EMDB-1852: EM map of the negative stained SMG-1-8-9 complex.

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1852
Title	EM map of the negative stained SMG-1-8-9 complex.
Map	This is the EM map of the negatively stained SMG-1-8-9 complex
Sample	Human SMG-1 kinase bound to SMG-9 and SMG-8
Keywords	Nonsense-mediated mRNA decay, NMD, SMG-1, SMG-8, SMG-9, SMG1C
Authors	Arias-Palomo E, Yamashita A, Fernandez IS, Nunez-Ramirez R, Bamba Y, Izumi N, Ohno S, Llorca O
Date	Deposition: 2010-12-17, Header release: 2011-01-21, Map release: 2011-12-23, Last update: 2011-12-23
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 0.05, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 0.05, Made by UCSF CHIMERA
Supplemental images	EMD1852.png
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	EMDB-1851 Cite EMDB-1853 Cite Cite: data citing same article
Similar strucutres (beta)	Diagram EMDB-1246 EMDB-1108 EMDB-1853 PDB-2r1g List of similar structure data about Omokage system

Article
Citation - Primary
Article	Genes Dev., Vol. 25, Issue 2, Page 153-64, Year 2011
Title	The nonsense-mediated mRNA decay SMG-1 kinase is regulated by large-scale conformational changes controlled by SMG-8.
Authors	Ernesto Arias-Palomo, Akio Yamashita, Israel S Fernández, Rafael Núñez-Ramírez, Yumi Bamba, Natsuko Izumi, Shigeo Ohno, Oscar Llorca Centro de Investigaciones Biológicas (CIB), Spanish National Research Council (Consejo Superior de Investigaciones Científicas, CSIC), 28040 Madrid, Spain.
Keywords	HEK293 Cells, HeLa Cells, Humans, Models, Molecular, Phosphatidylinositol 3-Kinases (chemistry, 2.7.1.-), Protein Kinases (chemistry, 2.7.-), Protein Multimerization (physiology), Protein Structure, Quaternary, Recombinant Proteins (metabolism), SMG-8 protein, human (2.7.-), SMG1 protein, human (2.7.1.137), Trans-Activators (metabolism), UPF1 protein, human
Links	DOI: 10.1101/gad.606911, PubMed: 21245168, PMC: PMC3022261

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= B= C: 336 A
Alpha=beta=gamma: 90 degrees

Pixel Spacing

X= Y= Z: 4.2 A

CCP4 map header info

Annotation Details

This is the EM map of the negatively stained SMG-1-8-9 complex

Sample
Name	Human SMG-1 kinase bound to SMG-9 and SMG-8
Number of Components	3
Oligomeric State	One molecule of SMG-1 binds to one molecule of SMG-9 and one molecule of SMG-8
Theoretical Mass	0.58MDa
Component #1: protein - SMG-1
Scientific name	SMG-1
Theoretical Mass	0.41 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Homo sapiens
Common Name of Species	Human
NCBI taxonomy	9606
Recombinant expression	Yes
Engineered Source	Vector: pEF_Flag-HA-SBP Expression system: 293T cells
Links	Gene Ontology: GO:0000184
Component #2: protein - SMG-9
Scientific name	SMG-9
Theoretical Mass	0.06 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Homo sapiens
Common Name of Species	Human
NCBI taxonomy	9606
Recombinant expression	Yes
Engineered Source	Expression system: 293T Cells Vector: pSR_Strep-HA
Links	Gene Ontology: GO:0000184
Component #3: protein - SMG-8
Scientific name	SMG-8
Theoretical Mass	0.11 MDa
Oligomeric Details	Monomer
Number of Copies	1
Scientific Name of Species	Homo sapiens
Common Name of Species	Human
NCBI taxonomy	9606
Recombinant expression	Yes
Engineered Source	Vector: pSR_Strep-HA Expression system: 293T Cells
Links	Gene Ontology: GO:0000184

Experiment
Sample Preparation
Staining	Protein was adsorbed for 1 minute, washed in two water drops and stained with 2% w/v uranyl formate for 1 minute.
Specimen Support Details	400 mesh copper grid
Specimen State	particle
Buffer	Details: 10 mM HEPES-KOH at pH7.5, 150 mM NaCl, 20% glycerol, 10 mM MgCl2 pH: 7.5
Vitrification
Cryogen Name	NONE
Instrument	NONE
Imaging
Microscope	OTHER
Details	Microscope JEOL JEM-1230
Electron Gun
Electron Source	TUNGSTEN HAIRPIN
Accelerating Voltage	100 kV
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 50000
Astigmatism	Objective lens astigmatism was corrected at 80,000 times magnification
Nominal Cs	2.9 mm
Imaging Mode	BRIGHT FIELD
Defocus	500 nm - 1200 nm
Specimen Holder
Holder	Side entry single tilt holder
Model	JEOL
Tilt Angle	0 degrees - 20 degrees
Temperature	294 K
Camera
Detector	Kodak SO163 film
Image Acquisition
Scanner	OTHER
Sampling Size	10.5
Quant Bit Number	16
Details	Minolta Dimage Scan Multi PRO scanner

Processing
Method	single particle reconstruction
3D reconstruction
Algorithm	Projection Matching
Software	EMAN, Xmipp
CTF Correction	Each micrograph
Resolution By Author	24 A
Resolution Method	FSC at 0.5 cut-off
Single Particle
Number of Projections	13853
Details	Particles were collected manually.

Data from EMDB

Header (meta data in XML format)

Map data

Images

FTP directory

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.5 MB .webm (WebM/VP8 format), 5.4 MB Session file for UCSF-Chimera, 26.8 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.3 MB .webm (WebM/VP8 format), 5 MB Session file for UCSF-Chimera, 26.8 KB