3D Electron Microscopy (3D-EM) Data Navigator [English / 日本語]
Top Gallery List Diagram Statistics Viewer Documents
Movie pageYodrodumi (structure viewer)
PDBj>EM Navigator>Detail page - EMDB-1325

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, Image by UCSF CHIMERA

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

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

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar-shape strucutres
Search for similar-shape assemblies throgh:
EMDB + EM entries in PDB
all of EMDB & PDB (Omokage search)
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
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
Single Particle
Applied SymmetryC1 (asymmetric)
Download
Data from EMDB
Header (meta data in XML format)emd-1325.xml (5.9 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