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The microtubule nucleating gamma-tubulin small complex assembles into a structure with microtubule-like thirteen fold symmetry

by helical reconstruction, at 8 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 2.5, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 2.5, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1731
AuthorsKollman JM, Polka JK, Zelter A, Davis TN, Agard DA
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 2.5, Made by UCSF CHIMERA

#2: Surface view colored by cylindrical radius, Surface level: 2.5, Made by UCSF CHIMERA

Supplemental images

emd-1731.jpg
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)

Diagram

PDB-2ymf

EMDB-1703

EMDB-1617
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleNature, Vol. 466, Issue 7308, Page 879-82, Year 2010
TitleMicrotubule nucleating gamma-TuSC assembles structures with 13-fold microtubule-like symmetry.
AuthorsJustin M Kollman, Jessica K Polka, Alex Zelter, Trisha N Davis, David A Agard
Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, and Keck Advanced Microscopy Center, University of California, San Francisco, San Francisco, California 94158, USA.
KeywordsBuffers, Cryoelectron Microscopy, Cytoskeletal Proteins (chemistry), Microtubule-Associated Proteins (chemistry), Microtubules (chemistry), Models, Biological, Models, Molecular, Multiprotein Complexes (chemistry), Nuclear Proteins (chemistry), SPC110 protein, S cerevisiae, SPC97 protein, S cerevisiae, SPC98 protein, S cerevisiae, Saccharomyces cerevisiae (chemistry), Saccharomyces cerevisiae Proteins (chemistry), Tubulin (chemistry)
LinksDOI: 10.1038/nature09207, PubMed: 20631709, PMC: PMC2921000
Map
FileEMD-1731.map ( map file in CCP4 format, 131074 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)
Contour Level:2.5 (by author), 2.5 (movie #1):
Minimum - Maximum: -3.00519 - 6.27779
Average (Standard dev.): 1.00001 (0.999949)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 320 320 320
Origin : 0 0 0
Limit : 319 319 319
Spacing : 320 320 320
Unit CellA = 380.8 A , B = 380.8 A , C = 380.8 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 1.19 A , Y = 1.19 A , Z = 1.19 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.191.191.19
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z380.800380.800380.800
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-100-100-100
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-3.0056.2781.000
Annotation DetailsThis is the map of the gamma-tubulin small complex - Spc110p filament. The filament axis is along the Z axis.
Supplement
Images
Images

emd-1731.jpg
Sample
NameGamma-tubulin small complex in complex with Spc110p(1-220)
Number of Components4
DetailsThe stoichiometry of gamma-TuSC to Spc110p is not known.
Component #1: protein - gamma-tubulin
Scientific nameTub4p
Common Namegamma-tubulin
Theoretical Mass0.0526 MDa
Oligomeric DetailsHelical filament
Number of Copies2
Scientific Name of SpeciesSaccharomyces cerevisiae (NCBI Taxonomy: 4932)

Common Name of SpeciesBaker's yeast
Recombinant expressionYes
Natural SourceCell Location: Spindle pole body
Engineered SourceVector: pAZ37
Exp System: Spodoptera frugiperda (baculovirus infected)
LinksInterPro: IPR:002454
Component #2: protein - Spindle pole body component p97
Scientific nameSpc97p
Common NameSpindle pole body component p97
Theoretical Mass0.0968 MDa
Oligomeric DetailsHelical filament
Number of Copies1
Scientific Name of SpeciesSaccharomyces cerevisiae (NCBI Taxonomy: 4932)
Common Name of SpeciesBaker'syeast
Recombinant expressionYes
Natural SourceCell Location: Spindle pole body
Engineered SourceExp System: Spodoptera frugiperda (baculovirus infected)
Vector: pDV45
LinksInterPro: IPR:015698
Component #3: protein - Spindle pole body component 98p
Scientific nameSpc98p
Common NameSpindle pole body component 98p
Theoretical Mass98.3 MDa
Oligomeric DetailsHelical filament
Number of Copies1
Scientific Name of SpeciesSaccharomyces cerevisiae (NCBI Taxonomy: 4932)
Common Name of SpeciesBaker's yeast
Recombinant expressionYes
Natural SourceCell Location: Spindle pole body
Engineered SourceVector: pDV46
Exp System: Spodoptera frugiperda (baculovirus infected)
LinksInterPro: IPR:015696
Component #4: protein - Spc110p
Scientific nameSpc110p
Theoretical Mass0.023 MDa
DetailsConstruct includes the first 220 residues of Spc110p
Oligomeric DetailsHelical filament
Number of Copies1
Scientific Name of SpeciesSaccharomyces cerevisiae (NCBI Taxonomy: 4932)
Common Name of SpeciesBaker's yeast
Recombinant expressionYes
Natural SourceCell Location: Spindle pole body
Engineered SourceVector: pAZ34
Exp System: Spodoptera frugiperda (baculovirus infected)
Experiment
Sample Preparation
Helical ParametersDelta Z: 22.2 A
Delta Phi: 54.3 degrees
Hand: LEFT HANDED
StainingSample was applied to C-FLAT holey carbon grids, blotted, and flash frozen in liquid ethane
Specimen Conc2 mg/ml
Specimen Support Details200 mesh copper grid
Specimen Statefilament
BufferpH: 7.6
Details: 100 mM KCl, 1mM GTP, 1mM MgCl2, 2mM EGTA, 40 mM Hepes
Vitrification
MethodBlotted 3s before plunging
Cryogen NameETHANE
DetailsVitrification instrument: Vitrobot
Humidity100
InstrumentFEI VITROBOT
Imaging
MicroscopeFEI TECNAI F20
Date23-SEP-2009
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 60000 X,
AstigmatismAstigmatism corrected at 250,000 times magnification
Nominal Cs2.2 mm
Imaging ModeBRIGHT FIELD
Defocus800 nm - 3000 nm
Specimen Holder
HolderOxford side-entry cryo stage ( OTHER )
Camera
DetectorTVIPS TemCam-F816
Image Acquisition
Processing
Methodhelical reconstruction
3 D reconstruction
AlgorithmIterative helical real space reconstruction
Euler Angles DetailsSPIDER:theta 90 degrees, phi 90 degrees
SoftwareSpider
CTF CorrectionWhole micrograph
Resolution By Author8
Resolution MethodFSC 0.5 cutoff
Download
Data from EMDB
Header (meta data in XML format)emd-1731.xml (10.8 KB)
Map dataemd_1731.map.gz (110.5 MB)
Imagesemd-1731.jpg (193.8 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1731
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 26.1 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.7 MB
Session file for UCSF-Chimera, 26.1 KB