[English] 日本語
Yorodumi
- EMDB-15119: 13pf undecorated microtubule from recombinant human tubulin (alph... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-15119
Title13pf undecorated microtubule from recombinant human tubulin (alpha1B, beta3) with spliced unmodified C-terminal tail on alpha1B.
Map dataHuman microtubules (alpha1B, beta3) with spliced unmodified C-terminal tail on alpha1B.
Sample
  • Organelle or cellular component: 13pf microtubule from recombinant human tubulin with spliced unmodified C-terminal tail on alpha1B.
    • Protein or peptide: Tubulin alpha-1B with spliced C-terminal tail
    • Protein or peptide: Tubulin beta-3
Keywordstubulin / no tail / recombinant / semisynthetic / STRUCTURAL PROTEIN
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 3.74 Å
AuthorsEbberink E / Fernandes S / Hatzopoulos GN / Agashe N / Guidotti N / Reichart T / Reymond L / Velluz MC / Schneider FZ / Pourroy C ...Ebberink E / Fernandes S / Hatzopoulos GN / Agashe N / Guidotti N / Reichart T / Reymond L / Velluz MC / Schneider FZ / Pourroy C / Janke C / Gonczy P / Aumeier C / Fierz B
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Nat Chem / Year: 2023
Title: Tubulin engineering by semi-synthesis reveals that polyglutamylation directs detyrosination.
Authors: Eduard Ebberink / Simon Fernandes / Georgios Hatzopoulos / Ninad Agashe / Po-Han Chang / Nora Guidotti / Timothy M Reichart / Luc Reymond / Marie-Claire Velluz / Fabian Schneider / Cédric ...Authors: Eduard Ebberink / Simon Fernandes / Georgios Hatzopoulos / Ninad Agashe / Po-Han Chang / Nora Guidotti / Timothy M Reichart / Luc Reymond / Marie-Claire Velluz / Fabian Schneider / Cédric Pourroy / Carsten Janke / Pierre Gönczy / Beat Fierz / Charlotte Aumeier /
Abstract: Microtubules, a critical component of the cytoskeleton, carry post-translational modifications (PTMs) that are important for the regulation of key cellular processes. Long-lived microtubules, in ...Microtubules, a critical component of the cytoskeleton, carry post-translational modifications (PTMs) that are important for the regulation of key cellular processes. Long-lived microtubules, in neurons particularly, exhibit both detyrosination of α-tubulin and polyglutamylation. Dysregulation of these PTMs can result in developmental defects and neurodegeneration. Owing to a lack of tools to study the regulation and function of these PTMs, the mechanisms that govern such PTM patterns are not well understood. Here we produce fully functional tubulin carrying precisely defined PTMs within its C-terminal tail. We ligate synthetic α-tubulin tails-which are site-specifically glutamylated-to recombinant human tubulin heterodimers by applying a sortase- and intein-mediated tandem transamidation strategy. Using microtubules reconstituted with these designer tubulins, we find that α-tubulin polyglutamylation promotes its detyrosination by enhancing the activity of the tubulin tyrosine carboxypeptidase vasohibin/small vasohibin-binding protein in a manner dependent on the length of polyglutamyl chains. We also find that modulating polyglutamylation levels in cells results in corresponding changes in detyrosination, corroborating the link between the detyrosination cycle to polyglutamylation.
History
DepositionJun 8, 2022-
Header (metadata) releaseJun 21, 2023-
Map releaseJun 21, 2023-
UpdateAug 23, 2023-
Current statusAug 23, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_15119.png

Downloads & links

-
Map

FileDownload / File: emd_15119.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman microtubules (alpha1B, beta3) with spliced unmodified C-terminal tail on alpha1B.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 600 pix.
= 498. Å		0.83 Å/pix.
x 600 pix.
= 498. Å		0.83 Å/pix.
x 600 pix.
= 498. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.054
Minimum - Maximum-0.08231881 - 0.23393734
Average (Standard dev.)0.0006047964 (±0.017694604)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 498.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_15119_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_15119_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_15119_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : 13pf microtubule from recombinant human tubulin with spliced unmo...

EntireName: 13pf microtubule from recombinant human tubulin with spliced unmodified C-terminal tail on alpha1B.
Components
  • Organelle or cellular component: 13pf microtubule from recombinant human tubulin with spliced unmodified C-terminal tail on alpha1B.
    • Protein or peptide: Tubulin alpha-1B with spliced C-terminal tail
    • Protein or peptide: Tubulin beta-3

-
Supramolecule #1: 13pf microtubule from recombinant human tubulin with spliced unmo...

SupramoleculeName: 13pf microtubule from recombinant human tubulin with spliced unmodified C-terminal tail on alpha1B.
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

-
Macromolecule #1: Tubulin alpha-1B with spliced C-terminal tail

MacromoleculeName: Tubulin alpha-1B with spliced C-terminal tail / type: protein_or_peptide / ID: 1
Details: internal 6xHis tag in 40-loop; Spliced C-terminal tail without glutamylation, splicing scar: InsC440 and V441F
Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MRECISIHVG QAGVQIGNA C WELYCLEH GI QPDGQMP SDK TIHHHH HHGGGDDSFN TFFSETGAG K HVPRAVFV DL EPTVIDE VRT GTYRQL FHPE QLITG KEDAA NNYA RGHYTI GKE IIDLVLD RI RKLADQCT G LQGFLVFHS FGGGTGSGFT ...String:
MRECISIHVG QAGVQIGNA C WELYCLEH GI QPDGQMP SDK TIHHHH HHGGGDDSFN TFFSETGAG K HVPRAVFV DL EPTVIDE VRT GTYRQL FHPE QLITG KEDAA NNYA RGHYTI GKE IIDLVLD RI RKLADQCT G LQGFLVFHS FGGGTGSGFT SLLMERLSV D YGKKSKLE FS IYPAPQV STA VVEPYN SILT THTTL EHSDC AFMV DNEAIY DIC RRNLDIE RP TYTNLNRL I SQIVSSITA SLRFDGALNV DLTEFQTNL V PYPRIHFP LA TYAPVIS AEK AYHEQL SVAE ITNAC FEPAN QMVK CDPRHG KYM ACCLLYR GD VVPKDVNA A IATIKTKRS IQFVDWCPTG FKVGINYQP P TVVPGGDL AK VQRAVCM LSN TTAIAE AWAR LDHKF DLMYA KRAF VHWYVG EGM EEGEFSE AR EDMAALEK D YEEVGVDSC FEGEGEEEGE EY

-
Macromolecule #2: Tubulin beta-3

MacromoleculeName: Tubulin beta-3 / type: protein_or_peptide / ID: 2 / Details: C-terminal FLAG-tag / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPSGNYVGDS DLQLERISVY YNEASSHKYV PRAILVDLEP GTMDSVRSGA FGHLFRPDNF IFGQSGAGNN WAKGHYTEGA ELVDSVLDVV RKECENCDCL QGFQLTHSLG GGTGSGMGTL LISKVREEYP DRIMNTFSVV ...String:
MREIVHIQAG QCGNQIGAKF WEVISDEHGI DPSGNYVGDS DLQLERISVY YNEASSHKYV PRAILVDLEP GTMDSVRSGA FGHLFRPDNF IFGQSGAGNN WAKGHYTEGA ELVDSVLDVV RKECENCDCL QGFQLTHSLG GGTGSGMGTL LISKVREEYP DRIMNTFSVV PSPKVSDTVV EPYNATLSIH QLVENTDETY CIDNEALYDI CFRTLKLATP TYGDLNHLVS ATMSGVTTSL RFPGQLNADL RKLAVNMVPF PRLHFFMPGF APLTARGSQQ YRALTVPELT QQMFDAKNMM AACDPRHGRY LTVATVFRGR MSMKEVDEQM LAIQSKNSSY FVEWIPNNVK VAVCDIPPRG LKMSSTFIGN STAIQELFKR ISEQFTAMFR RKAFLHWYTG EGMDEMEFTE AESNMNDLVS EYQQYQDATA EEEGEMYEDD EEESEAQGPK ENLYFQSSGG DYKDDDDK

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

-
Sample preparation

BufferpH: 6.8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 9.46 Å
Applied symmetry - Helical parameters - Δ&Phi: -27.67 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.74 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 115123
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

+
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