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- EMDB-51008: Structure of the Position 4 to 11 Open gamma-Tubulin Ring Complex... -

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Basic information

Entry
Database: EMDB / ID: EMD-51008
TitleStructure of the Position 4 to 11 Open gamma-Tubulin Ring Complex from Pig Brain
Map data
Sample
  • Complex: Gamma-Tubulin Ring Complex from native pig brain
    • Protein or peptide: Structure of the Position 3 to 11 Open gamma-Tubulin Ring Complex from Pig Brain
KeywordsTubulin Complex / STRUCTURAL PROTEIN
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.37 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_51008.png

Downloads & links

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Map

FileDownload / File: emd_51008.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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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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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4133 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.005
Minimum - Maximum-0.00986188 - 0.034393333
Average (Standard dev.)-0.00008805651 (±0.0011714789)
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_51008_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_51008_half_map_2.map
Projections & Slices
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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
    • Protein or peptide: Structure of the Position 3 to 11 Open gamma-Tubulin Ring Complex from 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: all
Source (natural)Organism: Sus scrofa (pig)

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Macromolecule #1: Structure of the Position 3 to 11 Open gamma-Tubulin Ring Complex...

MacromoleculeName: Structure of the Position 3 to 11 Open gamma-Tubulin Ring Complex from Pig Brain
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Sus scrofa (pig)
SequenceString: MPREIITLQL GQCGNQIGFE FWKQLCAEHG ISPEGIVEEF ATEGTDRKDV FFYQADDEHY IPRAVLLDLE PRVIHSILNS PYAKLYNPEN IYLSEHGGGA GNNWASGFSQ GEKIHEDIFD IIDREADGSD SLEGFVLCHS IAGGTGSGLG SYLLERLNDR YPKKLVQTYS ...String:
MPREIITLQL GQCGNQIGFE FWKQLCAEHG ISPEGIVEEF ATEGTDRKDV FFYQADDEHY IPRAVLLDLE PRVIHSILNS PYAKLYNPEN IYLSEHGGGA GNNWASGFSQ GEKIHEDIFD IIDREADGSD SLEGFVLCHS IAGGTGSGLG SYLLERLNDR YPKKLVQTYS VFPNQDEMSD VVVQPYNSLL TLKRLTQNAD CVVVLDNTAL NRIATDRLHI QNPSFSQINQ LVSTIMSAST TTLRYPGYMN NDLIGLIASL IPTPRLHFLM TGYTPLTTDQ SVASVRKTTV LDVMRRLLQP KNVMVSTGRD RQTNHCYIAI LNIIQGEVDP TQVHKSLQRI RERKLANFIP WGPASIQVAL SRKSPYLPSA HRVSGLMMAN HTSISSLFES SCQQYDKLRK REAFLEQFRK EDIFKENFDE LDRSREVVQE LIDEYHAATR PDYISWGTQE Q

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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: 4.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 172015
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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