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Composition and three-dimensional EM structure of double affinity-purified, human prespliceosomal A complexes.

by single particle reconstruction, at 45 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.065, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.065, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1325
TitleComposition and three-dimensional EM structure of double affinity-purified, human prespliceosomal A complexes.
MapHuman spliceosomal A complex
SampleHuman prespliceosomal A Complex
AuthorsBehzadnia N, Golas MM, Hartmuth K, Sander B, Kastner B, Deckert J, Dube P, Will CL, Urlaub H, Stark H, Luhrmann R
DateDeposition: 2007-02-16, Header release: 2007-02-16, Map release: 2009-02-16, Last update: 2012-10-10
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.065, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 0.065, Made by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleEMBO J., Vol. 26, Issue 6, Page 1737-48, Year 2007
TitleComposition and three-dimensional EM structure of double affinity-purified, human prespliceosomal A complexes.
AuthorsNastaran Behzadnia, Monika M Golas, Klaus Hartmuth, Bjoern Sander, Berthold Kastner, Jochen Deckert, Prakash Dube, Cindy L Will, Henning Urlaub, Holger Stark, Reinhard Lührmann
Department of Cellular Biochemistry, MPI of Biophysical Chemistry, Göttingen, Germany.
KeywordsBase Pairing (genetics), Humans, Immunoblotting, Immunoprecipitation, Mass Spectrometry, Microscopy, Electron, Models, Molecular, Oligonucleotides, Proteins (analysis), RNA Precursors (chemistry), Spliceosomes (chemistry), Tobramycin
LinksDOI: 10.1038/sj.emboj.7601631, PubMed: 17332742, PMC: PMC1829389
Map
Fileemd_1325.map.gz ( map file in CCP4 format, 3908 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
100 pix
4.9 A/pix
= 490. A
100 pix
4.9 A/pix
= 490. A
100 pix
4.9 A/pix
= 490. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.06 (by emdb), 0.065 (movie #1):
Minimum - Maximum: -0.240983 - 0.564643
Average (Standard dev.): 0.00325364 (0.0341388)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions100100100
Origin000
Limit999999
Spacing100100100
Unit CellA= B= C: 490 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 4.9 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z4.94.94.9
M x/y/z100100100
origin x/y/z0.0000.0000.000
length x/y/z490.000490.000490.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-72-72-72
NX/NY/NZ144144144
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-0.2410.5650.003
Annotation DetailsHuman spliceosomal A complex
Supplement
Images
Images
Sample
NameHuman prespliceosomal A Complex
Number of Components1
Component #1: cellular-component - Prespliceosome
Scientific nameHuman prespliceosomal A Complex
Common NamePrespliceosome
Oligomeric Detailsmonomer
Scientific Name of SpeciesHomo sapiens
Common Name of SpeciesHuman
NCBI taxonomy9606
Recombinant expressionNo
Natural SourceOrganelle: nucleus
Cell: HeLa
Experiment
Sample Preparation
Specimen Stateparticle
Vitrification
Cryogen NameETHANE
Imaging
MicroscopeFEI/PHILIPS CM200FEG
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Illumination ModeSPOT SCAN
Lens
MagnificationNominal: 88000, Calibrated: 122000
Imaging ModeBRIGHT FIELD
Specimen Holder
ModelOTHER
Tilt Angle0 degrees - 45 degrees
Camera
DetectorTVIPS TEMCAM-F415 (4k x 4k)
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmRCT
SoftwareIMAGIC
Resolution By Author45 A
Resolution MethodFSC
Download
Data from EMDB
Header (meta data in XML format)emd-1325.xml (5.8 KB)
Map dataemd_1325.map.gz (2 MB)
Images1325.png (99.9 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1325
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.4 MB
Session file for UCSF-Chimera, 25.5 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.6 MB
Session file for UCSF-Chimera, 25.5 KB