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- EMDB-1636: A dimeric structure for archaeal methylation-guide small ribonucl... -

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Basic information

Entry
Database: EMDB / ID: EMD-1636
TitleA dimeric structure for archaeal methylation-guide small ribonucleoproteins
Map dataStructure of an archaeal methylation-guide RNP
Sample
  • Sample: Methanocaldococcus jannaschii methylation-guide sRNP
  • Protein or peptide: Ribonucleoprotein
Biological speciesMethanocaldococcus jannaschii (archaea)
Methodsingle particle reconstruction / negative staining / Resolution: 27.0 Å
AuthorsBleichert F / Gagnon KT / Brown II BA / Maxwell ES / Leschziner AE / Unger VM / Baserga SJ
CitationJournal: Science / Year: 2009
Title: A dimeric structure for archaeal box C/D small ribonucleoproteins.
Authors: Franziska Bleichert / Keith T Gagnon / Bernard A Brown / E Stuart Maxwell / Andres E Leschziner / Vinzenz M Unger / Susan J Baserga /
Abstract: Methylation of ribosomal RNA (rRNA) is required for optimal protein synthesis. Multiple 2'-O-ribose methylations are carried out by box C/D guide ribonucleoproteins [small ribonucleoproteins (sRNPs) ...Methylation of ribosomal RNA (rRNA) is required for optimal protein synthesis. Multiple 2'-O-ribose methylations are carried out by box C/D guide ribonucleoproteins [small ribonucleoproteins (sRNPs) and small nucleolar ribonucleoproteins (snoRNPs)], which are conserved from archaea to eukaryotes. Methylation is dictated by base pairing between the specific guide RNA component of the sRNP or snoRNP and the target rRNA. We determined the structure of a reconstituted and catalytically active box C/D sRNP from the archaeon Methanocaldococcus jannaschii by single-particle electron microscopy. We found that archaeal box C/D sRNPs unexpectedly formed a dimeric structure with an alternative organization of their RNA and protein components that challenges the conventional view of their architecture. Mutational analysis demonstrated that this di-sRNP structure was relevant for the enzymatic function of archaeal box C/D sRNPs.
History
DepositionJul 15, 2009-
Header (metadata) releaseJul 15, 2009-
Map releaseOct 20, 2009-
UpdateOct 20, 2009-
Current statusOct 20, 2009Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.9
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.9
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD1636_imag...

Downloads & links

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Map

FileDownload / File: emd_1636.map.gz / Format: CCP4 / Size: 1001 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of an archaeal methylation-guide RNP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.38 Å/pix.
x 64 pix.
= 344.32 Å		5.38 Å/pix.
x 64 pix.
= 344.32 Å		5.38 Å/pix.
x 64 pix.
= 344.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5.38 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.9 / Movie #1: 2.9
Minimum - Maximum-7.14815 - 22.583200000000001
Average (Standard dev.)0.00381789 (±0.973699)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-32-32-32
Dimensions646464
Spacing646464
CellA=B=C: 344.32 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.385.385.38
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z344.320344.320344.320
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-32-32-32
NC/NR/NS646464
D min/max/mean-7.14822.5830.004

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Supplemental data

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Sample components

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Entire : Methanocaldococcus jannaschii methylation-guide sRNP

EntireName: Methanocaldococcus jannaschii methylation-guide sRNP
Components
  • Sample: Methanocaldococcus jannaschii methylation-guide sRNP
  • Protein or peptide: Ribonucleoprotein

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Supramolecule #1000: Methanocaldococcus jannaschii methylation-guide sRNP

SupramoleculeName: Methanocaldococcus jannaschii methylation-guide sRNP / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 366 KDa

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Macromolecule #1: Ribonucleoprotein

MacromoleculeName: Ribonucleoprotein / type: protein_or_peptide / ID: 1 / Name.synonym: RNP / Recombinant expression: Yes
Source (natural)Organism: Methanocaldococcus jannaschii (archaea)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

BufferpH: 7 / Details: 20mM Hepes, 500mM NaCl, 1.5mM MgCl2
StainingType: NEGATIVE / Details: Sandwiched, 2% uranyl formate
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI 12
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Average electron dose: 20 e/Å2
Tilt angle min0
Electron beamAcceleration voltage: 120 kV / Electron source: LAB6
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal magnification: 52000
Sample stageSpecimen holder: Eucentric / Specimen holder model: OTHER / Tilt angle max: 50

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 27.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 8775

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Atomic model buiding 1

Initial modelPDB ID:

2nnw

SoftwareName: Situs, Chimera
RefinementSpace: REAL

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Atomic model buiding 2

Initial modelPDB ID:

1xbi

SoftwareName: Situs, Chimera
RefinementSpace: REAL

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