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The role of the kinesin-13 neck in microtubule depolymerization.

by helical reconstruction, at 20 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 10, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 10, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1441
TitleThe role of the kinesin-13 neck in microtubule depolymerization.
MapA realspace map of kinesin-13-bound, 15 protofilament microtubules, calculated from averaged layer line data using Fourier-Bessel synthesis
SampleMalarial kinesin-13 motor core ADP
AuthorsMoores CA, Hekmat-Nejad M, Sakowicz R, Milligan RA
DateDeposition: 2007-10-08, Header release: 2007-10-08, Map release: 2007-10-08, Last update: 2013-02-20
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 10, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 10, Made by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

Cite: data citing same article

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleCell Cycle, Vol. 5, Issue 16, Page 1812-5, Year 2006
TitleThe role of the kinesin-13 neck in microtubule depolymerization.
AuthorsCarolyn A Moores, Jeremy Cooper, Mike Wagenbach, Yulia Ovechkina, Linda Wordeman, Ronald A Milligan
School of Crystallography, Birkbeck College, London, UK.
KeywordsAdenosine Triphosphate (chemistry), Adenylyl Imidodiphosphate (chemistry, 25612-73-1), Cell Division (physiology), Kinesin (chemistry, 3.6.1.-), Microtubules (chemistry), Models, Molecular, Molecular Motor Proteins (chemistry), Peptide Fragments (chemistry), Protein Binding, Protein Conformation, Recombinant Proteins (chemistry), Tubulin (chemistry), mitotic centromere-associated kinesin, hamster
LinksPubMed: 16929184
Map
Fileemd_1441.map.gz ( map file in CCP4 format, 2910 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
73 pix
4.97 A/pix
= 362.81 A
101 pix
4.97 A/pix
= 501.97 A
101 pix
4.97 A/pix
= 501.97 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:28, 10 (movie #1):
Minimum - Maximum: -37 - 48
Average (Standard dev.): 1.62657 (10.558)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions10110173
Origin000
Limit10010072
Spacing10110173
Unit CellA: 501.97 A, B: 501.97 A, C: 362.81 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 4.97 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z4.974.974.97
M x/y/z10110173
origin x/y/z0.0000.0000.000
length x/y/z501.970501.970362.810
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-60-60-59
NX/NY/NZ120120120
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS10110173
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-37.00048.0001.627
Annotation DetailsA realspace map of kinesin-13-bound, 15 protofilament microtubules, calculated from averaged layer line data using Fourier-Bessel synthesis
Supplement
Images
Images
Sample
NameMalarial kinesin-13 motor core ADP
Oligomeric Statemonomeric kinesin binds to each tubulin dimer
Number of Components2
DetailsMolecular weight of kinesin motor core is 40kD
Component #1: protein - pKinI
Scientific namekinesin-13 motor core
Common NamepKinI
Theoretical Mass0.04 MDa
Experimental Mass0.04 MDa
Oligomeric Detailsmonomer
Scientific Name of SpeciesPlasmodium falciparum

Common Name of SpeciesMalaria
NCBI taxonomy5833
Recombinant expressionYes
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Component #2: protein - tubulin
Scientific nametubulin
Theoretical Mass0.1 MDa
Experimental Mass0.1 MDa
Oligomeric Detailshelical polymer
Scientific Name of SpeciesPlasmodium falciparum
Common Name of SpeciesMalaria
NCBI taxonomy5833
Recombinant expressionNo
Natural SourceCell: neurone
Cell Location: cytoplasmic
Organ Or Tissue: brain
Experiment
Sample Preparation
Specimen Conc3 mg/ml
Specimen Support Details400 mesh quantifoil grid 2/2
Helical ParametersHand: LEFT HANDED
Specimen Statefilament
BufferDetails: 20mM Pipes, 2mM MgCl2, 1mM EGTA, 1mM DTT,5mM ADP
pH: 6.8
Vitrification
Cryogen NameETHANE
Humidity98
Temperature277 Kelvin
InstrumentHOMEMADE PLUNGER
Methodblot for 3-4s before plunging
DetailsVitrification instrument: plunger. vitrification performed in humidified cold room
Imaging
MicroscopeFEI/PHILIPS CM200FEG
Date2002-08-01
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage120 kV
Electron Dose10 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 38000
Astigmatismobjective lens astigmatism was corrected at
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus950 nm - 2200 nm
Specimen Holder
Holderside entry, nitrogen cooled
ModelGATAN LIQUID NITROGEN
Temperature95 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
Number of Digital Images50
Sampling Size20
ScannerPERKIN ELMER
Processing
Methodhelical reconstruction
3D reconstruction
AlgorithmFourier Bessel synthesis
SoftwarePhoelix
CTF Correctioneach microtubule
Resolution By Author20 A
Resolution Methodlayer line phase information
DetailsFinal map calculated from 184 moire repeats
Download
Data from EMDB
Header (meta data in XML format)emd-1441.xml (8.1 KB)
Map dataemd_1441.map.gz (443.8 KB)
Images1441.gif (89.2 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1441
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 27.1 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.9 MB
Session file for UCSF-Chimera, 27.1 KB