3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Nucleotide-induced conformations in the neck region of dimeric kinesin.
by helical reconstruction, at 25 A resolution
#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 / ID | EM DATA BANK (EMDB) / 1039 |
|---|---|
| Authors | Skiniotis G |
| EMDB Sites |  EMDB @PDBe (EU), EMDB @RCSB (USA) |
| Structure Visualization | |
| Movies |  Movie 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 | |
| Structure viewers |  Yorodumi,  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 | |
| Article | EMBO J., Vol. 22, Issue 7, Page 1518-28, Year 2003 |
|---|---|
| Title | Nucleotide-induced conformations in the neck region of dimeric kinesin. |
| Authors | Georgios Skiniotis, Thomas Surrey, Stephan Altmann, Heinz Gross, Young-Hwa Song, Eckhard Mandelkow, Andreas Hoenger European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany. |
| Keywords |  Adenosine 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 |
| Links | PubMed: 12660159, DOI: 10.1093/emboj/cdg164, PMC: PMC152908 |
 Map | |||||||||||||||||||||||||
| File |  EMD-1039.map ( map file in CCP4 format, 4001 KB ) | ||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Projections & Slices | Size of images:
Images are generated by Spider package. | ||||||||||||||||||||||||
| Density |
| ||||||||||||||||||||||||
| Data Type | float (32-bit) | ||||||||||||||||||||||||
| Space Group Number | 1 | ||||||||||||||||||||||||
| Map Geometry |
| ||||||||||||||||||||||||
| Unit Cell | A = 552.6 A , B = 552.6 A , C = 552.6 A , alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees | ||||||||||||||||||||||||
| Pixel Spacing | X = 5.526 A , Y = 5.526 A , Z = 5.526 A | ||||||||||||||||||||||||
| CCP4 map header info | |||||||||||||||||||||||||
| Annotation Details | rat 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 | |
|---|---|
 Sample | |
| Name | Rat kinesin dimer with an SH3 domain complexed to subtilisin treated microtubules in the presence of AMP-PNP. |
|---|---|
| Oligomeric State | dimer |
| Number of Components | 2 |
| Component #1: protein - molecular motor | |
| Scientific name | rat kinesin |
| Common Name | molecular motor |
| Experimental Mass | 0.98 MDa |
| Oligomeric Details | dimer |
| Number of Copies | 1 |
| Scientific Name of Species | Rattus norvegicus (NCBI Taxonomy: 10116)
|
| Common Name of Species | rat kinesin |
| Recombinant expression | Yes |
| Engineered Source | Exp System: Escherichia coli (NCBI Taxonomy: 562) Vector: pET3 |
| Component #2: protein - microtubule | |
| Scientific name | tubulin |
| Common Name | microtubule |
| Experimental Mass | 0.11 MDa |
| Oligomeric Details | hetero-dimer |
| Number of Copies | 1 |
| Scientific Name of Species | Rattus norvegicus (NCBI Taxonomy: 10116) |
| Common Name of Species | rat kinesin |
| Recombinant expression | No |
| Natural Source | Cell: neuronal cells Cell Location: cytoplasm Organ Or Tissue: brain |
 Experiment | |
| Sample Preparation | |
| Specimen Conc | 0.5 mg/ml |
|---|---|
| Staining | ice-embeded |
| Specimen Support Details | holey grids |
| Helical Parameters | Axial Symmetry: p1 Hand: LEFT HANDED |
| Specimen State | filament |
| Buffer | Details: PIPES 80 mM, MgCl2 1 mM, GTP 1 mM, Taxol 20 uM, DMSO 7.5% pH: 6.8 |
| Vitrification | |
| Cryogen Name | ETHANE |
| Temperature | 93 Kelvin |
| Imaging | |
| Microscope | FEI/PHILIPS CM200FEG/ST |
| Electron Gun | |
| Electron Source | FIELD EMISSION GUN |
| Accelerating Voltage | 200 kV |
| Electron Dose | 5 e/A**2 |
| Illumination Mode | FLOOD BEAM |
| Lens | |
| Magnification | Nominal: 38000 X, |
| Astigmatism | was corrected at 180,000 times mag. |
| Nominal Cs | 2 mm |
| Imaging Mode | BRIGHT FIELD |
| Defocus | 2000 nm - 2500 nm |
| Specimen Holder | |
| Holder | side entry ( GATAN LIQUID NITROGEN ) |
| Tilt Angle | 0 degrees - 0 degrees |
| Camera | |
| Detector | Kodak SO163 film |
| Image Acquisition | |
| Number of Digital Images | 12 |
| Sampling Size | 21 microns |
| Quant Bit Number | 8 |
| Scanner | ZEISS SCAI |
 Processing | |
| Method | helical reconstruction |
|---|---|
| 3 D reconstruction | |
| Algorithm | layer lines, Bessel orders |
| Software | PHOELIX, SUPRIM |
| Resolution By Author | 25 |
| Resolution Method | FSC at 0.5 |
| Details | Final map from 24 averaged datasets = 12 helical tubes |
| Download | |||
| Data from EMDB | |||
| Header (meta data in XML format) | emd-1039.xml (8 KB) | ||
|---|---|---|---|
| Map data | emd_1039.map.gz (2.9 MB) | ||
| Images |  1039.gif (65.3 KB) | ||
| FTP directory | ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1039 | ||
| Movie files | |||
| movie #1 |
| ||
| movie #2 |
| ||
Top
Gallery
List
Diagram
Statistics
Documents
PDBj
EM Navigator
Detail page - EMDB-1039
Z (Sec.)
Y (Row.)
X (Col.)
Contact