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- PDB-9h9r: Full gamma-tubulin ring complex composed of the Candida albicans ... -

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Basic information

Entry
Database: PDB / ID: 9h9r
TitleFull gamma-tubulin ring complex composed of the Candida albicans gamma-tubulin small complex in complex with Spc72 CM1
Components
  • Mto2p-binding domain-containing protein
  • Spc98p
  • Spindle pole body component
  • Tubulin gamma chain
KeywordsCELL CYCLE / cytoskeleton / microtubule / microtubule nucleation / complex / template / cap / gamma-tubulin / gamma-tubulin ring complex / gamma-tubulin small complex / Spc72 / CM1 / CM1 motif / GCP2 / GCP3 / Spc97 / Spc98 / Candida / albicans / gamma-TuRC / gamma-TuSC / yeast / fungi
Function / homology
Function and homology information


gamma-tubulin complex / microtubule nucleation / gamma-tubulin binding / spindle pole body / spindle assembly / cytoplasmic microtubule organization / meiotic cell cycle / spindle pole / mitotic cell cycle / microtubule ...gamma-tubulin complex / microtubule nucleation / gamma-tubulin binding / spindle pole body / spindle assembly / cytoplasmic microtubule organization / meiotic cell cycle / spindle pole / mitotic cell cycle / microtubule / 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 / Mto2p-binding domain-containing protein
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.2 Å
AuthorsVermeulen, B.J.A. / Pfeffer, S.
Funding support Germany, 6items
OrganizationGrant numberCountry
German Research Foundation (DFG)Schi 295/4-4 Germany
German Research Foundation (DFG)PF 963/1-4 Germany
German Research Foundation (DFG)PF 963/4-1 Germany
Other private
German Research Foundation (DFG)INST 35/1314-1 FUGG Germany
German Research Foundation (DFG)INST 35/1134-1 FUGG Germany
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into the interplay between microtubule polymerases, γ-tubulin complexes and their receptors.
Authors: Anjun Zheng / Bram J A Vermeulen / Martin Würtz / Annett Neuner / Nicole Lübbehusen / Matthias P Mayer / Elmar Schiebel / Stefan Pfeffer /
Abstract: The γ-tubulin ring complex (γ-TuRC) is a structural template for controlled nucleation of microtubules from α/β-tubulin heterodimers. At the cytoplasmic side of the yeast spindle pole body, the ...The γ-tubulin ring complex (γ-TuRC) is a structural template for controlled nucleation of microtubules from α/β-tubulin heterodimers. At the cytoplasmic side of the yeast spindle pole body, the CM1-containing receptor protein Spc72 promotes γ-TuRC assembly from seven γ-tubulin small complexes (γ-TuSCs) and recruits the microtubule polymerase Stu2, yet their molecular interplay remains unclear. Here, we determine the cryo-EM structure of the Candida albicans cytoplasmic nucleation unit at 3.6 Å resolution, revealing how the γ-TuRC is assembled and conformationally primed for microtubule nucleation by the dimerised Spc72 CM1 motif. Two coiled-coil regions of Spc72 interact with the conserved C-terminal α-helix of Stu2 and thereby position the α/β-tubulin-binding TOG domains of Stu2 in the vicinity of the microtubule assembly site. Collectively, we reveal the function of CM1 motifs in γ-TuSC oligomerisation and the recruitment of microtubule polymerases to the γ-TuRC.
History
DepositionOct 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin gamma chain
B: Tubulin gamma chain
C: Spindle pole body component
D: Spc98p
E: Mto2p-binding domain-containing protein
F: Mto2p-binding domain-containing protein
G: Tubulin gamma chain
H: Tubulin gamma chain
I: Spindle pole body component
J: Spc98p
K: Mto2p-binding domain-containing protein
L: Mto2p-binding domain-containing protein
M: Tubulin gamma chain
N: Tubulin gamma chain
O: Spindle pole body component
P: Spc98p
Q: Mto2p-binding domain-containing protein
R: Mto2p-binding domain-containing protein
S: Tubulin gamma chain
T: Tubulin gamma chain
U: Spindle pole body component
V: Spc98p
W: Mto2p-binding domain-containing protein
X: Mto2p-binding domain-containing protein
Y: Tubulin gamma chain
Z: Tubulin gamma chain
a: Spindle pole body component
b: Spc98p
c: Mto2p-binding domain-containing protein
d: Mto2p-binding domain-containing protein
e: Tubulin gamma chain
f: Tubulin gamma chain
g: Spindle pole body component
h: Spc98p
i: Mto2p-binding domain-containing protein
j: Mto2p-binding domain-containing protein
k: Tubulin gamma chain
l: Tubulin gamma chain
m: Spindle pole body component
n: Spc98p
o: Mto2p-binding domain-containing protein
p: Mto2p-binding domain-containing protein


Theoretical massNumber of molelcules
Total (without water)3,175,99042
Polymers3,175,99042
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Tubulin gamma chain


Mass: 56228.242 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: FOB64_001277 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A8H6F519
#2: Protein
Spindle pole body component


Mass: 104692.742 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: CAALFM_CR06740WA, orf19.8327 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q59PZ2
#3: Protein
Spc98p


Mass: 95318.438 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: SPC98, CAALFM_CR01990CA, orf19.10131 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A0A1D8PS42
#4: Protein
Mto2p-binding domain-containing protein


Mass: 70622.578 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candida albicans (yeast) / Gene: CAALFM_C701460CA, orf19.13936 / Cell line (production host): Sf21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5AGV5
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Full gamma-tubulin ring complex composed of the Candida albicans gamma-tubulin small complex in complex with Spc72 CM1
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Candida albicans (yeast)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm) / Cell: Sf21
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R2/1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 1000 nm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 47 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 2 / Num. of real images: 33781
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
9RELION3.1initial Euler assignment
10RELION3final Euler assignment
12RELION33D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 8.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 8261 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT

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