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- EMDB-55044: CM1-activated gTuRC in complex with nascent wildtype microtubules -

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Basic information

Entry
Database: EMDB / ID: EMD-55044
TitleCM1-activated gTuRC in complex with nascent wildtype microtubules
Map dataConsensus refinement map
Sample
  • Complex: gamma-tubulin ring complex
KeywordsMicrotubule / cytoskeleton / g-tubulin ring complex / tubulin / STRUCTURAL PROTEIN / CDK5RAP2 / CM1 / nucleation
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.62 Å
AuthorsLlorca O / Serna M / Lopez-Perrote A
Funding support Spain, European Union, 2 items
OrganizationGrant numberCountry
Agencia Estatal de Investigacion (AEI)MCIN/AEI/10.13039/501100011033 Spain
European Regional Development FundPID2023-146110NB-I00European Union
CitationJournal: Nat Commun / Year: 2026
Title: Structural basis of human γTuRC closure during CM1-activated microtubule nucleation.
Authors: Marina Serna / Cláudia Brito / Silvia Speroni / Fabian Zimmermann / Andrés Lopez-Perrote / Maria Gili / Cristina Lacasa / Jens Lüders / Thomas Surrey / Oscar Llorca /
Abstract: Microtubule nucleation by the γ-tubulin ring complex (γTuRC) is spatiotemporally regulated and in higher eukaryotes is thought to involve a transition from an inactive open to an active closed ...Microtubule nucleation by the γ-tubulin ring complex (γTuRC) is spatiotemporally regulated and in higher eukaryotes is thought to involve a transition from an inactive open to an active closed conformation that matches the microtubule geometry. However, γTuRC activators only promote a partially closed conformation, raising the question of whether complete closure is required for activation. Combining in vitro nucleation assays and cryo-EM, we find that centrosomin motif 1 (CM1), a conserved element of several γTuRC regulators, potently accelerates human γTuRC-mediated microtubule nucleation by facilitating complete closure of γTuRC as the nascent microtubule assembles. A 3.7 Å cryo-EM structure identifies the γTuRC latch and several interactions involved in conformational closure. Notably, the distinct subunits that keep γTuRC open and inactive in higher eukaryotes also participate in its closure and activation. This work provides additional insight into the logic of the human γTuRC architecture and its activation by CM1.
History
DepositionSep 9, 2025-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_55044.png

Downloads & links

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Map

FileDownload / File: emd_55044.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationConsensus refinement map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.11 Å/pix.
x 224 pix.
= 472.64 Å		2.11 Å/pix.
x 224 pix.
= 472.64 Å		2.11 Å/pix.
x 224 pix.
= 472.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.007
Minimum - Maximum-0.018799473 - 0.04259582
Average (Standard dev.)0.00052730134 (±0.0033861827)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 472.63998 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_55044_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Consensus map sharpened using deepEMhancer

Fileemd_55044_additional_1.map
AnnotationConsensus map sharpened using deepEMhancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened consensus map

Fileemd_55044_additional_2.map
AnnotationSharpened consensus map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half 2 map of the consensus refinement

Fileemd_55044_half_map_1.map
AnnotationHalf 2 map of the consensus refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half 1 map of the consensus refinement

Fileemd_55044_half_map_2.map
AnnotationHalf 1 map of the consensus refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : gamma-tubulin ring complex

EntireName: gamma-tubulin ring complex
Components
  • Complex: gamma-tubulin ring complex

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Supramolecule #1: gamma-tubulin ring complex

SupramoleculeName: gamma-tubulin ring complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #2-#3, #1, #5
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6.9
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR / Details: 15 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 310 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: EPU
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 9011 / Average electron dose: 40.3 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: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 494718
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL / In silico model: CryoSPARC Ab Initio Reconstruction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.62 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5.0) / Number images used: 22226
Initial angle assignmentType: ANGULAR RECONSTITUTION / Software: (Name: cryoSPARC (ver. 4.7.0), RELION (ver. 5.0))
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 5.0)
Final 3D classificationSoftware: (Name: RELION (ver. 5.0), cryoSPARC (ver. 4.7.0), cryoDRGN2)
Details: Several 3D classification and heterogeneity analysis methods
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

7as4

source_name: PDB, initial_model_type: experimental model

6x0u

source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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