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Nucleotide-induced conformations in the neck region of dimeric kinesin.

by helical reconstruction, at 25 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 54.470584561, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 54.470584561, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1039
TitleNucleotide-induced conformations in the neck region of dimeric kinesin.
Maprat kinesin dimer with an SH3 domain cloned within the neck region -rKS379-, complexed to subtilisin treated microtubules in the presence of AMP-PNP
SampleRat kinesin dimer with an SH3 domain complexed to subtilisin treated microtubules in the presence of AMP-PNP.
AuthorsSkiniotis G
DateDeposition: 2003-02-28, Header release: 2003-02-28, Map release: 2003-03-28, 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: 54.470584561, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 54.470584561, Made by UCSF CHIMERA

Supplemental images

1039.gif
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

EMDB-1037
Cite

EMDB-1038
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EMDB-1040
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EMDB-1041
Cite

Cite: data citing same article

Similar strucutres (beta)

Diagram

EMDB-1037

EMDB-1041

EMDB-1038

EMDB-1040

EMDB-1030

EMDB-1025
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleEMBO J., Vol. 22, Issue 7, Page 1518-28, Year 2003
TitleNucleotide-induced conformations in the neck region of dimeric kinesin.
AuthorsGeorgios Skiniotis, Thomas Surrey, Stephan Altmann, Heinz Gross, Young-Hwa Song, Eckhard Mandelkow, Andreas Hoenger
European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.
KeywordsAdenosine Monophosphate (chemistry, 61-19-8), Cloning, Molecular, Cryoelectron Microscopy, Dimerization, Kinesin (chemistry, 3.6.1.-), Models, Molecular, Protein Conformation, Recombinant Fusion Proteins (chemistry), Recombinant Proteins (chemistry), src Homology Domains
LinksPubMed: 12660159, DOI: 10.1093/emboj/cdg164, PMC: PMC152908
Map
FileEMD-1039.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:63.6, 54.4705846 (movie #1):
Minimum - Maximum: 0 - 100
Average (Standard dev.): 40.3611 (10.6337)
Data Typefloat (32-bit)
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100100
Origin000
Limit999999
Spacing100100100
Unit CellA= B= C: 552.6 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 5.526 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z5.5265.5265.526
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z552.600552.600552.600
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,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean0.000100.00040.361
Annotation Detailsrat kinesin dimer with an SH3 domain cloned within the neck region -rKS379-, complexed to subtilisin treated microtubules in the presence of AMP-PNP
Supplement
Images
Images

1039.gif
Sample
NameRat kinesin dimer with an SH3 domain complexed to subtilisin treated microtubules in the presence of AMP-PNP.
Oligomeric Statedimer
Number of Components2
Component #1: protein - molecular motor
Scientific namerat kinesin
Common Namemolecular motor
Experimental Mass0.98 MDa
Oligomeric Detailsdimer
Number of Copies1
Scientific Name of SpeciesRattus norvegicus

Common Name of Speciesrat kinesin
NCBI taxonomy10116
Recombinant expressionYes
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Vector: pET3
Component #2: protein - microtubule
Scientific nametubulin
Common Namemicrotubule
Experimental Mass0.11 MDa
Oligomeric Detailshetero-dimer
Number of Copies1
Scientific Name of SpeciesRattus norvegicus
Common Name of Speciesrat kinesin
NCBI taxonomy10116
Recombinant expressionNo
Natural SourceCell: neuronal cells
Cell Location: cytoplasm
Organ Or Tissue: brain
Experiment
Sample Preparation
Specimen Conc0.5 mg/ml
Stainingice-embeded
Specimen Support Detailsholey grids
Helical ParametersAxial Symmetry: p1
Hand: LEFT HANDED
Specimen Statefilament
BufferDetails: PIPES 80 mM, MgCl2 1 mM, GTP 1 mM, Taxol 20 uM, DMSO 7.5%
pH: 6.8
Vitrification
Cryogen NameETHANE
Temperature93 Kelvin
Imaging
MicroscopeFEI/PHILIPS CM200FEG/ST
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose5 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 38000
Astigmatismwas corrected at 180,000 times mag.
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus2000 nm - 2500 nm
Specimen Holder
Holderside entry
ModelGATAN LIQUID NITROGEN
Tilt Angle0 degrees - 0 degrees
Camera
DetectorKodak SO163 film
Image Acquisition
Number of Digital Images12
Sampling Size21
Quant Bit Number8
ScannerZEISS SCAI
Processing
Methodhelical reconstruction
3D reconstruction
Algorithmlayer lines, Bessel orders
SoftwarePHOELIX, SUPRIM
Resolution By Author25 A
Resolution MethodFSC at 0.5
DetailsFinal map from 24 averaged datasets = 12 helical tubes
Download
Data from EMDB
Header (meta data in XML format)emd-1039.xml (8 KB)
Map dataemd_1039.map.gz (2.9 MB)
Images1039.gif (65.3 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1039
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), 4.7 MB
Session file for UCSF-Chimera, 19.7 KB