[English] 日本語
Yorodumi
- EMDB-1041: Nucleotide-induced conformations in the neck region of dimeric ki... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 1041
TitleNucleotide-induced conformations in the neck region of dimeric kinesin.
Samplerat kinesin monomer ric354 complexed to microtubule in the absence of nucleotide
SourceRattus norvegicus / mammal / rat kinesin / ドブネズミ, どぶねずみ /
Map datarat kinesin monomer rk354 complexed to microtubules in the absence of nucleotide
Methodhelical reconstruction, at 25 A resolution
AuthorsSkiniotis G
CitationEMBO J., 2003, 22, 1518-1528

EMBO J., 2003, 22, 1518-1528 StrPapers
Nucleotide-induced conformations in the neck region of dimeric kinesin.
Georgios Skiniotis / Thomas Surrey / Stephan Altmann / Heinz Gross / Young-Hwa Song / Eckhard Mandelkow / Andreas Hoenger

DateDeposition: Feb 28, 2003 / Header (metadata) release: Feb 28, 2003 / Map release: Mar 28, 2003 / Last update: Feb 28, 2003

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 55.87245372
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 55.87245372
  • 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_1041.map.gz (map file in CCP4 format, 3908 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
100 pix
5.53 A/pix
= 552.6 A
100 pix
5.53 A/pix
= 552.6 A
100 pix
5.53 A/pix
= 552.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 5.526 A
Density
Contour Level:66.7, 55.8724537 (movie #1):
Minimum - Maximum0 - 100
Average (Standard dev.)45.1461 (9.89639)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100100
Origin000
Limit999999
Spacing100100100
CellA=B=C: 552.6 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

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
D min/max/mean0.000100.00045.146

-
Supplemental data

-
Sample components

-
Entire rat kinesin monomer ric354 complexed to microtubule in the absenc...

EntireName: rat kinesin monomer ric354 complexed to microtubule in the absence of nucleotide
Oligomeric State: monomer / Number of components: 2

-
Component #1: protein, rat kinesin

ProteinName: rat kinesin / a.k.a: molecular motor / Oligomeric Details: dimer / Number of Copies: 1 / Recombinant expression: Yes
MassExperimental: 390 kDa
SourceSpecies: Rattus norvegicus / mammal / rat kinesin / ドブネズミ, どぶねずみ /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pET3

-
Component #2: protein, tubulin

ProteinName: tubulin / a.k.a: microtubule / Oligomeric Details: hetero-dimer / Recombinant expression: No / Number of Copies: 1
MassExperimental: 110 kDa
SourceSpecies: Rattus norvegicus / mammal / rat kinesin / ドブネズミ, どぶねずみ /
Source (natural)Location in cell: cytoplasm / Cell: neuronal cells / Organ or tissue: brain

+
Experimental details

-
Sample preparation

Specimen statefilament
Helical parametersAxial symmetry: C1 (asymmetric) / Hand: LEFT HANDED
Sample solutionSpecimen conc.: 0.5 mg/ml
Buffer solution: PIPES 80 mM, MgCl2 1 mM, GTP 1 mM, Taxol 20 uM, DMSO 7.5%
pH: 6.8
Support filmholey grids
Stainingice-embedded
VitrificationCryogen name: ETHANE / Temperature: 93 K

-
Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200FEG/ST
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 5 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 38000 X (nominal) / Astigmatism: was corrected at 180,000 times mag. / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 2500 nm
Specimen HolderHolder: side entry / Model: GATAN LIQUID NITROGEN
CameraDetector: KODAK SO-163 FILM

-
Image acquisition

Image acquisitionNumber of digital images: 10 / Scanner: ZEISS SCAI / Sampling size: 21 microns / Bit depth: 8

-
Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: layer lines, Bessel orders / Software: PHOELIX, SUPRIM / Resolution: 25 A / Resolution method: FSC 0.5
Details: Final map from 20 averaged datasets = 10 helical tubes

+
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