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-5205

Structure of microtubule decorated with PRC1

by helical reconstruction, at 18 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 14, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 14, Image by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5205
TitleStructure of microtubule decorated with PRC1
MapThis is an image of section of microtubule decorated with PRC1
SamplePRC1
AuthorsSubramanian R, Wilson-Kubalek EM, Arthur CP, Bick MJ, Campbell EA, Darst SA, Milligan RA, Kapoor TM
DateDeposition: 2010-06-30, Header release: 2010-09-10, Map release: 2010-09-10, Last update: 2010-10-19
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 14, Image by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 14, Image 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-shape strucutres
Search for similar-shape assemblies throgh:
EMDB + EM entries in PDB
all of EMDB & PDB (Omokage search)
Article
Citation - Primary
ArticleCell, Vol. 142, Issue 3, Page 433-43, Year 2010
TitleInsights into antiparallel microtubule crosslinking by PRC1, a conserved nonmotor microtubule binding protein.
AuthorsRadhika Subramanian, Elizabeth M Wilson-Kubalek, Christopher P Arthur, Matthew J Bick, Elizabeth A Campbell, Seth A Darst, Ronald A Milligan, Tarun M Kapoor
Laboratory of Chemistry and Cell Biology, The Rockefeller University, New York, NY 10065, USA.
KeywordsCell Cycle Proteins (chemistry), Cryoelectron Microscopy, Humans, Microtubules (metabolism), Models, Molecular, PRC1 protein, human, Protein Structure, Tertiary, Spectrin (metabolism, 12634-43-4)
LinksPII: S0092-8674(10)00781-6, DOI: 10.1016/j.cell.2010.07.012, PubMed: 20691902, PMC: PMC2966277
Map
Fileemd_5205.map.gz ( map file in CCP4 format, 11766 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
103 pix
5.345 A/pix
= 550.535 A
171 pix
5.345 A/pix
= 913.995 A
171 pix
5.345 A/pix
= 913.995 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:2.5 (by author), 14 (movie #1):
Minimum - Maximum: -32 - 50
Average (Standard dev.): 0.847337 (10.7397)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions171171103
Origin000
Limit170170102
Spacing171171103
Unit CellA: 913.995 A, B: 913.995 A, C: 550.535 A
Alpha=beta=gamma: 90 degrees
Pixel Spacing
XYZ
EMDB info.5.3455.3455.345
CCP4 map header5.3455.3455.345
EM Navigator Movie #13.473.473.47
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z5.3455.3455.345
M x/y/z171171103
origin x/y/z0.0000.0000.000
length x/y/z913.995913.995550.535
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-99-99-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS171171103
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-32.00050.0000.847
Annotation DetailsThis is an image of section of microtubule decorated with PRC1
Supplement
Images
Images
Sample
NamePRC1
Number of Components2
DetailsDecorated microtubules
Component #1: protein - PRC1
Scientific nameMicrotubule
Common NamePRC1
Scientific Name of Speciesunidentified
NCBI taxonomy32644
Recombinant expressionYes
Experiment
Sample Preparation
Helical ParametersHand: LEFT HANDED
Specimen Statefilament
Vitrification
Cryogen NameETHANE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI F20
Date02-FEB-2010
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage120 kV
Electron Dose10 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 35000
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus900 nm - 2000 nm
Specimen Holder
HolderEucentric
ModelGATAN LIQUID NITROGEN
Tilt Angle0 degrees - 0 degrees
Temperature93 K ( 93 - 93 K)
Camera
DetectorGENERIC GATAN
Image Acquisition
#1
Number of Digital Images10
Processing
Methodhelical reconstruction
3D reconstruction
AlgorithmFourier Bessel inversion
SoftwarePHOELIX
CTF CorrectionCTF correction of each micrograph
Resolution By Author18 A
Resolution MethodCoherent phase determination
Download
Data from EMDB
Header (meta data in XML format)emd-5205.xml (6.3 KB)
Map dataemd_5205.map.gz (1.6 MB)
Imagesemd_5205_1.png (296.1 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5205
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.2 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, 26.2 KB