[English] 日本語
Yorodumi
- EMDB-11835: Structure of the Candida albicans gamma-Tubulin Small Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11835
TitleStructure of the Candida albicans gamma-Tubulin Small Complex
Map datagamma-Tubulin Small Complex density map
Sample
  • Complex: gamma-Tubulin Small Complex
    • Protein or peptide: Tubulin gamma chain
    • Protein or peptide: Spindle pole body component
    • Protein or peptide: Spindle pole body component
Function / homology
Function and homology information


gamma-tubulin small complex / mitotic spindle pole body / equatorial microtubule organizing center / gamma-tubulin complex / microtubule nucleation / spindle pole body / gamma-tubulin binding / spindle assembly / cytoplasmic microtubule organization / meiotic cell cycle ...gamma-tubulin small complex / mitotic spindle pole body / equatorial microtubule organizing center / gamma-tubulin complex / microtubule nucleation / spindle pole body / gamma-tubulin binding / spindle assembly / cytoplasmic microtubule organization / meiotic cell cycle / spindle pole / mitotic cell cycle / microtubule / GTPase activity / GTP binding / cytoplasm
Similarity search - Function
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 ...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, 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 / Tubulin gamma chain / Spindle pole body component
Similarity search - Component
Biological speciesCandida albicans (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsZupa E / Pfeffer S
Funding support Germany, 1 items
OrganizationGrant numberCountry
German Research Foundation (DFG)Schi 295/4-4 Germany
CitationJournal: Nat Commun / Year: 2020
Title: The cryo-EM structure of a γ-TuSC elucidates architecture and regulation of minimal microtubule nucleation systems.
Authors: Erik Zupa / Anjun Zheng / Annett Neuner / Martin Würtz / Peng Liu / Anna Böhler / Elmar Schiebel / Stefan Pfeffer /
Abstract: The nucleation of microtubules from αβ-tubulin subunits is mediated by γ-tubulin complexes, which vary in composition across organisms. Aiming to understand how de novo microtubule formation is ...The nucleation of microtubules from αβ-tubulin subunits is mediated by γ-tubulin complexes, which vary in composition across organisms. Aiming to understand how de novo microtubule formation is achieved and regulated by a minimal microtubule nucleation system, we here determined the cryo-electron microscopy structure of the heterotetrameric γ-tubulin small complex (γ-TuSC) from C. albicans at near-atomic resolution. Compared to the vertebrate γ-tubulin ring complex (γ-TuRC), we observed a vastly remodeled interface between the SPC/GCP-γ-tubulin spokes, which stabilizes the complex and defines the γ-tubulin arrangement. The relative positioning of γ-tubulin subunits indicates that a conformational rearrangement of the complex is required for microtubule nucleation activity, which follows opposing directionality as predicted for the vertebrate γ-TuRC. Collectively, our data suggest that the assembly and regulation mechanisms of γ-tubulin complexes fundamentally differ between the microtubule nucleation systems in lower and higher eukaryotes.
History
DepositionOct 13, 2020-
Header (metadata) releaseNov 4, 2020-
Map releaseNov 4, 2020-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7anz
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11835.png

Downloads & links

-
Map

FileDownload / File: emd_11835.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationgamma-Tubulin Small Complex density map
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.18757834 - 0.6726366
Average (Standard dev.)0.00051714294 (±0.01081325)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z273.920273.920273.920
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1880.6730.001

-
Supplemental data

-
Sample components

-
Entire : gamma-Tubulin Small Complex

EntireName: gamma-Tubulin Small Complex
Components
  • Complex: gamma-Tubulin Small Complex
    • Protein or peptide: Tubulin gamma chain
    • Protein or peptide: Spindle pole body component
    • Protein or peptide: Spindle pole body component

-
Supramolecule #1: gamma-Tubulin Small Complex

SupramoleculeName: gamma-Tubulin Small Complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Candida albicans gamma-Tubulin Small Complex expressed and purified from SF21 cells
Source (natural)Organism: Candida albicans (yeast)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
Molecular weightTheoretical: 306.7 KDa

-
Macromolecule #1: Tubulin gamma chain

MacromoleculeName: Tubulin gamma chain / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Candida albicans (yeast)
Molecular weightTheoretical: 56.532543 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MPGETITLQV GQCGNQVGLQ YWQQLATEHG IQSDGSSTPY PKDINDLQLQ ELNNSGSSPQ SYPQQTKPNG KYRNDHPELF FTLSDSNTY TPRSILIDME PSVIAKSTSA LPMFNPRNVH LSNQGNGAAN NWINGYKYGT EEEETLLNLI DREVDKCDNL S NFQLFHSV ...String:
MPGETITLQV GQCGNQVGLQ YWQQLATEHG IQSDGSSTPY PKDINDLQLQ ELNNSGSSPQ SYPQQTKPNG KYRNDHPELF FTLSDSNTY TPRSILIDME PSVIAKSTSA LPMFNPRNVH LSNQGNGAAN NWINGYKYGT EEEETLLNLI DREVDKCDNL S NFQLFHSV AGGTGSGVGS KMLEVISDRY GHKKLLNTFS IFPSNEDTSD VVVQPYNTIL TLKRLIDYSD ATFVFHNDSL NR IENILFN NNSNIQHDDN DLFLGANKLI ALVSASVSNP LRFPGYMYSS MESIVSNLIP TPDLKFLTSS IAPFSTQKHN YLN EYDMLL ELSNDRYKTN RVGGDTSYIS MLNYLIGYNL DQREIRKGIL KSQQRISFVP WVARSVLVVH GKKSPYLKNT NLEG IQVTN NTSMIDVFTK ILKQFDLLIK RKAYLNRYYS SVEEENEVME MFNESRESVK SIIDEYKACK EITYLDDDDE DDLED GDGG GGGNGNGYNN IDDADMGI

-
Macromolecule #2: Spindle pole body component

MacromoleculeName: Spindle pole body component / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Candida albicans (yeast)
Molecular weightTheoretical: 101.660453 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MNTFSSPPNV IREYNDSTYQ SPLNSQFHQS PFLQTQSPDY VSLREEEDDN NDKNLDIMSS CIVDSVIYKS QKIAGPLLSQ ISNLNIQQA LIIRELLFTL LGHEGHYIQY SKRYDPTSQI SRIEGPDYKI AKNLDISLKV ITKKLVKFGK FYSGLKSFIQ V FDNNKFGK ...String:
MNTFSSPPNV IREYNDSTYQ SPLNSQFHQS PFLQTQSPDY VSLREEEDDN NDKNLDIMSS CIVDSVIYKS QKIAGPLLSQ ISNLNIQQA LIIRELLFTL LGHEGHYIQY SKRYDPTSQI SRIEGPDYKI AKNLDISLKV ITKKLVKFGK FYSGLKSFIQ V FDNNKFGK IVQKFCSEVR KFLSSYQQVL INVEHEFKFN KNFNLNMLDS LLHQEISNEM THLYQIGIEI SRITEERQKM SQ AEIMGNF EPTTLANTSM NGINSEPNLY YGKFDCCKGG LLLQVIQERM VYYKGDPTSL DFLTQLFDIV SSDYIGMLNQ WLL EGVIND PFDEFMIREK RVPDSFMEIF QSKSEYYWNE LFLIKIDGLL NQFQNSTIQS KILNTGKYLN IFKRCTGLHN FESL KEKLT TITSLAAPDL ELKIDEFYHR ANKMLMKLLF DGYNFPSVVN IFQRLFLFAD SFQIDNFIDS TFSELKRGKL KISVS RLQK QYDDIFKEKI ENKVGVRPSV YDVLKKNQKL SVTSESLYKV VEELMEKNSD YLISDNNLRG IFHRVASLRD DSRLTI SST ADSATENVKD EPTITSVDLT IPLPFPLNLV LNQQLSYQYE IMFKLLINIK FISKYNSSNW QEMNYSKIWT NSHFNSS VK KWILRCRVLH SRICSFIHEL ENYIVHDVIE HNFEEIKNLI HTTATNLATS ELGSDINDEG DNIFNGSLIR GTFNNNSI F DSKVHKHRTT TYVEGISTVE QLIQKFLDYS STLLNDSLLT REESLRQLRK MLDFIFHFNN YIVQVKKVLV LLNHELFNE YSKEFPTKFE KPMDQESIDK RFANLSDTFL MQYEKFGENL VTFLATIKQV GERENQGLLE LSNRLELCFP E

-
Macromolecule #3: Spindle pole body component

MacromoleculeName: Spindle pole body component / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Candida albicans (yeast)
Molecular weightTheoretical: 92.29618 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MALNKVQLIK LYSNRLVKSL VPVEFGEAFI QSIINDLQTT LLNTSSEEQN LSIIINKLKM QFLSNNLKNE WVEFQNIVNS LSKFKSLDQ ICNYLAFLDA LRDEKPEDIL STSTASLSPG KQNLMINTVN TALTLSQLIE PYYDTLSEQT ILTYLPYTML G SDSKIFTF ...String:
MALNKVQLIK LYSNRLVKSL VPVEFGEAFI QSIINDLQTT LLNTSSEEQN LSIIINKLKM QFLSNNLKNE WVEFQNIVNS LSKFKSLDQ ICNYLAFLDA LRDEKPEDIL STSTASLSPG KQNLMINTVN TALTLSQLIE PYYDTLSEQT ILTYLPYTML G SDSKIFTF SNNYTRLEIP KDINNSFSSL LREVFEFAIL YKQLAIVVDR YKGTLVSAIK TAYIAILEAQ LNKYVNDINN IF NNKPNSI LVVYNSIFPW ISILRFLYRV SNRLNRLDGY EFLTFIYSFT NHGDPKIRGI AVTAFTEVVK PYYNIVEHWI VKG ELIDNN NEFFIIFDQE QNEFNSIIKL LPKKIPAFIK SSDKIFQIGK TLIFLNKYCR ELKWVNQYNV KYSAILFNNH QGLA SMTTN EMIKLIDSQY NEILTFLTQI IQGNNKLFTH VYNFKRFYFM ETNDFIDAIM VKGKDVFNES SVNISSTYLR KVLQD AIQI SSVKNFEYVD RLDSRVLNPQ HGNLGWESFT IEYKIDDLPM SYLFEGHQHL QYLKMFHFLW KLRQLNNLLN WHFEMF NEL NHNVVTKLSS RNRRPLAKSL SIITSIRFHF TQFLNELIAY LSYDVIEENF QQHIVRKLFY NKNDQDLLLN KSFMNLS EI DPNNDLPKFN VNLLTIDELV ELHGTYIDSI INSSLLNEKL KGNETNISYI DQIFNILQTI FNFINTSQEF YSLVVTFG L LVRSDSNANK IELEQDQEDL EFQLHKIKRK IYKDIYQHDY KRQLNDLKND LNRDYNLKDL SKLL

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
Component:
ConcentrationFormulaName
50.0 mMC4H11NO3Tris
NaClSodium chlorideSodium Chloride
0.5 mMC14H24N2O10EGTA
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: OTHER / Details: Gatan Solarus 950 plasma cleaner
VitrificationCryogen name: ETHANE / Chamber humidity: 75 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3838 pixel / Number grids imaged: 2 / Number real images: 1399 / Average electron dose: 2.1 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 1860000
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: EMDB MAP
EMDB ID:

2799


Details: two spokes segmented from the EMD-2799
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) / Software - details: Beta version
Final 3D classificationSoftware - Name: RELION (ver. 3.0) / Software - details: Beta version
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) / Software - details: Beta version
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Software - details: Beta version / Number images used: 274326

-
Atomic model buiding 1

Initial model(PDB ID:

3rip

,

1z5w

)
Output model

PDB-7anz:
Structure of the Candida albicans gamma-Tubulin Small Complex

+
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