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- EMDB-51016: Consensus cryo-EM reconstruction of the S. scrofa gamma-TuRC -

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Basic information

Entry
Database: EMDB / ID: EMD-51016
TitleConsensus cryo-EM reconstruction of the S. scrofa gamma-TuRC
Map data
Sample
  • Complex: Gamma-Tubulin Ring Complex from native pig brain
KeywordsTubulin Complex / STRUCTURAL PROTEIN
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsMunoz-Hernandez H / Wieczorek M
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
Swiss National Science FoundationTMSGI3_211309 Switzerland
Swiss National Science Foundation310030_208120 Switzerland
CitationJournal: Dev Cell / Year: 2024
Title: Partial closure of the γ-tubulin ring complex by CDK5RAP2 activates microtubule nucleation.
Authors: Yixin Xu / Hugo Muñoz-Hernández / Rościsław Krutyhołowa / Florina Marxer / Ferdane Cetin / Michal Wieczorek /
Abstract: Microtubule nucleation is templated by the γ-tubulin ring complex (γ-TuRC), but its structure deviates from the geometry of α-/β-tubulin in the microtubule, explaining the complex's poor ...Microtubule nucleation is templated by the γ-tubulin ring complex (γ-TuRC), but its structure deviates from the geometry of α-/β-tubulin in the microtubule, explaining the complex's poor nucleating activity. Several proteins may activate the γ-TuRC, but the mechanisms underlying activation are not known. Here, we determined the structure of the porcine γ-TuRC purified using CDK5RAP2's centrosomin motif 1 (CM1). We identified an unexpected conformation of the γ-TuRC bound to multiple protein modules containing MZT2, GCP2, and CDK5RAP2, resulting in a long-range constriction of the γ-tubulin ring that brings it in closer agreement with the 13-protofilament microtubule. Additional CDK5RAP2 promoted γ-TuRC decoration and stimulated the microtubule-nucleating activities of the porcine γ-TuRC and a reconstituted, CM1-free human complex in single-molecule assays. Our results provide a structural mechanism for the control of microtubule nucleation by CM1 proteins and identify conformational transitions in the γ-TuRC that prime it for microtubule nucleation.
History
DepositionJul 12, 2024-
Header (metadata) releaseOct 9, 2024-
Map releaseOct 9, 2024-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51016.png

Downloads & links

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Map

FileDownload / File: emd_51016.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.41 Å/pix.
x 384 pix.
= 542.707 Å		1.41 Å/pix.
x 384 pix.
= 542.707 Å		1.41 Å/pix.
x 384 pix.
= 542.707 Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4133 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.008226908 - 0.030569505
Average (Standard dev.)0.000072098235 (±0.0009851144)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 542.7072 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_51016_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_51016_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Gamma-Tubulin Ring Complex from native pig brain

EntireName: Gamma-Tubulin Ring Complex from native pig brain
Components
  • Complex: Gamma-Tubulin Ring Complex from native pig brain

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Supramolecule #1: Gamma-Tubulin Ring Complex from native pig brain

SupramoleculeName: Gamma-Tubulin Ring Complex from native pig brain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#24
Source (natural)Organism: Sus scrofa (pig)

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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: 7.5
GridModel: Quantifoil R2/1 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.9 µm / Nominal defocus min: 0.9 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 494171
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE

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