[English] 日本語
Yorodumi
- EMDB-5205: Structure of microtubule decorated with PRC1 -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 5205
TitleStructure of microtubule decorated with PRC1
SamplePRC1
SourceUnidentified
Map dataThis is an image of section of microtubule decorated with PRC1
Methodhelical reconstruction, at 18 A resolution
AuthorsSubramanian R / Wilson-Kubalek EM / Arthur CP / Bick MJ / Campbell EA / Darst SA / Milligan RA / Kapoor TM
CitationCell, 2010, 142, 433-443

Cell, 2010, 142, 433-443 StrPapers
Insights into antiparallel microtubule crosslinking by PRC1, a conserved nonmotor microtubule binding protein.
Radhika Subramanian / Elizabeth M Wilson-Kubalek / Christopher P Arthur / Matthew J Bick / Elizabeth A Campbell / Seth A Darst / Ronald A Milligan / Tarun M Kapoor

DateDeposition: Jun 30, 2010 / Header (metadata) release: Sep 10, 2010 / Map release: Sep 10, 2010 / Last update: Jun 30, 2010

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 14
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 14
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
Map

Fileemd_5205.map.gz (map file in CCP4 format, 11766 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
103 pix
5.35 A/pix
= 550.535 A
171 pix
5.35 A/pix
= 913.995 A
171 pix
5.35 A/pix
= 913.995 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel size
XYZ
EMDB info.5.3455.3455.345
CCP4 map header5.3455.3455.345
EM Navigator Movie #13.473.473.47
Density
Contour Level:2.5 (by author), 14 (movie #1):
Minimum - Maximum-32 - 50
Average (Standard dev.)0.847337 (10.7397)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions171171103
Origin000
Limit170170102
Spacing171171103
CellA: 913.995 A / B: 913.995 A / C: 550.535 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

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
D min/max/mean-32.00050.0000.847

-
Supplemental data

-
Sample components

-
Entire PRC1

EntireName: PRC1 / Details: Decorated microtubules / Number of components: 2

-
Component #1: protein, Microtubule

ProteinName: Microtubule / a.k.a: PRC1 / Recombinant expression: Yes
SourceSpecies: Unidentified

+
Experimental details

-
Sample preparation

Specimen statefilament
Helical parametersHand: LEFT HANDED
VitrificationInstrument: NONE / Cryogen name: ETHANE

-
Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20 / Date: Feb 2, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 10 e/A2 / Electron beam tilt params: 0 / Illumination mode: FLOOD BEAM
LensMagnification: 35000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 900 - 2000 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 93 K ( 93 - 93 K)
CameraDetector: GENERIC GATAN

-
Image acquisition

Image acquisitionNumber of digital images: 10

-
Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: Fourier Bessel inversion / Software: PHOELIX / CTF correction: CTF correction of each micrograph / Resolution: 18 A / Resolution method: Coherent phase determination

+
About Yorodumi

-
News

-
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

-
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

+
Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more