EMDB-1232: Structure of the Sec13-31 COPII coat cage.

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1232
Authors	Stagg SM, Gurkan C, Fowler DM, LaPointe P, Foss TR, Potter CS, Carragher B, Balch WE
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: 3.3, Made by UCSF CHIMERA #2: Surface view colored by radius, Surface level: 3.3, Made by UCSF CHIMERA
Supplemental images	1232.gif EMD-1232.png
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Similar strucutres (beta)	Diagram EMDB-5524 EMDB-5408 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Nature, Vol. 439, Issue 7073, Page 234-8, Year 2006
Title	Structure of the Sec13/31 COPII coat cage.
Authors	Scott M Stagg, Cemal Gürkan, Douglas M Fowler, Paul LaPointe, Ted R Foss, Clinton S Potter, Bridget Carragher, William E Balch National Resource for Automated Molecular Microscopy, Departments of Cell, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, USA.
Keywords	Animals, COP-Coated Vesicles (chemistry), Capsid Proteins (chemistry), Carrier Proteins, Cell Line, Cryoelectron Microscopy, Endoplasmic Reticulum (metabolism), Humans, Light, Models, Molecular, Protein Structure, Quaternary, SEC13 protein, human, SEC31A protein, human, SEC31B protein, human, Scattering, Radiation, Vesicular Transport Proteins
Links	DOI: 10.1038/nature04339, PubMed: 16407955

File

Projections & Slices

Size of images:

Images are generated by Spider package.

Density

Data Type

float (32-bit)

Space Group Number

Map Geometry

Unit Cell

A = 868.992 A , B = 868.992 A , C = 868.992 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees

Pixel Spacing

X = 4.526 A , Y = 4.526 A , Z = 4.526 A

CCP4 map header info

Annotation Details

This is a 30 angstrom resolution map of the self-assembing Sec13/31 cage.

Sample
Name	Oligomeric assembly of Sec13-31
Number of Components	2
Oligomeric State	24-mer of Sec13-31 heterotetramers forming a cuboctahedron
Theoretical Mass	8.14 MDa
Component #1: protein - Sec13
Scientific name	Sec13
Theoretical Mass	33 MDa
Experimental Mass	33 MDa
Details	SEC13R
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	Human
Recombinant expression	Yes
Engineered Source	Exp System: Baculovirus infected Tn5 insect cells Vector: pFastBac
Links	Gene Ontology: GO:0006886, InterPro: IPR:001680
Component #2: protein - Sec31
Scientific name	Sec31
Theoretical Mass	139 MDa
Experimental Mass	139 MDa
Details	SEC31L1
Scientific Name of Species	Homo sapiens (NCBI Taxonomy: 9606)
Common Name of Species	Human
Recombinant expression	Yes
Engineered Source	Vector: pFastBac Exp System: Baculovirus infected Tn5 insect cells
Links	InterPro: IPR:001680, Gene Ontology: GO:0030127

Experiment
Sample Preparation
Specimen Conc	0.9 mg/ml
Specimen Support Details	Quantifoil 2/2, 400 mesh copper grid
Specimen State	particle
Buffer	Details: 50mM MES pH 6.5, 225mM KOAc, 1mM MgCl2 pH: 6.5
Vitrification
Method	Temperature of chamber was 4 degrees C. 0 seconds drain time. Single blot. 0 mm offset. 4 ul sample applied to grid. Blot for 3.0 seconds before plunging.
Cryogen Name	ETHANE
Details	Vitrification instrument: FEI Vitrobot. Grid plasma cleaned for 30s with Fischione 1020 plasma cleaner using 75-25 Argon-Oxygen mix.
Humidity	100
Instrument	FEI VITROBOT
Temperature	93 Kelvin
Imaging
Microscope	FEI TECNAI 20
Date	02-FEB-2005
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	200 kV
Electron Dose	20 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 50000 X,
Astigmatism	objective lens astigmatism was corrected at 50,000X magnification
Nominal Cs	2 mm
Imaging Mode	BRIGHT FIELD
Defocus	800 nm - 2500 nm
Specimen Holder
Holder	Side entry liquid nitrogen-cooled cryo specimen holder. ( GATAN LIQUID NITROGEN )
Temperature	94 Kelvin
Camera
Detector	Gatan Ultrascan 4Kx4K CCD camera
Image Acquisition
Quant Bit Number	16

Processing
Method	single particle reconstruction
3 D reconstruction
Algorithm	Iterative multi-reference alignment
Software	EMAN
CTF Correction	Phase correction for each particle.
Resolution By Author	30
Resolution Method	FSC at 0.5 cut-off
Single Particle
Number of Class Averages	92
Number of Projections	9777
Details	The images were acquired using the Leginon automated data aquisition system. The particles were automatically selected using the Selexon package. The CTF was automatically estimated using the ACE package

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), 3.1 MB .webm (WebM/VP8 format), 4.7 MB Session file for UCSF-Chimera, 26.4 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3 MB .webm (WebM/VP8 format), 4.2 MB Session file for UCSF-Chimera, 26.5 KB