[English] 日本語
- EMDB-1421: Electron cryomicroscopy reveals different F1+F2 protein States in... -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 1421
TitleElectron cryomicroscopy reveals different F1+F2 protein States in intact parainfluenza virions.
SampleF-Protein in intact Parainfluenzavirus 5
SourceParainfluenza virus 5 / virus
Map dataIn-situ 3D reconstruction of the ectodomain of the PIV5 F protein determined from cryo-negative stain electron micrographs
Methodsingle particle reconstruction, at 15 A resolution
AuthorsLudwig K / Schade B / Boettcher C / Korte T
CitationJ. Virol., 2008, 82, 3775-3781

J. Virol., 2008, 82, 3775-3781 StrPapers
Electron cryomicroscopy reveals different F1+F2 protein States in intact parainfluenza virions.
Kai Ludwig / Boris Schade / Christoph Böttcher / Thomas Korte / Nina Ohlwein / Bolormaa Baljinnyam / Michael Veit / Andreas Herrmann

DateDeposition: Sep 7, 2007 / Header (metadata) release: Sep 11, 2007 / Map release: Apr 7, 2008 / Last update: Sep 7, 2007

Structure visualization

  • Surface view with section colored by density value
  • Surface level: -100
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: -100
  • Imaged by UCSF CHIMERA
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_1421.map.gz (map file in CCP4 format, 1301 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
110 pix
1.56 A/pix
= 171.6 A
110 pix
1.56 A/pix
= 171.6 A
110 pix
1.56 A/pix
= 171.6 A



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.56 A
Contour Level:-95 (by emdb), -100 (movie #1):
Minimum - Maximum-128 - 122
Average (Standard dev.)-124.687 (18.0757)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 171.6 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
A/pix X/Y/Z1.561.561.56
M x/y/z110110110
origin x/y/z0.0000.0000.000
length x/y/z171.600171.600171.600
start NX/NY/NZ-30-30-49
MAP C/R/S123
start NC/NR/NS-54-55-55
D min/max/mean-128.000122.000-124.687

Supplemental data

Sample components

Entire F-Protein in intact Parainfluenzavirus 5

EntireName: F-Protein in intact Parainfluenzavirus 5
Details: sample of fusion active virions (proven by fluorescence spectroscopy)of PIV5 (strain W3A)
Number of components: 1 / Oligomeric State: F-Protein Homotrimer
MassTheoretical: 150 kDa

Component #1: protein, F-Protein

ProteinName: F-Protein / Oligomeric Details: Homotrimer / Recombinant expression: No
MassExperimental: 150 kDa
SourceSpecies: Parainfluenza virus 5 / virus / Strain: W3A
Source (natural)Location in cell: viral membrane

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: PBS (150 mM NaCl, 5.8 mM NaH2PO4/Na2HPO4) / pH: 7.4
Support film200 mesh carbon coated collodium-supported copper grids
Staining30 seconds absorption 60 seconds staining (1% phospho-tungstic acid, pH 7.4) vitrified in liquid ethane
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
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

Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 160 kV / Electron dose: 12 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 51064 X (calibrated)
Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1501 - 2066 nm
Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
Model: GATAN LIQUID NITROGEN / Temperature: 92 K
CameraDetector: KODAK SO-163 FILM

Image acquisition

Image acquisitionNumber of digital images: 175 / Scanner: PRIMESCAN / Sampling size: 4 microns / Bit depth: 8

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 5700
Details: well resolved spike-like proteins protruding from the viral membrane suitable for single particle analysis were interactively selected
Applied symmetry: C3 (3 fold cyclic)
3D reconstructionAlgorithm: Common lines / Software: Imagic / CTF correction: MSA-based / Resolution: 15 A / Resolution method: FSC 3 SIGMA

About Yorodumi


Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

Read more


Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more