3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Top Gallery List Diagram Statistics Viewer Documents
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - EMDB-1030

A new look at the microtubule binding patterns of dimeric kinesins.

by helical reconstruction, at 25 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 60.078065367, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 60.078065367, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1030
TitleA new look at the microtubule binding patterns of dimeric kinesins.
MapDrosophila Kinesin dimer AMP-PNP state
Sampledrosophila kinesin dimer AMP-PNP state
AuthorsHoenger A
DateDeposition: 2003-02-27, Header release: 2003-02-27, Map release: 2003-02-27, Last update: 2011-05-26
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 60.078065367, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 60.078065367, Made by UCSF CHIMERA

Supplemental images

1030.gif
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

EMDB-1031
Cite

EMDB-1032
Cite

EMDB-1033
Cite

EMDB-1034
Cite

EMDB-1035
Cite

Cite: data citing same article

Similar strucutres (beta)

Diagram

EMDB-1038

EMDB-1039

EMDB-1037

EMDB-1041

EMDB-1025

EMDB-1040
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleJ. Mol. Biol., Vol. 297, Issue 5, Page 1087-103, Year 2000
TitleA new look at the microtubule binding patterns of dimeric kinesins.
AuthorsA Hoenger, M Thormählen, R Diaz-Avalos, M Doerhoefer, K N Goldie, J Müller, E Mandelkow
Structure Programme, European Molecular Biology Laboratory, Meyerhofstrasse 1, Heidelberg, D-69117, Germany.
KeywordsAdenosine Triphosphate (metabolism, 56-65-5), Animals, Binding Sites, Biopolymers (chemistry), Decapodiformes, Dimerization, Disulfides (metabolism), Drosophila melanogaster, Kinesin (chemistry, 3.6.1.-), Kinetics, Microscopy, Electron, Microtubules (chemistry), Models, Biological, Models, Molecular, Molecular Motor Proteins (chemistry), Molecular Weight, Mutation (genetics), Neurospora crassa, Protein Binding, Protein Structure, Quaternary, Protein Structure, Tertiary, Rats, Thermodynamics, Tubulin (metabolism)
LinksPubMed: 10764575, DOI: 10.1006/jmbi.2000.3627, PII: S0022-2836(00)93627-1
Map
FileEMD-1030.map ( map file in CCP4 format, 4001 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:67.1, 60.0780654 (movie #1):
Minimum - Maximum: 0 - 100
Average (Standard dev.): 49.2952 (9.01098)
Data Typefloat (32-bit)
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 100 100 100
Origin : 0 0 0
Limit : 99 99 99
Spacing : 100 100 100
Unit CellA = 567.6 A , B = 567.6 A , C = 567.6 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 5.676 A , Y = 5.676 A , Z = 5.676 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z5.6765.6765.676
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z567.600567.600567.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
start NC,NX/NR,NY/NS,NZ000
NC,NX/NR,NY/NS,NZ100100100
D min/max/mean0.000100.00049.295
Annotation DetailsDrosophila Kinesin dimer AMP-PNP state
Supplement
Images
Images

1030.gif
Sample
Namedrosophila kinesin dimer AMP-PNP state
Oligomeric Statedimer
Number of Components2
Component #1: protein - molecular motor
Scientific namedrosophila kinesin
Common Namemolecular motor
Oligomeric Detailsdimer
Number of Copies1
Scientific Name of SpeciesDrosophila melanogaster (NCBI Taxonomy: 7227)

Common Name of Speciesfruit fly
Recombinant expressionYes
Component #2: protein - microtubules
Scientific nametubulin
Common Namemicrotubules
Oligomeric Detailshetero dimer
Number of Copies1
Scientific Name of SpeciesDrosophila melanogaster (NCBI Taxonomy: 7227)
Common Name of Speciesfruit fly
Recombinant expressionNo
Natural SourceCell: neuronal cells
Cell Location: cytoplasm
Organ Or Tissue: brain
Experiment
Sample Preparation
Specimen Conc0.5 mg/ml
Stainingice-embedded
Specimen Support Detailsholey grids
Helical ParametersAxial Symmetry: p1
Hand: LEFT HANDED
Specimen Statefilament
BufferDetails: Pipes 20mM, 50 mM NaCl, 5mM mgcl,1mM Mg-ATP, 20um taxol.
pH: 6.9
Vitrification
Cryogen NameETHANE
Temperature93 Kelvin
InstrumentHOMEMADE PLUNGER
DetailsVitrification instrument: self made
Imaging
MicroscopeFEI/PHILIPS CM120T
Electron Gun
Electron SourceLAB6
Accelerating Voltage100 kV
Electron Dose5 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 35000 X,
Imaging ModeBRIGHT FIELD
Defocus1500 nm - 2000 nm
Specimen Holder
Holderside-entry ( GATAN LIQUID NITROGEN )
Tilt Angle0 degrees - 0 degrees
Camera
DetectorKodak SO163 film
Image Acquisition
Number of Digital Images10
Sampling Size21 microns
Quant Bit Number16
ScannerZEISS SCAI
Processing
Methodhelical reconstruction
3 D reconstruction
Algorithmhelical
SoftwarePhoelix, Suprim
Resolution By Author25
Resolution MethodFSC at 0.5
DetailsFinal maps from 20 averaged datasets = 10 helical tubes
Download
Data from EMDB
Header (meta data in XML format)emd-1030.xml (7.6 KB)
Map dataemd_1030.map.gz (2.7 MB)
Images1030.gif (28.6 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1030
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 19.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 19.7 KB