[English] 日本語
- EMDB-2141: 6A Electron cryomicroscopy structure of immature Dengue virus ser... -

Open data

ID or keywords:


no data

Basic information

Database: EMDB / ID: 2141
Title6A Electron cryomicroscopy structure of immature Dengue virus serotype 1
Keywordsflavivirus / dengue virus serotype 1 / immature / e protein / prM protein / capsid protein
SampleImmature Dengue virus serotype 1
SourceDengue virus 1 / virus
Map dataimmature Dengue virus 1
Methodsingle particle (icosahedral) reconstruction, at 6 Å resolution
AuthorsKostyuchenko VA / Zhang Q / Tan LC / Ng TS / Lok SM
CitationJ. Virol., 2013, 87, 7700-7707

J. Virol., 2013, 87, 7700-7707 Yorodumi Papers
Immature and mature dengue serotype 1 virus structures provide insight into the maturation process.
Victor A Kostyuchenko / Qian Zhang / Joanne L Tan / Thiam-Seng Ng / Shee-Mei Lok

Validation ReportPDB-ID: 4b03

SummaryFull reportAbout validation report
DateDeposition: Jun 25, 2012 / Header (metadata) release: Jul 9, 2012 / Map release: Jun 5, 2013 / Last update: Jun 19, 2013

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-4b03
  • Surface level: 2.5
  • Imaged by UCSF CHIMERA
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-4b03
  • Imaged by Jmol
  • Download
3D viewer

View / / Stereo:
Slabnear <=> far

fix: /
Orientation Rotation
Misc. /
Supplemental images

Downloads & links


Fileemd_2141.map.gz (map file in CCP4 format, 843751 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
600 pix
1.2 Å/pix.
= 720. Å
600 pix
1.2 Å/pix.
= 720. Å
600 pix
1.2 Å/pix.
= 720. Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.2 Å
Contour Level:2.5 (by author), 2.5 (movie #1):
Minimum - Maximum-11.73692226 - 8.14927101
Average (Standard dev.)-0.03639847 (0.68797463)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA=B=C: 720 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21.21.2
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z720.000720.000720.000
start NX/NY/NZ-32-32-32
MAP C/R/S123
start NC/NR/NS-300-300-300
D min/max/mean-11.7378.149-0.036

Supplemental data

Sample components

Entire Immature Dengue virus serotype 1

EntireName: Immature Dengue virus serotype 1 / Number of components: 1
MassTheoretical: 14.5 MDa / Experimental: 14.5 MDa
Measured by: estimation based on components' amino acid sequences

Component #1: virus, Dengue virus 1

VirusName: Dengue virus 1 / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: STRAIN
MassTheoretical: 14.5 MDa / Experimental: 14.5 MDa
SpeciesSpecies: Dengue virus 1 / virus / Strain: PVP159 (DEN1/SG/07K3640DK1/2008)
Source (natural)Host Species: Aedes aegypti / arthropod / / Host category: INVERTEBRATES
Shell #1Name of element: E / Diameter: 600 Å / T number(triangulation number): 1

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionpH: 7.5
Support filmthin carbon film on lacey carbon support, copper grid, plasma cleaned and glow discharged
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 100 K / Humidity: 100 % / Method: blot 1 second before plunging

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Apr 11, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 17.7 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 75000 X (nominal), 75000 X (calibrated)
Astigmatism: Astigmatism was corrected at 250,000 magnification
Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 700 - 3500 nm / Energy filter: FEI
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 100 K ( 99 - 101 K)
CameraDetector: GENERIC GATAN (4k x 4k)

Image acquisition

Image acquisitionNumber of digital images: 838 / Bit depth: 16 / Details: CCD data

Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 7169 / Details: particles were manually selected / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: MPSA / Software: GPU-adapted, EMAN1
CTF correction: Wiener filter weighting each particle during 3D reconstruction
Resolution: 6 Å / Resolution method: FSC 0.143

Atomic model buiding

Modeling #1Software: Chimera / Refinement protocol: rigid body / Refinement space: REAL
Details: Protocol: rigid body. Fit in map feature in Chimera, whole structure was fitted as a rigid body with no apparent need to fit domains separately
Input PDB model: 3c6e
Chain ID: A, C
Output model

About Yorodumi


Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

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 / 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)

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