EMDB-1421: Electron cryomicroscopy reveals different F1+F2 protei...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1421
Title	Electron cryomicroscopy reveals different F1+F2 protein States in intact parainfluenza virions.
Map	In-situ 3D reconstruction of the ectodomain of the PIV5 F protein determined from cryo-negative stain electron micrographs
Sample	F-Protein in intact Parainfluenzavirus 5
Authors	Ludwig K, Schade B, Boettcher C, Korte T
Date	Deposition: 2007-09-07, Header release: 2007-09-11, Map release: 2008-04-07, Last update: 2012-10-24
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie Page #1: Surface view with section colored by density value, Surface level: -100, Made by UCSF CHIMERA #2: Surface view colored by cylindrical radius, Surface level: -100, Made by UCSF CHIMERA
Supplemental images	1421.gif emd_1421.tif
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data

Article
Citation - Primary
Article	J. Virol., Vol. 82, Issue 7, Page 3775-81, Year 2008
Title	Electron cryomicroscopy reveals different F1+F2 protein States in intact parainfluenza virions.
Authors	Kai Ludwig, Boris Schade, Christoph Böttcher, Thomas Korte, Nina Ohlwein, Bolormaa Baljinnyam, Michael Veit, Andreas Herrmann Forschungszentrum für Elektronenmikroskopie, Freie Universität Berlin, Fabeckstr. 36a, D-14195 Berlin, Germany.
Keywords	Animals, Cattle, Cell Fusion, Cell Line, Chick Embryo, Cryoelectron Microscopy, Image Processing, Computer-Assisted, Paramyxoviridae (ultrastructure), Protein Structure, Tertiary, Viral Proteins (ultrastructure), Virion (ultrastructure)
Links	DOI: 10.1128/JVI.02154-07, PubMed: 18216117, PMC: PMC2268498

Map

File

EMD-1421.map ( map file in CCP4 format, 1332 KB )

Projections & Slices

Size of images:

Axes	Z (Sec.)	Y (Row.)	X (Col.)
Surface
Projections
Slices (1/3)
Slices (1/2)
Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)

Contour Level:	-95 (by emdb), -100 (movie #1):
Minimum - Maximum:	-128 - 122
Average (Standard dev.):	-124.687 (18.0757)

Data Type

signed byte

Space Group Number

Map Geometry

Axis order	X	Y	Z
Dimensions	110	110	110
Origin	-55	-54	-55
Limit	54	55	54
Spacing	110	110	110

Unit Cell

A= B= C: 171.6 A
Alpha=beta=gamma: 90 degrees

Pixel Spacing

X= Y= Z: 1.56 A

CCP4 map header info

mode	envelope stored as signed bytes (from -128 lowest to 127 highest)
A/pix X/Y/Z	1.56	1.56	1.56
M x/y/z	110	110	110
origin x/y/z	0.000	0.000	0.000
length x/y/z	171.600	171.600	171.600
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ	-30	-30	-49
NX/NY/NZ	60	60	100
MAP C/R/S	1	2	3
start NC/NR/NS	-54	-55	-55
NC/NR/NS	110	110	110
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean	-128.000	122.000	-124.687

Annotation Details

In-situ 3D reconstruction of the ectodomain of the PIV5 F protein determined from cryo-negative stain electron micrographs

Supplement
Images
Images	1421.gif emd_1421.tif

Sample
Name	F-Protein in intact Parainfluenzavirus 5
Number of Components	1
Oligomeric State	F-Protein Homotrimer
Theoretical Mass	0.15MDa
Details	sample of fusion active virions (proven by fluorescence spectroscopy)of PIV5 (strain W3A)
Component #1: protein - F-Protein
Scientific name	F-Protein
Experimental Mass	0.15 MDa
Oligomeric Details	Homotrimer
Scientific Name of Species	Parainfluenza virus 5
NCBI taxonomy	11207
Strain	W3A
Recombinant expression	No
Natural Source	Cell Location: viral membrane

Experiment
Sample Preparation
Staining	30 seconds absorption 60 seconds staining (1% phospho-tungstic acid, pH 7.4) vitrified in liquid ethane
Specimen Support Details	200 mesh carbon coated collodium-supported copper grids
Specimen State	particle
Buffer	Details: PBS (150 mM NaCl, 5.8 mM NaH2PO4/Na2HPO4) pH: 7.4
Vitrification
Cryogen Name	ETHANE
Instrument	HOMEMADE PLUNGER
Method	A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a redetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen,and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.
Details	Vitrification instrument: self-construction
Imaging
Microscope	FEI TECNAI F20
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	160 kV
Electron Dose	12 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 50000, Calibrated: 51064
Astigmatism	objective lens astigmatism was corrected at 100,000 times magnification
Nominal Cs	2 mm
Imaging Mode	BRIGHT FIELD
Defocus	1501 nm - 2066 nm
Specimen Holder
Holder	Side entry liquid nitrogen-cooled cryo specimen holder
Model	GATAN LIQUID NITROGEN
Temperature	92 K
Camera
Detector	Kodak SO163 film
Image Acquisition
Number of Digital Images	175
Sampling Size	4
Quant Bit Number	8
Scanner	PRIMESCAN

Processing
Method	single particle reconstruction
3D reconstruction
Algorithm	Common lines
Software	Imagic
CTF Correction	MSA-based
Resolution By Author	15 A
Resolution Method	FSC (3-sigma)
Single Particle
Number of Projections	5700
Details	well resolved spike-like proteins protruding from the viral membrane suitable for single particle analysis were interactively selected

Download

Data from EMDB

Header (meta data in XML format)

emd-1421.xml (8.4 KB)

Map data

emd_1421.map.gz (75.5 KB)

Images

1421.gif (43.5 KB)

emd_1421.tif (258.8 KB)

FTP directory

ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1421

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.5 MB .webm (WebM/VP8 format), 4.5 MB Session file for UCSF-Chimera, 26.3 KB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 3.2 MB .webm (WebM/VP8 format), 4.1 MB Session file for UCSF-Chimera, 26.3 KB