[English] 日本語
- EMDB-1467: Human Parvovirus B19 (empty wildtype particle) -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 1467
TitleHuman Parvovirus B19 (empty wildtype particle)
Map dataHuman Parvovirus B19 (eB19, empty wildtype particle)
SampleHuman Parvovirus B19 (empty wildtype particle):
Keywordsicosahedral / empty viral particle / B19
SourceHuman parvovirus B19 (Human Parvovirus B19)
Methodsingle particle reconstruction / cryo EM / 11.3 Å resolution
AuthorsKaufmann B / Chipman PR / Modrow S / Rossmann MG
CitationJournal: J. Virol. / Year: 2008
Title: Visualization of the externalized VP2 N termini of infectious human parvovirus B19.
Authors: Bärbel Kaufmann / Paul R Chipman / Victor A Kostyuchenko / Susanne Modrow / Michael G Rossmann
DateDeposition: Feb 5, 2008 / Header (metadata) release: Feb 7, 2008 / Map release: Mar 31, 2009 / Last update: Mar 31, 2009

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 18
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 18
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


Fileemd_1467.map.gz (map file in CCP4 format, 5344 KB)
Projections & slices

Image control

AxesZ (Sec.)X (Row.)Y (Col.)
111 pix
2.82 Å/pix.
= 312.63 Å
111 pix
2.82 Å/pix.
= 312.63 Å
111 pix
2.82 Å/pix.
= 312.63 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.81649 Å
Contour Level:11, 18 (movie #1):
Minimum - Maximum-10.31 - 34.561
Average (Standard dev.)2.24292 (8.7631)


Space Group Number1
Map Geometry
Axis orderYXZ
CellA=B=C: 312.63 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.81648648648652.81648648648652.8164864864865
M x/y/z111111111
origin x/y/z0.0000.0000.000
length x/y/z312.630312.630312.630
start NX/NY/NZ-55-55-55
MAP C/R/S213
start NC/NR/NS-55-55-55
D min/max/mean-10.31034.5612.243

Supplemental data

Sample components

Entire Human Parvovirus B19 (empty wildtype particle)

EntireName: Human Parvovirus B19 (empty wildtype particle)
Details: icosahedral, empty viral particle, non-enveloped protein shell
Number of components: 1
Oligomeric State: 60 VP subunits form icosahedral protein shell
MassTheoretical: 3.6 MDa

Component #1: virus, Human parvovirus B19

VirusName: Human parvovirus B19 / a.k.a: Human Parvovirus B19 / Class: OTHER
Details: empty wildtype particles purified from human plasma, no ssDNA genome encapsidated
Empty: Yes / Enveloped: No / Isolate: SPECIES
MassTheoretical: 3.6 MDa
SpeciesSpecies: Human parvovirus B19 (Human Parvovirus B19)
Source (natural)Host Species: Homo sapiens (human) / Host category: VERTEBRATES

Experimental details

Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 1 mg/ml / Buffer solution: 25mM Tris-HCl / pH: 7.5
Support film400 mesh copper
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 predetermined 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: guillotine-style plunge freezing device

Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM300FEG/T / Details: low dose
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 22 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 45000 X (nominal), 47000 X (calibrated) / Astigmatism: live FFT at 200K / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1250 - 3660 nm
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 98 K
CameraDetector: KODAK SO-163 FILM

Image acquisition

Image acquisitionNumber of digital images: 31 / Scanner: ZEISS SCAI / Sampling size: 14 microns / Bit depth: 8

Image processing

ProcessingMethod: single particle reconstruction / Details: manual particle selection / Number of projections: 1959 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: model-based approach using Fourier methods / Software: EMPFT, POR, P3DR / CTF correction: each particle
Details: final map includes data to 10.5 Ang resolution (fsc 0.3 cut-off), magnification of final map standardized to a map calculated from B19 VP2 VLP model coordinates (PDB accession no 1S58) resulting in final pixel separation of 2.8165Ang
Resolution: 11.3 Å / Resolution method: FSC 0.5

About Yorodumi


Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at EBI / Contact to PDBj

Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

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

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

Read more


Thousand views of thousand structures

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

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more