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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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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
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
#1
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