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- EMDB-21069: Desnity map of lumenal bridge in reconstruction of the native hum... -

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Basic information

Entry
Database: EMDB / ID: EMD-21069
TitleDesnity map of lumenal bridge in reconstruction of the native human gamma-tubulin ring complex
Map data
Sample
  • Complex: Native human gamma-tubulin ring complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWieczorek M / Urnavicius L / Ti S / Molloy KR / Chait BT / Kapoor TM
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesR35 GM130234 United States
Human Frontier Science ProgramLT000025/18-L1 United States
CitationJournal: Cell / Year: 2020
Title: Asymmetric Molecular Architecture of the Human γ-Tubulin Ring Complex.
Authors: Michal Wieczorek / Linas Urnavicius / Shih-Chieh Ti / Kelly R Molloy / Brian T Chait / Tarun M Kapoor /
Abstract: The γ-tubulin ring complex (γ-TuRC) is an essential regulator of centrosomal and acentrosomal microtubule formation, yet its structure is not known. Here, we present a cryo-EM reconstruction of the ...The γ-tubulin ring complex (γ-TuRC) is an essential regulator of centrosomal and acentrosomal microtubule formation, yet its structure is not known. Here, we present a cryo-EM reconstruction of the native human γ-TuRC at ∼3.8 Å resolution, revealing an asymmetric, cone-shaped structure. Pseudo-atomic models indicate that GCP4, GCP5, and GCP6 form distinct Y-shaped assemblies that structurally mimic GCP2/GCP3 subcomplexes distal to the γ-TuRC "seam." We also identify an unanticipated structural bridge that includes an actin-like protein and spans the γ-TuRC lumen. Despite its asymmetric architecture, the γ-TuRC arranges γ-tubulins into a helical geometry poised to nucleate microtubules. Diversity in the γ-TuRC subunits introduces large (>100,000 Å) surfaces in the complex that allow for interactions with different regulatory factors. The observed compositional complexity of the γ-TuRC could self-regulate its assembly into a cone-shaped structure to control microtubule formation across diverse contexts, e.g., within biological condensates or alongside existing filaments.
History
DepositionDec 4, 2019-
Header (metadata) releaseDec 18, 2019-
Map releaseJan 1, 2020-
UpdateJan 22, 2020-
Current statusJan 22, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0198
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0198
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21069.png

Downloads & links

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Map

FileDownload / File: emd_21069.map.gz / Format: CCP4 / Size: 190.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 368 pix.
= 491.28 Å		1.34 Å/pix.
x 368 pix.
= 491.28 Å		1.34 Å/pix.
x 368 pix.
= 491.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.335 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0198 / Movie #1: 0.0198
Minimum - Maximum-0.06930334 - 0.12975727
Average (Standard dev.)0.0000968121 (±0.0017707656)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions368368368
Spacing368368368
CellA=B=C: 491.28003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3351.3351.335
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z491.280491.280491.280
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS368368368
D min/max/mean-0.0690.1300.000

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Supplemental data

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Sample components

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Entire : Native human gamma-tubulin ring complex

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

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Supramolecule #1: Native human gamma-tubulin ring complex

SupramoleculeName: Native human gamma-tubulin ring complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Relion 3.0 initial model generation
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 307228
Initial angle assignmentType: OTHER / Details: Relion 3.0
Final angle assignmentType: OTHER / Details: Relion 3.0

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