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- EMDB-2420: Electron microscopy of the CSM/RNA complex from Sulfolobus solfat... -

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Basic information

Entry
Database: EMDB / ID: EMD-2420
TitleElectron microscopy of the CSM/RNA complex from Sulfolobus solfataricus
Map dataStructure of CSM/RNA complex
Sample
  • Sample: CSM/RNA complex from Sulfolobus solfataricus
  • Protein or peptide: CSM complex
KeywordsCRISPR / CSM / Sulfolobus solfataricus
Biological speciesSulfolobus solfataricus (archaea)
Methodsingle particle reconstruction / Resolution: 30.0 Å
AuthorsRouillon C / Zhou M / Zhang J / Politis A / Beilsten V / Cannone G / Graham S / Robinson CV / Spagnolo L / White MF
CitationJournal: Mol Cell / Year: 2013
Title: Structure of the CRISPR interference complex CSM reveals key similarities with cascade.
Authors: Christophe Rouillon / Min Zhou / Jing Zhang / Argyris Politis / Victoria Beilsten-Edmands / Giuseppe Cannone / Shirley Graham / Carol V Robinson / Laura Spagnolo / Malcolm F White /
Abstract: The Clustered Regularly Interspaced Palindromic Repeats (CRISPR) system is an adaptive immune system in prokaryotes. Interference complexes encoded by CRISPR-associated (cas) genes utilize small RNAs ...The Clustered Regularly Interspaced Palindromic Repeats (CRISPR) system is an adaptive immune system in prokaryotes. Interference complexes encoded by CRISPR-associated (cas) genes utilize small RNAs for homology-directed detection and subsequent degradation of invading genetic elements, and they have been classified into three main types (I-III). Type III complexes share the Cas10 subunit but are subclassifed as type IIIA (CSM) and type IIIB (CMR), depending on their specificity for DNA or RNA targets, respectively. The role of CSM in limiting the spread of conjugative plasmids in Staphylococcus epidermidis was first described in 2008. Here, we report a detailed investigation of the composition and structure of the CSM complex from the archaeon Sulfolobus solfataricus, using a combination of electron microscopy, mass spectrometry, and deep sequencing. This reveals a three-dimensional model for the CSM complex that includes a helical component strikingly reminiscent of the backbone structure of the type I (Cascade) family.
History
DepositionJul 19, 2013-
Header (metadata) releaseAug 28, 2013-
Map releaseApr 23, 2014-
UpdateMay 21, 2014-
Current statusMay 21, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2420.png

Downloads & links

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Map

FileDownload / File: emd_2420.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of CSM/RNA complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
7.2 Å/pix.
x 64 pix.
= 460.8 Å		7.2 Å/pix.
x 64 pix.
= 460.8 Å		7.2 Å/pix.
x 64 pix.
= 460.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 7.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 3.34 / Movie #1: 5
Minimum - Maximum-8.59251308 - 18.895511630000001
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-4-4-4
Dimensions646464
Spacing646464
CellA=B=C: 460.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.27.27.2
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z460.800460.800460.800
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS-4-4-4
NC/NR/NS646464
D min/max/mean-8.59318.896-0.000

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Supplemental data

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Sample components

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Entire : CSM/RNA complex from Sulfolobus solfataricus

EntireName: CSM/RNA complex from Sulfolobus solfataricus
Components
  • Sample: CSM/RNA complex from Sulfolobus solfataricus
  • Protein or peptide: CSM complex

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Supramolecule #1000: CSM/RNA complex from Sulfolobus solfataricus

SupramoleculeName: CSM/RNA complex from Sulfolobus solfataricus / type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 428 KDa

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Macromolecule #1: CSM complex

MacromoleculeName: CSM complex / type: protein_or_peptide / ID: 1 / Recombinant expression: Yes
Source (natural)Organism: Sulfolobus solfataricus (archaea)
Recombinant expressionOrganism: Sulfolobus solfataricus (archaea)

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
DateDec 13, 2012
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Number images used: 7829

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