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- EMDB-2102: Structure of a stalled transfer intermediate of Sm proteins from ... -

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Entry
Database: EMDB / ID: EMD-2102
TitleStructure of a stalled transfer intermediate of Sm proteins from the assembly chaperone pICln to the SMN-complex
Map dataReconstruction of the 8S complex
Sample
  • Sample: 8S complex: a stalled Sm protein transfer intermediate from the assembly chaperone pICln to the SMN-complex
  • Protein or peptide: 8S complex
KeywordssnRNP / spliceosome / assembly chaperone / SMN-complex
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsChari A / Grimm C / Fischer U / Stark H
CitationJournal: Mol Cell / Year: 2013
Title: Structural basis of assembly chaperone- mediated snRNP formation.
Authors: Clemens Grimm / Ashwin Chari / Jann-Patrick Pelz / Jochen Kuper / Caroline Kisker / Kay Diederichs / Holger Stark / Hermann Schindelin / Utz Fischer /
Abstract: Small nuclear ribonucleoproteins (snRNPs) represent key constituents of major and minor spliceosomes. snRNPs contain a common core, composed of seven Sm proteins bound to snRNA, which forms in a step- ...Small nuclear ribonucleoproteins (snRNPs) represent key constituents of major and minor spliceosomes. snRNPs contain a common core, composed of seven Sm proteins bound to snRNA, which forms in a step-wise and factor-mediated reaction. The assembly chaperone pICln initially mediates the formation of an otherwise unstable pentameric Sm protein unit. This so-called 6S complex docks subsequently onto the SMN complex, which removes pICln and enables the transfer of pre-assembled Sm proteins onto snRNA. X-ray crystallography and electron microscopy was used to investigate the structural basis of snRNP assembly. The 6S complex structure identifies pICln as an Sm protein mimic, which enables the topological organization of the Sm pentamer in a closed ring. A second structure of 6S bound to the SMN complex components SMN and Gemin2 uncovers a plausible mechanism of pICln elimination and Sm protein activation for snRNA binding. Our studies reveal how assembly factors facilitate formation of RNA-protein complexes in vivo.
History
DepositionMay 17, 2012-
Header (metadata) releaseOct 3, 2012-
Map releaseJan 30, 2013-
UpdateMar 6, 2013-
Current statusMar 6, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.017
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.017
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2102.png

Downloads & links

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Map

FileDownload / File: emd_2102.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the 8S complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.5 Å/pix.
x 80 pix.
= 200. Å		2.5 Å/pix.
x 80 pix.
= 200. Å		2.5 Å/pix.
x 80 pix.
= 200. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.017 / Movie #1: 0.017
Minimum - Maximum-0.23855253 - 1.32832515
Average (Standard dev.)0.00943616 (±0.07313307)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 200.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.52.52.5
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z200.000200.000200.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ128128168
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-0.2391.3280.009

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Supplemental data

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Sample components

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Entire : 8S complex: a stalled Sm protein transfer intermediate from the a...

EntireName: 8S complex: a stalled Sm protein transfer intermediate from the assembly chaperone pICln to the SMN-complex
Components
  • Sample: 8S complex: a stalled Sm protein transfer intermediate from the assembly chaperone pICln to the SMN-complex
  • Protein or peptide: 8S complex

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Supramolecule #1000: 8S complex: a stalled Sm protein transfer intermediate from the a...

SupramoleculeName: 8S complex: a stalled Sm protein transfer intermediate from the assembly chaperone pICln to the SMN-complex
type: sample / ID: 1000 / Details: Sample was monodisperse
Oligomeric state: One heterooctamer composed of pICln, SmD1, SmD2, SmE, SmF, SmG, SMN and Gemin2
Number unique components: 1
Molecular weightExperimental: 125 KDa / Theoretical: 125 KDa / Method: Gel filtration, Sedimentation

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Macromolecule #1: 8S complex

MacromoleculeName: 8S complex / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Organelle: Cytoplasm / Location in cell: Cytosol
Molecular weightExperimental: 125 KDa / Theoretical: 125 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pet28

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration10 mg/mL
BufferpH: 7.5 / Details: 20 mM HEPES, 150 mM NaCl, 5 mM DTT
StainingType: NEGATIVE
Details: Grids were floated on 2 % Uranyl Formate solution for 1 minute.
GridDetails: Custom made holey grid with thin carbon support.
VitrificationCryogen name: NONE / Instrument: OTHER / Details: negative stain

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
DateJan 12, 2012
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Number real images: 48 / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 160 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 109000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2 mm
Sample stageSpecimen holder model: SIDE ENTRY, EUCENTRIC

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Imagic / Number images used: 10000

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Atomic model buiding 1

Initial modelPDB ID:

4f77
PDB Unreleased entry

SoftwareName: Amira
DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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