[English] 日本語
Yorodumi
- EMDB-1731: The microtubule nucleating gamma-tubulin small complex assembles ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1731
TitleThe microtubule nucleating gamma-tubulin small complex assembles into a structure with microtubule-like thirteen fold symmetry
Map dataThis is the map of the gamma-tubulin small complex - Spc110p filament. The filament axis is along the Z axis.
Sample
  • Sample: Gamma-tubulin small complex in complex with Spc110p(1-220)
  • Protein or peptide: Tub4p
  • Protein or peptide: Spc97p
  • Protein or peptide: Spc98p
  • Protein or peptide: Spc110p
KeywordsMicrotubule / nucleation / tubulin / filament
Function / homology
Function and homology information


inner plaque of spindle pole body / microtubule nucleation by spindle pole body / outer plaque of spindle pole body / gamma-tubulin small complex / regulation of microtubule nucleation / microtubule nucleator activity / mitotic spindle pole body / gamma-tubulin complex / gamma-tubulin ring complex / meiotic spindle organization ...inner plaque of spindle pole body / microtubule nucleation by spindle pole body / outer plaque of spindle pole body / gamma-tubulin small complex / regulation of microtubule nucleation / microtubule nucleator activity / mitotic spindle pole body / gamma-tubulin complex / gamma-tubulin ring complex / meiotic spindle organization / microtubule nucleation / spindle pole body / gamma-tubulin binding / positive regulation of cytoplasmic translation / mitotic sister chromatid segregation / spindle assembly / cytoplasmic microtubule organization / mitotic spindle organization / meiotic cell cycle / structural constituent of cytoskeleton / spindle / spindle pole / mitotic cell cycle / microtubule / GTP binding / nucleus / cytoplasm
Similarity search - Function
: / : / Gamma tubulin / Gamma tubulin / Gamma tubulin complex component, C-terminal / Gamma-tubulin complex component, C-terminal domain superfamily / Gamma tubulin complex component C-terminal / Gamma-tubulin complex component protein / Gamma tubulin complex component protein, N-terminal / Gamma tubulin complex component N-terminal ...: / : / Gamma tubulin / Gamma tubulin / Gamma tubulin complex component, C-terminal / Gamma-tubulin complex component, C-terminal domain superfamily / Gamma tubulin complex component C-terminal / Gamma-tubulin complex component protein / Gamma tubulin complex component protein, N-terminal / Gamma tubulin complex component N-terminal / 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
Spindle pole body component SPC97 / Tubulin gamma chain / Spindle pole body component SPC98
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodhelical reconstruction / cryo EM / negative staining / Resolution: 8.0 Å
AuthorsKollman JM / Polka JK / Zelter A / Davis TN / Agard DA
CitationJournal: Nature / Year: 2010
Title: Microtubule nucleating gamma-TuSC assembles structures with 13-fold microtubule-like symmetry.
Authors: Justin M Kollman / Jessica K Polka / Alex Zelter / Trisha N Davis / David A Agard /
Abstract: Microtubules are nucleated in vivo by gamma-tubulin complexes. The 300-kDa gamma-tubulin small complex (gamma-TuSC), consisting of two molecules of gamma-tubulin and one copy each of the accessory ...Microtubules are nucleated in vivo by gamma-tubulin complexes. The 300-kDa gamma-tubulin small complex (gamma-TuSC), consisting of two molecules of gamma-tubulin and one copy each of the accessory proteins Spc97 and Spc98, is the conserved, essential core of the microtubule nucleating machinery. In metazoa multiple gamma-TuSCs assemble with other proteins into gamma-tubulin ring complexes (gamma-TuRCs). The structure of gamma-TuRC indicated that it functions as a microtubule template. Because each gamma-TuSC contains two molecules of gamma-tubulin, it was assumed that the gamma-TuRC-specific proteins are required to organize gamma-TuSCs to match 13-fold microtubule symmetry. Here we show that Saccharomyces cerevisiae gamma-TuSC forms rings even in the absence of other gamma-TuRC components. The yeast adaptor protein Spc110 stabilizes the rings into extended filaments and is required for oligomer formation under physiological buffer conditions. The 8-A cryo-electron microscopic reconstruction of the filament reveals 13 gamma-tubulins per turn, matching microtubule symmetry, with plus ends exposed for interaction with microtubules, implying that one turn of the filament constitutes a microtubule template. The domain structures of Spc97 and Spc98 suggest functions for conserved sequence motifs, with implications for the gamma-TuRC-specific proteins. The gamma-TuSC filaments nucleate microtubules at a low level, and the structure provides a strong hypothesis for how nucleation is regulated, converting this less active form to a potent nucleator.
History
DepositionMay 14, 2010-
Header (metadata) releaseJun 28, 2010-
Map releaseNov 1, 2010-
UpdateDec 23, 2015-
Current statusDec 23, 2015Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd-1731.jpg

Downloads & links

-
Map

FileDownload / File: emd_1731.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is the map of the gamma-tubulin small complex - Spc110p filament. The filament axis is along the Z axis.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.19 Å/pix.
x 320 pix.
= 380.8 Å		1.19 Å/pix.
x 320 pix.
= 380.8 Å		1.19 Å/pix.
x 320 pix.
= 380.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.19 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-3.00519 - 6.27779
Average (Standard dev.)1.00001 (±0.999949)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 380.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.191.191.19
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z380.800380.800380.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-3.0056.2781.000

-
Supplemental data

-
Sample components

-
Entire : Gamma-tubulin small complex in complex with Spc110p(1-220)

EntireName: Gamma-tubulin small complex in complex with Spc110p(1-220)
Components
  • Sample: Gamma-tubulin small complex in complex with Spc110p(1-220)
  • Protein or peptide: Tub4p
  • Protein or peptide: Spc97p
  • Protein or peptide: Spc98p
  • Protein or peptide: Spc110p

-
Supramolecule #1000: Gamma-tubulin small complex in complex with Spc110p(1-220)

SupramoleculeName: Gamma-tubulin small complex in complex with Spc110p(1-220)
type: sample / ID: 1000
Details: The stoichiometry of gamma-TuSC to Spc110p is not known.
Number unique components: 4

-
Macromolecule #1: Tub4p

MacromoleculeName: Tub4p / type: protein_or_peptide / ID: 1 / Name.synonym: gamma-tubulin / Number of copies: 2 / Oligomeric state: Helical filament / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Location in cell: Spindle pole body
Molecular weightTheoretical: 52.6 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (baculovirus infected) / Recombinant plasmid: pAZ37
SequenceInterPro: Gamma tubulin

-
Macromolecule #2: Spc97p

MacromoleculeName: Spc97p / type: protein_or_peptide / ID: 2 / Name.synonym: Spindle pole body component p97 / Number of copies: 1 / Oligomeric state: Helical filament / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker'syeast / Location in cell: Spindle pole body
Molecular weightTheoretical: 96.8 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (baculovirus infected) / Recombinant plasmid: pDV45
SequenceInterPro: INTERPRO: IPR015698

-
Macromolecule #3: Spc98p

MacromoleculeName: Spc98p / type: protein_or_peptide / ID: 3 / Name.synonym: Spindle pole body component 98p / Number of copies: 1 / Oligomeric state: Helical filament / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Location in cell: Spindle pole body
Molecular weightTheoretical: 98.3 MDa
Recombinant expressionOrganism: Spodoptera frugiperda (baculovirus infected) / Recombinant plasmid: pDV46
SequenceInterPro: INTERPRO: IPR015696

-
Macromolecule #4: Spc110p

MacromoleculeName: Spc110p / type: protein_or_peptide / ID: 4 / Name.synonym: Spc110p
Details: Construct includes the first 220 residues of Spc110p
Number of copies: 1 / Oligomeric state: Helical filament / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Location in cell: Spindle pole body
Molecular weightTheoretical: 23 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (baculovirus infected) / Recombinant plasmid: pAZ34

-
Experimental details

-
Structure determination

Methodnegative staining, cryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration2 mg/mL
BufferpH: 7.6
Details: 100 mM KCl, 1mM GTP, 1mM MgCl2, 2mM EGTA, 40 mM Hepes
StainingType: NEGATIVE
Details: Sample was applied to C-FLAT holey carbon grids, blotted, and flash frozen in liquid ethane
GridDetails: 200 mesh copper grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blotted 3s before plunging

-
Electron microscopy

MicroscopeFEI TECNAI F20
Alignment procedureLegacy - Astigmatism: Astigmatism corrected at 250,000 times magnification
DateSep 23, 2009
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.2 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 60000
Sample stageSpecimen holder: Oxford side-entry cryo stage / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 22.2 Å
Applied symmetry - Helical parameters - Δ&Phi: 54.3 °
Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider
CTF correctionDetails: Whole micrograph
Final angle assignmentDetails: SPIDER:theta 90 degrees, phi 90 degrees

+
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