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Archaeoglobus fulgidus methylation-guide sRNP

by single particle reconstruction, at 26 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 3, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 3, Made by UCSF CHIMERA

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5421
TitleArchaeoglobus fulgidus methylation-guide sRNP
MapProjection matching single particle reconstruction of Archaeoglobus fulgidus box C/D sRNP, 26 Angstrom resolution
SampleArchaeoglobus fulgidus methylation-guide sRNP
Keywordsarchaea, box C/D sRNP, single particle EM, rRNA modification, RNA-protein complex, non-coding RNA
AuthorsBower-Phipps KR, Taylor DW, Wang HW, Baserga SJ
DateDeposition: 2012-05-08, Header release: 2012-06-05, Map release: 2012-07-09, Last update: 2012-07-09
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 3, Made by UCSF CHIMERA

#2: Surface view colored by radius, Surface level: 3, Made by UCSF CHIMERA

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

Cite: data citing same article

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleRNA, Vol. 18, Issue 8, Page 1527-40, Year 2012
TitleThe box C/D sRNP dimeric architecture is conserved across domain Archaea.
AuthorsKathleen R Bower-Phipps, David W Taylor, Hong-Wei Wang, Susan J Baserga
Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA.
KeywordsArchaea (classification), Archaeal Proteins (chemistry), Base Sequence, Methylation, Molecular Sequence Data, Mutagenesis, Protein Binding, Protein Conformation, Protein Multimerization, RNA, Archaeal (genetics), RNA, Small Nucleolar (genetics), Ribonucleoproteins, Small Nucleolar (chemistry)
LinksDOI: 10.1261/rna.033134.112, PubMed: 22753779, PMC: PMC3404373
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.

Density
Contour Level:3 (by author), 3 (movie #1):
Minimum - Maximum: -5.50738192 - 17.90023232
Average (Standard dev.): 0.0008348 (0.99800557)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin000
Limit127127127
Spacing128128128
Unit CellA= B= C: 345.6 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.7 A
CCP4 map header info
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
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-5.50717.9000.001
Annotation DetailsProjection matching single particle reconstruction of Archaeoglobus fulgidus box C/D sRNP, 26 Angstrom resolution
Supplement
Images
Images
Sample
NameArchaeoglobus fulgidus methylation-guide sRNP
Number of Components1
Oligomeric StateFour copies of each box C/D core protein could be docked in this map.
Theoretical Mass0.308MDa
Component #1: protein - box C/D sRNP
Scientific nameribonucleoprotein
Common Namebox C/D sRNP
Theoretical Mass0.308 MDa
Scientific Name of SpeciesArchaeoglobus fulgidus
NCBI taxonomy2234
Recombinant expressionYes
Experiment
Sample Preparation
Staining2% uranyl formate
Specimen Stateparticle
BufferDetails: 20mM HEPES, 500mM NaCl, 1.5mM MgCl2
pH: 7.5
Vitrification
Cryogen NameNONE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI 12
Date09-SEP-2011
Detailslow-dose conditions
Electron Gun
Electron SourceLAB6
Accelerating Voltage120 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 42000
Imaging ModeBRIGHT FIELD
Specimen Holder
ModelSIDE ENTRY, EUCENTRIC
Camera
DetectorGATAN ULTRASCAN 4000 (4k x 4k)
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmProjection matching
SoftwareSPIDER
Resolution By Author26 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections6336
Applied SymmetryC1 (asymmetric)
Atomic Model Fitting
Model #0
Refinement SpaceREAL
SoftwareChimera, Situs
PDB Entry ID1RLG
Model #1
Refinement SpaceREAL
SoftwareChimera, Situs
PDB Entry ID1NT2
Download
Data from EMDB
Header (meta data in XML format)emd-5421.xml (6.4 KB)
Map dataemd_5421.map.gz (5.8 MB)
Imagesemd_5421_1.png (1009.7 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5421
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 26.6 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.6 MB
Session file for UCSF-Chimera, 26.6 KB