANE
DetailsVitrification instrument: Vitrobot
Humidity90
InstrumentFEI VITROBOT
Temperature4 Kelvin
Imaging
MicroscopeFEI TECNAI F20
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage120 kV
Electron Dose10 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 29000
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Energy FilterEnergy Filter: Field Emission Gun
Specimen Holder
Holdereucentric
ModelGATAN LIQUID NITROGEN
Camera
DetectorGATAN ULTRASCAN 4000 (4k x 4k)
Image Acquisition
Number of Digital Images10
Sampling Size3.5
Quant Bit Number8
Processing
Methodhelical reconstruction
3D reconstruction
AlgorithmFourier methods
Softwarephoelix
CTF Correctioneach image
Resolution By Author35 A
Resolution Methodphase overplots
Atomic Model Fitting
Model #0
DetailsProtocol: Rigid body. The crystal structure was manually docked into the EM density using the chimera software package.
Refinement Protocolrigid body
Refinement SpaceREAL
PDB Entry ID3ERR
PDB Chain ID3ERR_A
Download
Data from EMDB
Header (meta data in XML format)emd-1581.xml (7.2 KB)
Map dataemd_1581.map.gz (1.3 MB)
Images1581.gif (103.1 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1581
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 26.1 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.6 MB
Session file for UCSF-Chimera, 26.1 KB