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- EMDB-5421: Archaeoglobus fulgidus methylation-guide sRNP -

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Basic information

Entry
Database: EMDB / ID: 5421
TitleArchaeoglobus fulgidus methylation-guide sRNP
Keywordsarchaea / box C/D sRNP / single particle EM / rRNA modification / RNA-protein complex / non-coding RNA
SampleArchaeoglobus fulgidus methylation-guide sRNP
SourceArchaeoglobus fulgidus / archaea / thermophilic / アーキオグロブス・フルギダス
Map dataProjection matching single particle reconstruction of Archaeoglobus fulgidus box C/D sRNP, 26 Angstrom resolution
Methodsingle particle reconstruction, at 26 A resolution
AuthorsBower-Phipps KR / Taylor DW / Wang HW / Baserga SJ
CitationRNA, 2012, 18, 1527-1540

RNA, 2012, 18, 1527-1540 StrPapers
The box C/D sRNP dimeric architecture is conserved across domain Archaea.
Kathleen R Bower-Phipps / David W Taylor / Hong-Wei Wang / Susan J Baserga

DateDeposition: May 8, 2012 / Header (metadata) release: Jun 5, 2012 / Map release: Jul 9, 2012 / Last update: May 8, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_5421.map.gz (map file in CCP4 format, 8193 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
2.7 A/pix
= 345.6 A
128 pix
2.7 A/pix
= 345.6 A
128 pix
2.7 A/pix
= 345.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.7 A
Density
Contour Level:3 (by author), 3 (movie #1):
Minimum - Maximum-5.50738192 - 17.90023232
Average (Standard dev.)0.0008348 (0.99800557)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin000
Limit127127127
Spacing128128128
CellA=B=C: 345.6 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z2.72.72.7
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z345.600345.600345.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-5.50717.9000.001

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Supplemental data

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Sample components

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Entire Archaeoglobus fulgidus methylation-guide sRNP

EntireName: Archaeoglobus fulgidus methylation-guide sRNP / Number of components: 1
Oligomeric State: Four copies of each box C/D core protein could be docked in this map.
MassTheoretical: 308 kDa

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Component #1: protein, ribonucleoprotein

ProteinName: ribonucleoprotein / a.k.a: box C/D sRNP / Recombinant expression: Yes
MassTheoretical: 308 kDa
SourceSpecies: Archaeoglobus fulgidus / archaea / thermophilic / アーキオグロブス・フルギダス

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 20mM HEPES, 500mM NaCl, 1.5mM MgCl2 / pH: 7.5
Staining2% uranyl formate
VitrificationInstrument: NONE / Cryogen name: NONE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 12 / Date: Sep 9, 2011 / Details: low-dose conditions
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 42000 X (nominal) / Imaging mode: BRIGHT FIELD
Specimen HolderModel: SIDE ENTRY, EUCENTRIC
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 6336 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Projection matching / Software: SPIDER / Resolution: 26 A / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: Chimera, Situs / Refinement space: REAL
Input PDB model: 1RLG
Modeling #2Software: Chimera, Situs / Refinement space: REAL
Input PDB model: 1NT2

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