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- EMDB-1325: Composition and three-dimensional EM structure of double affinity... -

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Basic information

Entry
Database: EMDB / ID: EMD-1325
TitleComposition and three-dimensional EM structure of double affinity-purified, human prespliceosomal A complexes.
Map dataHuman spliceosomal A complex
Sample
  • Sample: Human prespliceosomal A Complex
  • Organelle or cellular component: Human prespliceosomal A Complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 45.0 Å
AuthorsBehzadnia N / Golas MM / Hartmuth K / Sander B / Kastner B / Deckert J / Dube P / Will CL / Urlaub H / Stark H / Luhrmann R
CitationJournal: EMBO J / Year: 2007
Title: Composition and three-dimensional EM structure of double affinity-purified, human prespliceosomal A complexes.
Authors: Nastaran Behzadnia / Monika M Golas / Klaus Hartmuth / Bjoern Sander / Berthold Kastner / Jochen Deckert / Prakash Dube / Cindy L Will / Henning Urlaub / Holger Stark / Reinhard Lührmann /
Abstract: Little is known about the higher-order structure of prespliceosomal A complexes, in which pairing of the pre-mRNA's splice sites occurs. Here, human A complexes were isolated under physiological ...Little is known about the higher-order structure of prespliceosomal A complexes, in which pairing of the pre-mRNA's splice sites occurs. Here, human A complexes were isolated under physiological conditions by double-affinity selection. Purified complexes contained stoichiometric amounts of U1, U2 and pre-mRNA, and crosslinking studies indicated that these form concomitant base pairing interactions with one another. A complexes contained nearly all U1 and U2 proteins plus approximately 50 non-snRNP proteins. Unexpectedly, proteins of the hPrp19/CDC5 complex were also detected, even when A complexes were formed in the absence of U4/U6 snRNPs, demonstrating that they associate independent of the tri-snRNP. Double-affinity purification yielded structurally homogeneous A complexes as evidenced by electron microscopy, and allowed for the first time the generation of a three-dimensional structure. A complexes possess an asymmetric shape (approximately 260 x 200 x 195 angstroms) and contain a main body with various protruding elements, including a head-like domain and foot-like protrusions. Complexes isolated here are well suited for in vitro assembly studies to determine factor requirements for the A to B complex transition.
History
DepositionFeb 16, 2007-
Header (metadata) releaseFeb 16, 2007-
Map releaseFeb 16, 2009-
UpdateOct 10, 2012-
Current statusOct 10, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.065
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.065
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1325.png

Downloads & links

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Map

FileDownload / File: emd_1325.map.gz / Format: CCP4 / Size: 3.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman spliceosomal A complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.9 Å/pix.
x 100 pix.
= 490. Å		4.9 Å/pix.
x 100 pix.
= 490. Å		4.9 Å/pix.
x 100 pix.
= 490. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.9 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.06 / Movie #1: 0.065
Minimum - Maximum-0.240983 - 0.564643
Average (Standard dev.)0.00325364 (±0.0341388)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 490 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
start NX/NY/NZ-72-72-72
NX/NY/NZ144144144
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS100100100
D min/max/mean-0.2410.5650.003

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Supplemental data

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Sample components

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Entire : Human prespliceosomal A Complex

EntireName: Human prespliceosomal A Complex
Components
  • Sample: Human prespliceosomal A Complex
  • Organelle or cellular component: Human prespliceosomal A Complex

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Supramolecule #1000: Human prespliceosomal A Complex

SupramoleculeName: Human prespliceosomal A Complex / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Human prespliceosomal A Complex

SupramoleculeName: Human prespliceosomal A Complex / type: organelle_or_cellular_component / ID: 1 / Name.synonym: Prespliceosome / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Cell: HeLa / Organelle: nucleus

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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

VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k)
Tilt angle min0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 122000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal magnification: 88000
Sample stageSpecimen holder model: OTHER / Tilt angle max: 45

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 45.0 Å / Resolution method: OTHER / Software - Name: IMAGIC

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