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Architecture of the Dam1 kinetochore ring complex and implications for microtubule-driven assembly and force-coupling mechanisms.

by single particle reconstruction, at 29 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 7.278150038, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 7.278150038, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1373
AuthorsWang H-W, Ramey VH, Westermann S, Leschziner AE, Welburn JPI, Nakajima Y, Drubin DG, Barnes G, Nogales E
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 7.278150038, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 7.278150038, Made by UCSF CHIMERA

Supplemental images

1373.gif
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

EMDB-1371
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EMDB-1372
Cite

Cite: data citing same article

Similar strucutres (beta)

Diagram

EMDB-1372

PDB-3j3c
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleNat. Struct. Mol. Biol., Vol. 14, Issue 8, Page 721-6, Year 2007
TitleArchitecture of the Dam1 kinetochore ring complex and implications for microtubule-driven assembly and force-coupling mechanisms.
AuthorsHong-Wei Wang, Vincent H Ramey, Stefan Westermann, Andres E Leschziner, Julie P I Welburn, Yuko Nakajima, David G Drubin, Georjana Barnes, Eva Nogales
Life Sciences Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd., Berkeley, California 94720, USA.
KeywordsCell Cycle Proteins (chemistry), DAM1 protein, S cerevisiae, Kinetochores (chemistry), Microtubule-Associated Proteins (chemistry), Microtubules (chemistry), Models, Molecular, Molecular Structure, Phosphorylation, Protein Structure, Tertiary, Saccharomyces cerevisiae (metabolism), Saccharomyces cerevisiae Proteins (chemistry)
LinksDOI: 10.1038/nsmb1274, PubMed: 17643123
Map
FileEMD-1373.map ( map file in CCP4 format, 8789 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:2.44, 7.27815 (movie #1):
Minimum - Maximum: -5.74718 - 30.2408
Average (Standard dev.): -0.000191472 (0.976579)
Data Typefloat (32-bit)
Space Group Number1
Map Geometry
Axis Order : X Y Z
Dimensions : 130 130 130
Origin : 0 0 0
Limit : 129 129 129
Spacing : 130 130 130
Unit CellA = 520 A , B = 520 A , C = 520 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees
Pixel SpacingX = 4 A , Y = 4 A , Z = 4 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z444
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z520.000520.000520.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS130130130
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-5.74730.241-0.000
Annotation DetailsThis is the single particle reconstruction of the DeltaC Dam1 mutant complex in its dimeric form.
Supplement
Images
Images

1373.gif
Sample
NameDam1 DeltC mutant complex
Oligomeric StateDimeric decamer
Number of Components1
Experimental Mass0.2 MDa
Theoretical Mass0.2 MDa
DetailsThe sample was mainly composed of dimers and little percentage of monomers and trimers.
Component #1: protein - Dam1 DeltC mutant complex
Scientific nameDam1 DeltC mutant complex
Theoretical Mass0.2 MDa
Experimental Mass0.2 MDa
Oligomeric Detailsdimer of decamer
Number of Copies2
Scientific Name of SpeciesSaccharomyces cerevisiae (NCBI Taxonomy: 4932)

Common Name of Speciesyeast
Recombinant expressionYes
Natural SourceCell Location: kinetochore
Engineered SourceExp System: Escherichia coli (NCBI Taxonomy: 562)
Experiment
Sample Preparation
Specimen Conc2 mg/ml
StainingThe complexes were negatively stained with 2% uranyl formate with the sandwich method between two layers of thin carbon film.
Specimen Support Details400 mesh copper grid
Specimen Stateparticle
BufferDetails: 500 mM NaCl, 20 mM sodium phosphate pH 6.8, 1 mM EDTA
pH: 6.8
Vitrification
Cryogen NameNONE
Imaging
MicroscopeFEI TECNAI 12
DetailsThe micrographs were taken at low dose mode.
Electron Gun
Electron SourceLAB6
Accelerating Voltage120 kV
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 49000 X,
Astigmatismobjective lens astigmatism was corrected at 120,000 magnification
Nominal Cs6.6 mm
Imaging ModeBRIGHT FIELD
Defocus700 nm - 1500 nm
Specimen Holder
HolderEucentric ( OTHER )
Tilt Angle0 degrees -
Camera
DetectorKodak SO163 film
Image Acquisition
Number of Digital Images200
Sampling Size12.7 microns
Od Range1.4
Quant Bit Number14
ScannerOTHER
DetailsThe micrographs were scanned on a Nikon Super Coolscan 8000 scanner
Processing
Methodsingle particle reconstruction
3 D reconstruction
AlgorithmRandom Conical Tilt and Projection Matching Refinement
SoftwareIMAGIC, SPIDER
Resolution By Author29
Resolution MethodFSC at 0.5 cut-off
Euler Angles DetailsSPIDER: theta 90 degrees, phi 90 degrees
Single Particle
Number of Class Averages50
Number of Projections5984
DetailsThe particles were selected using WEB program manually.
Download
Data from EMDB
Header (meta data in XML format)emd-1373.xml (7.7 KB)
Map dataemd_1373.map.gz (7.4 MB)
Images1373.gif (34.4 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1373
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 4.2 MB
Session file for UCSF-Chimera, 19.7 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 3.8 MB
Session file for UCSF-Chimera, 19.9 KB