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- PDB-9i8m: NEDD1-bound native vertebrate gamma-tubulin ring complex from Xen... -

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Basic information

Entry
Database: PDB / ID: 9i8m
TitleNEDD1-bound native vertebrate gamma-tubulin ring complex from Xenopus laevis, focused reconstruction
Components
  • (Gamma-tubulin complex ...) x 5
  • Mitotic-spindle organizing protein 1
  • NEDD1 gamma-tubulin ring complex targeting factor L homeolog
KeywordsCELL CYCLE / cytoskeleton / microtubule / microtubule nucleation / complex / template / cap / gamma-tubulin / gamma-tubulin ring complex / nedd1 / neural precursor cell-expressed developmentally down-regulated 1
Function / homology
Function and homology information


microtubule nucleation by interphase microtubule organizing center / microtubule minus-end binding / gamma-tubulin complex localization / interphase microtubule organizing center / gamma-tubulin complex / gamma-tubulin ring complex / microtubule nucleation / gamma-tubulin binding / mitotic spindle assembly / spindle assembly ...microtubule nucleation by interphase microtubule organizing center / microtubule minus-end binding / gamma-tubulin complex localization / interphase microtubule organizing center / gamma-tubulin complex / gamma-tubulin ring complex / microtubule nucleation / gamma-tubulin binding / mitotic spindle assembly / spindle assembly / cytoplasmic microtubule organization / centriole / meiotic cell cycle / spindle / spindle pole / mitotic cell cycle / microtubule / ciliary basal body / centrosome / cytoplasm
Similarity search - Function
: / Mitotic-spindle organizing protein 1 / Mitotic-spindle organizing gamma-tubulin ring associated / Gamma-tubulin complex component 6, N-terminal / Gamma-tubulin complex component 6 N-terminus / 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 ...: / Mitotic-spindle organizing protein 1 / Mitotic-spindle organizing gamma-tubulin ring associated / Gamma-tubulin complex component 6, N-terminal / Gamma-tubulin complex component 6 N-terminus / 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 / Anaphase-promoting complex subunit 4, WD40 domain / Anaphase-promoting complex subunit 4 WD40 domain / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
Gamma-tubulin complex component / Protein NEDD1 / Gamma-tubulin complex component / Gamma-tubulin complex component 6 / Gamma-tubulin complex component 3 homolog / Mitotic-spindle organizing protein 1 / Gamma-tubulin complex component
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.3 Å
AuthorsVermeulen, B.J.A. / Pfeffer, S.
Funding support Germany, 7items
OrganizationGrant numberCountry
German Research Foundation (DFG)DFG Schi 295/4-4 Germany
German Research Foundation (DFG)DFG Schi 295/11-1 Germany
German Research Foundation (DFG)DFG PF 963/1-4 Germany
German Research Foundation (DFG)DFG PF 963/4-1 Germany
German Research Foundation (DFG)INST 35/1314-1 FUGG Germany
German Research Foundation (DFG)INST 35/1503-1 FUGG Germany
German Research Foundation (DFG)INST 35/1134-1 FUGG Germany
CitationJournal: Nat Commun / Year: 2025
Title: Structural mechanisms for centrosomal recruitment and organization of the microtubule nucleator γ-TuRC.
Authors: Qi Gao / Florian W Hofer / Sebastian Filbeck / Bram J A Vermeulen / Martin Würtz / Annett Neuner / Charlotte Kaplan / Maja Zezlina / Cornelia Sala / Hyesu Shin / Oliver J Gruss / Elmar ...Authors: Qi Gao / Florian W Hofer / Sebastian Filbeck / Bram J A Vermeulen / Martin Würtz / Annett Neuner / Charlotte Kaplan / Maja Zezlina / Cornelia Sala / Hyesu Shin / Oliver J Gruss / Elmar Schiebel / Stefan Pfeffer /
Abstract: The γ-tubulin ring complex (γ-TuRC) acts as a structural template for microtubule formation at centrosomes, associating with two main compartments: the pericentriolar material and the centriole ...The γ-tubulin ring complex (γ-TuRC) acts as a structural template for microtubule formation at centrosomes, associating with two main compartments: the pericentriolar material and the centriole lumen. In the pericentriolar material, the γ-TuRC is involved in microtubule organization, while the function of the centriole lumenal pool remains unclear. The conformational landscape of the γ-TuRC, which is crucial for its activity, and its centrosomal anchoring mechanisms, which determine γ-TuRC activity and turnover, are not understood. Using cryo-electron tomography, we analyze γ-TuRCs in human cells and purified centrosomes. Pericentriolar γ-TuRCs simultaneously associate with the essential adapter NEDD1 and the microcephaly protein CDK5RAP2. NEDD1 forms a tetrameric structure at the γ-TuRC base through interactions with four GCP3/MZT1 modules and GCP5/6-specific extensions, while multiple copies of CDK5RAP2 engage the γ-TuRC in two distinct binding patterns to promote γ-TuRC closure and activation. In the centriole lumen, the microtubule branching factor Augmin tethers a condensed cluster of γ-TuRCs to the centriole wall with defined directional orientation. Centriole-lumenal γ-TuRC-Augmin is protected from degradation during interphase and released in mitosis to aid chromosome alignment. This study provides a unique view on γ-TuRC structure and molecular organization at centrosomes and identifies an important cellular function of centriole-lumenal γ-TuRCs.
History
DepositionFeb 5, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 19, 2025Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 19, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
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Revision 1.1Mar 26, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _em_admin.last_update
Revision 1.2Jul 9, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 9, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Gamma-tubulin complex component
B: Gamma-tubulin complex component 3 homolog
C: Gamma-tubulin complex component
D: Gamma-tubulin complex component 3 homolog
E: Gamma-tubulin complex component
F: Gamma-tubulin complex component 3 homolog
G: Gamma-tubulin complex component
H: Gamma-tubulin complex component 3 homolog
I: Gamma-tubulin complex component
J: Gamma-tubulin complex component
K: Gamma-tubulin complex component
L: Gamma-tubulin complex component 6
O: Gamma-tubulin complex component 3 homolog
Q: Gamma-tubulin complex component 3 homolog
R: Gamma-tubulin complex component 3 homolog
S: Gamma-tubulin complex component 3 homolog
T: Gamma-tubulin complex component 3 homolog
U: NEDD1 gamma-tubulin ring complex targeting factor L homeolog
V: NEDD1 gamma-tubulin ring complex targeting factor L homeolog
W: NEDD1 gamma-tubulin ring complex targeting factor L homeolog
X: NEDD1 gamma-tubulin ring complex targeting factor L homeolog
o: Mitotic-spindle organizing protein 1
p: Mitotic-spindle organizing protein 1
q: Mitotic-spindle organizing protein 1
r: Mitotic-spindle organizing protein 1
s: Mitotic-spindle organizing protein 1
t: Mitotic-spindle organizing protein 1


Theoretical massNumber of molelcules
Total (without water)2,150,23027
Polymers2,150,23027
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

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Gamma-tubulin complex ... , 5 types, 17 molecules ACEGBDFHOQRSTIKJL

#1: Protein
Gamma-tubulin complex component


Mass: 103468.312 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A8J0T6B8
#2: Protein
Gamma-tubulin complex component 3 homolog / Gamma-ring complex protein 109 / Xgrip109 / x109p


Mass: 103789.352 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: O73787
#3: Protein Gamma-tubulin complex component


Mass: 76122.961 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q642S3
#4: Protein Gamma-tubulin complex component


Mass: 117577.633 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A1L8HGZ5
#5: Protein Gamma-tubulin complex component 6


Mass: 193069.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A974HT83

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Protein , 2 types, 10 molecules UVWXopqrst

#6: Protein
NEDD1 gamma-tubulin ring complex targeting factor L homeolog


Mass: 73215.234 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: A0A8J0Q0Y8
#7: Protein
Mitotic-spindle organizing protein 1 / Mitotic-spindle organizing protein associated with a ring of gamma-tubulin 1


Mass: 7749.854 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) Xenopus laevis (African clawed frog) / References: UniProt: Q5U4M5

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Details

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: Tetramer of NEDD1 bound to the gamma-tubulin ring complex
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 51 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 299022 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.03638069
ELECTRON MICROSCOPYf_angle_d3.47851416
ELECTRON MICROSCOPYf_dihedral_angle_d19.32823091
ELECTRON MICROSCOPYf_chiral_restr0.2175874
ELECTRON MICROSCOPYf_plane_restr0.0256522

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