[English] 日本語
Yorodumi
- EMDB-0614: Deacetylated Microtubules -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0614
TitleDeacetylated Microtubules
Map data
SampleDeacetylated Microtubule:
Tubulin alpha-1B chain / Tubulin beta chain / (ligand) x 3
Function / homology
Function and homology information


cytoplasmic microtubule / microtubule-based process / cellular response to interleukin-4 / structural constituent of cytoskeleton / neuron migration / microtubule cytoskeleton organization / double-stranded RNA binding / mitotic cell cycle / microtubule / GTPase activity ...cytoplasmic microtubule / microtubule-based process / cellular response to interleukin-4 / structural constituent of cytoskeleton / neuron migration / microtubule cytoskeleton organization / double-stranded RNA binding / mitotic cell cycle / microtubule / GTPase activity / GTP binding / ubiquitin protein ligase binding / cytoplasm
Tubulin / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, C-terminal domain superfamily / Tubulin/FtsZ, GTPase domain superfamily / Tubulin, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin, conserved site / Beta tubulin, autoregulation binding site / Tubulin/FtsZ, C-terminal / Alpha tubulin / Beta tubulin
Tubulin beta chain / Tubulin alpha-1B chain
Biological speciesPig (pig)
Methodhelical reconstruction / cryo EM / Resolution: 4 Å
AuthorsEshun-Wilson L / Zhang R / Portran D / Nachury MV / Toso D / Lohr T / Vendruscolo M / Bonomi M / Fraser JS / Nogales E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2016222703 United States
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2019
Title: Effects of α-tubulin acetylation on microtubule structure and stability.
Authors: Lisa Eshun-Wilson / Rui Zhang / Didier Portran / Maxence V Nachury / Daniel B Toso / Thomas Löhr / Michele Vendruscolo / Massimiliano Bonomi / James S Fraser / Eva Nogales /
Abstract: Acetylation of K40 in α-tubulin is the sole posttranslational modification to mark the luminal surface of microtubules. It is still controversial whether its relationship with microtubule ...Acetylation of K40 in α-tubulin is the sole posttranslational modification to mark the luminal surface of microtubules. It is still controversial whether its relationship with microtubule stabilization is correlative or causative. We have obtained high-resolution cryo-electron microscopy (cryo-EM) reconstructions of pure samples of αTAT1-acetylated and SIRT2-deacetylated microtubules to visualize the structural consequences of this modification and reveal its potential for influencing the larger assembly properties of microtubules. We modeled the conformational ensembles of the unmodified and acetylated states by using the experimental cryo-EM density as a structural restraint in molecular dynamics simulations. We found that acetylation alters the conformational landscape of the flexible loop that contains αK40. Modification of αK40 reduces the disorder of the loop and restricts the states that it samples. We propose that the change in conformational sampling that we describe, at a location very close to the lateral contacts site, is likely to affect microtubule stability and function.
Validation ReportPDB-ID: 6o2s

SummaryFull reportAbout validation report
History
DepositionFeb 24, 2019-
Header (metadata) releaseMar 20, 2019-
Map releaseMay 22, 2019-
UpdateNov 27, 2019-
Current statusNov 27, 2019Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6o2s
  • Surface level: 4
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6o2s
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_0614.map.gz / Format: CCP4 / Size: 515 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.07 Å/pix.
x 513 pix.
= 548.91 Å
1.07 Å/pix.
x 513 pix.
= 548.91 Å
1.07 Å/pix.
x 513 pix.
= 548.91 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 4 / Movie #1: 4
Minimum - Maximum-7.4073935 - 13.9379425
Average (Standard dev.)-0.00012911075 (±0.93751955)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions513513513
Spacing513513513
CellA=B=C: 548.91003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z513513513
origin x/y/z0.0000.0000.000
length x/y/z548.910548.910548.910
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ513513513
MAP C/R/S321
start NC/NR/NS000
NC/NR/NS513513513
D min/max/mean-7.40713.938-0.000

-
Supplemental data

-
Half map: Half map deposition

Fileemd_0614_half_map_1.map
AnnotationHalf map deposition
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: Half map deposition

Fileemd_0614_half_map_2.map
AnnotationHalf map deposition
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

+
Entire Deacetylated Microtubule

EntireName: Deacetylated Microtubule / Number of components: 6

+
Component #1: cellular-component, Deacetylated Microtubule

Cellular-componentName: Deacetylated Microtubule / Recombinant expression: No

+
Component #2: protein, Tubulin alpha-1B chain

ProteinName: Tubulin alpha-1B chain / Number of Copies: 52 / Recombinant expression: No
MassTheoretical: 50.204445 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: Brain

+
Component #3: protein, Tubulin beta chain

ProteinName: Tubulin beta chain / Number of Copies: 52 / Recombinant expression: No
MassTheoretical: 49.90777 kDa
SourceSpecies: Pig (pig)
Source (natural)Organ or tissue: Brain

+
Component #4: ligand, GUANOSINE-5'-TRIPHOSPHATE

LigandName: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate / Number of Copies: 52 / Recombinant expression: No
MassTheoretical: 0.52318 kDa

+
Component #5: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 52 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

+
Component #6: ligand, GUANOSINE-5'-DIPHOSPHATE

LigandName: GUANOSINE-5'-DIPHOSPHATE / Number of Copies: 52 / Recombinant expression: No
MassTheoretical: 0.443201 kDa

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: helical array / Method: cryo EM
Helical parametersAxial symmetry: C1 (asymmetric) / Delta z: 9.3 Å / Delta phi: -27.7 %deg;
Sample solutionSpecimen conc.: 10 mg/mL
Buffer solution: Contains 80 mM PIPES, 1 mM MgCl2, 1 mM EGTA, pH 6.8 with KOH (stored at 4 degrees Celsius).
pH: 6.8
Support filmunspecified
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 310.15 K / Humidity: 100 % / Details: Blotted for 4 seconds at blot force 10..

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Details: Preliminary grid screening was performed manually and all of the alignments were initially done using a gold calibration grid.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500.0 X (nominal), 23364.0 X (calibrated) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500.0 - 2500.0 nm / Energy filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: (77.0 - 77.0 K)
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

-
Image acquisition

Image acquisitionNumber of digital images: 287

-
Image processing

ProcessingMethod: helical reconstruction
3D reconstructionAlgorithm: FOURIER SPACE / Software: FREALIGN / CTF correction: CTFFIND4 / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

-
Atomic model buiding

Modeling #1Target criteria: 0.5 / Refinement space: REAL
Details: We use PHENIX to perform real space refinement and sharpen our cryoEM maps.
Input PDB model: 3JAR
Overall bvalue: 126
Output model

+
About Yorodumi

-
News

-
Aug 12, 2020. New: Covid-19 info

New: Covid-19 info

  • 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. New: 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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

Read more

-
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.

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