[English] 日本語
Yorodumi
- EMDB-5897: Cryo EM density of microtubules stabilized by taxol -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-5897
TitleCryo EM density of microtubules stabilized by taxol
Map datacryo-EM reconstruction of microtubule stabilized by taxol
Sample
  • Sample: microtubule stabilized by taxol
  • Protein or peptide: Alpha tubulin
  • Protein or peptide: Beta tubulin
  • Protein or peptide: kinesin
Keywordsmicrotubule / taxol
Function / homology
Function and homology information


structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / GTPase activity / GTP binding / metal ion binding / cytoplasm
Similarity search - Function
Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain ...Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
Tubulin alpha-1A chain / Tubulin beta chain
Similarity search - Component
Biological speciesSus scrofa (pig) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.5 Å
AuthorsAlushin GM / Lander GC / Kellogg EH / Zhang R / Baker D / Nogales E
CitationJournal: Cell / Year: 2014
Title: High-resolution microtubule structures reveal the structural transitions in αβ-tubulin upon GTP hydrolysis.
Authors: Gregory M Alushin / Gabriel C Lander / Elizabeth H Kellogg / Rui Zhang / David Baker / Eva Nogales /
Abstract: Dynamic instability, the stochastic switching between growth and shrinkage, is essential for microtubule function. This behavior is driven by GTP hydrolysis in the microtubule lattice and is ...Dynamic instability, the stochastic switching between growth and shrinkage, is essential for microtubule function. This behavior is driven by GTP hydrolysis in the microtubule lattice and is inhibited by anticancer agents like Taxol. We provide insight into the mechanism of dynamic instability, based on high-resolution cryo-EM structures (4.7-5.6 Å) of dynamic microtubules and microtubules stabilized by GMPCPP or Taxol. We infer that hydrolysis leads to a compaction around the E-site nucleotide at longitudinal interfaces, as well as movement of the α-tubulin intermediate domain and H7 helix. Displacement of the C-terminal helices in both α- and β-tubulin subunits suggests an effect on interactions with binding partners that contact this region. Taxol inhibits most of these conformational changes, allosterically inducing a GMPCPP-like state. Lateral interactions are similar in all conditions we examined, suggesting that microtubule lattice stability is primarily modulated at longitudinal interfaces.
History
DepositionFeb 9, 2014-
Header (metadata) releaseMar 5, 2014-
Map releaseJun 4, 2014-
UpdateJun 4, 2014-
Current statusJun 4, 2014Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j6g
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3j6g
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_5897.gif

Downloads & links

-
Map

FileDownload / File: emd_5897.map.gz / Format: CCP4 / Size: 4.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcryo-EM reconstruction of microtubule stabilized by taxol
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.74 Å/pix.
x 162 pix.
= 281.88 Å		1.74 Å/pix.
x 66 pix.
= 114.84 Å		1.74 Å/pix.
x 110 pix.
= 191.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.74 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 4.0 / Movie #1: 3
Minimum - Maximum-4.27395248 - 10.34669495
Average (Standard dev.)0.50004441 (±1.79294729)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-33-55-81
Dimensions66110162
Spacing66110162
CellA: 191.4 Å / B: 114.840004 Å / C: 281.88 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.741.741.74
M x/y/z11066162
origin x/y/z0.0000.0000.000
length x/y/z191.400114.840281.880
α/β/γ90.00090.00090.000
start NX/NY/NZ-95-75153
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-55-33-81
NC/NR/NS11066162
D min/max/mean-4.27410.3470.500

-
Supplemental data

-
Sample components

-
Entire : microtubule stabilized by taxol

EntireName: microtubule stabilized by taxol
Components
  • Sample: microtubule stabilized by taxol
  • Protein or peptide: Alpha tubulin
  • Protein or peptide: Beta tubulin
  • Protein or peptide: kinesin

-
Supramolecule #1000: microtubule stabilized by taxol

SupramoleculeName: microtubule stabilized by taxol / type: sample / ID: 1000 / Number unique components: 3

-
Macromolecule #1: Alpha tubulin

MacromoleculeName: Alpha tubulin / type: protein_or_peptide / ID: 1 / Oligomeric state: heterodimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Sus scrofa (pig) / synonym: porcine / Tissue: brain / Organelle: Cytoplasm / Location in cell: Cytoskeleton
Molecular weightTheoretical: 55 KDa

-
Macromolecule #2: Beta tubulin

MacromoleculeName: Beta tubulin / type: protein_or_peptide / ID: 2 / Oligomeric state: heterodimer / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Sus scrofa (pig) / synonym: porcine / Tissue: brain / Organelle: Cytoplasm / Location in cell: Cytoskeleton
Molecular weightTheoretical: 55 KDa

-
Macromolecule #3: kinesin

MacromoleculeName: kinesin / type: protein_or_peptide / ID: 3
Details: Human monomeric kinesin K349 cys-lite described in: Rice, S., Lin, A.W., Safer, D., Hart, C.L., Naber, N., Carragher, B.O., Cain, S.M., Pechatnikova, E., Wilson-Kubalek, E.M., Whittaker, M., ...Details: Human monomeric kinesin K349 cys-lite described in: Rice, S., Lin, A.W., Safer, D., Hart, C.L., Naber, N., Carragher, B.O., Cain, S.M., Pechatnikova, E., Wilson-Kubalek, E.M., Whittaker, M., et al. (1999). A structural change in the kinesin motor protein that drives motility. Nature 402, 778-784.
Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: human / Organelle: Cytoplasm / Location in cell: Cytoskeleton
Molecular weightTheoretical: 36 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

-
Sample preparation

Concentration0.25 mg/mL
BufferpH: 6.8
Details: 80mM PIPES, 1mM EGTA, 1mM MgCl2, 1mM DTT, 0.05% Nonidet P-40
GridDetails: 400 mesh C-flat 1.2/1.3, glow discharged in Edwards carbon evaporator
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 90.4 K / Instrument: FEI VITROBOT MARK II / Method: The grid was blotted for 2 seconds before plunging.

-
Electron microscopy

MicroscopeFEI TITAN
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnifacation.
DateMay 29, 2012
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 6.35 µm / Number real images: 149 / Average electron dose: 25.0 e/Å2 / Bits/pixel: 16
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 72000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 72000
Sample stageSpecimen holder: Gatan 626 holder / Specimen holder model: GATAN LIQUID NITROGEN

-
Image processing

DetailsInitial alignments performed with EMAN2/SPARX, including refinement of helical parameters with the IHRSR programs of Egelman. Final alignment and reconstruction performed with FREALIGN.
CTF correctionDetails: ctftilt
Final reconstructionApplied symmetry - Helical parameters - Δz: 8.96 Å
Applied symmetry - Helical parameters - Δ&Phi: 25.75 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 5.5 Å / Resolution method: OTHER / Software - Name: FREALIGN / Number images used: 24357

-
Atomic model buiding 1

Initial modelPDB ID:

1jff

SoftwareName: ROSETTA
DetailsStructure represents the minimized average structure of the 1% lowest energy structures from the refinement run.
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-3j6g:
Minimized average structure of microtubules stabilized by taxol

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more