EMDB-5421: Archaeoglobus fulgidus methylation-guide sRNP

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 5421
Authors	Bower-Phipps KR, Taylor DW, Wang HW, Baserga SJ
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie 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	EMDB figure
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	EMDB-5419 Cite EMDB-5420 Cite Cite: data citing same article
Similar strucutres (beta)	Diagram EMDB-1578 EMDB-5420 EMDB-1438 EMDB-1754 List of similar structure data about Omokage system

Article
Citation - Primary
Article	RNA, Vol. 18, Issue 8, Page 1527-40, Year 2012
Title	The box C/D sRNP dimeric architecture is conserved across domain Archaea.
Authors	Kathleen 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.
Keywords	Archaea (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)
Links	DOI: 10.1261/rna.033134.112, PubMed: 22753779, PMC: PMC3404373

File

Projections & Slices

Size of images:

Images are generated by Spider package.

Density

Data Type

Image stored as Reals

Space Group Number

Map Geometry

Unit Cell

A = 345.6 A , B = 345.6 A , C = 345.6 A ,
alpha = 90.0 degrees , beta = 90.0 degrees , gamma = 90.0 degrees

Pixel Spacing

X = 2.7 A , Y = 2.7 A , Z = 2.7 A

CCP4 map header info

Annotation Details

Projection matching single particle reconstruction of Archaeoglobus fulgidus box C/D sRNP, 26 Angstrom resolution

Sample
Name	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.
Theoretical Mass	0.308 MDa
Component #1: protein - box C/D sRNP
Scientific name	ribonucleoprotein
Common Name	box C/D sRNP
Theoretical Mass	0.308 MDa
Scientific Name of Species	Archaeoglobus fulgidus (NCBI Taxonomy: 2234)
Recombinant expression	Yes

Experiment
Sample Preparation
Staining	2% uranyl formate
Specimen State	particle
Buffer	Details: 20mM HEPES, 500mM NaCl, 1.5mM MgCl2 pH: 7.5
Vitrification
Cryogen Name	NONE
Instrument	NONE
Imaging
Microscope	FEI TECNAI 12
Date	09-SEP-2011
Details	low-dose conditions
Electron Gun
Electron Source	LAB6
Accelerating Voltage	120 kV
Electron Dose	20 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 42000 X,
Imaging Mode	BRIGHT FIELD
Specimen Holder
Holder	( SIDE ENTRY, EUCENTRIC )
Camera
Detector	GATAN Ultra4000 4k x 4k CCD
Image Acquisition

Processing
Method	single particle reconstruction
3 D reconstruction
Algorithm	Projection matching
Software	SPIDER
Resolution By Author	26
Resolution Method	FSC at 0.5 cut-off
Single Particle
Number of Projections	6336
Atomic Model Fitting
Model #0
Refinement Space	REAL
Software	Chimera, Situs
Model #1
Refinement Space	REAL
Software	Chimera, Situs

Data from EMDB

Header (meta data in XML format)

Map data

FTP directory

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