PDB-1na4: The structure of immature Yellow Fever virus particle - EM Navigator

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The structure of immature Yellow Fever virus particle

by single particle (icosahedral) reconstruction

Movie

Orientation:

#1: Biological unit as complete icosahedral assembly, Made by Jmol

#2: Biological unit as icosahedral pentamer, Made by Jmol

#3: Biological unit as icosahedral 23 hexamer, Made by Jmol

#4: Depositted structure unit, Made by Jmol

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 1na4
Title	The structure of immature Yellow Fever virus particle
Descriptor	major envelope protein E
Keywords	Virus, flavivirus, flaviviridae, yellow fever immature virus, prM particle, Icosahedral virus
Authors	Zhang, Y., Corver, J., Chipman, P.R., Lenches, E., Zhang, W., Pletnev, S.V., Sedlak, D., Baker, T.S., Strauss, J.H., Kuhn, R.J., Rossmann, M.G.
Date	Deposition: 2002-11-26, Release: 2003-12-09
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
Movies	Movie Page #1: Biological unit as complete icosahedral assembly, Made by Jmol #2: Biological unit as icosahedral pentamer, Made by Jmol #3: Biological unit as icosahedral 23 hexamer, Made by Jmol #4: Depositted structure unit, Made by Jmol
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	PDB-1n6g Cite Cite: data citing same article
Similar strucutres (beta)	Diagram PDB-2of6 PDB-1n6g PDB-3c6d PDB-1tge List of similar structure data about Omokage system

Article
Citation - primary
Article	EMBO J., Vol. 22, Issue 11, Page 2604-13, Year 2003
Title	Structures of immature flavivirus particles.
Authors	Ying Zhang, Jeroen Corver, Paul R Chipman, Wei Zhang, Sergei V Pletnev, Dagmar Sedlak, Timothy S Baker, James H Strauss, Richard J Kuhn, Michael G Rossmann Department of Biological Sciences, Lilly Hall, 915 West State Street, Purdue University, West Lafayette, IN 47907-2054, USA.
Keywords	Animals, Cell Line, Cryoelectron Microscopy, Dengue Virus (chemistry), Flavivirus (chemistry), Image Processing, Computer-Assisted, Lipid Bilayers (chemistry), Models, Molecular, Nucleocapsid (chemistry), Sindbis Virus (chemistry), Viral Proteins (chemistry), Yellow fever virus (chemistry)
Links	PubMed: 12773377, DOI: 10.1093/emboj/cdg270, PMC: PMC156766

Components
ID 1 : major envelope protein E
Image
Description	major envelope protein E
Type	polymer
Formula weight	43231.574 Da
Number of molecules	3
Source	Method: Isolated from a natural source Genus: Flavivirus NCBI taxonomy: ID:11089 Organism scientific: Yellow fever virus
Links	UniProt: P14336, Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Details	The samples were produced by adding ammonium chloride to the medium in the late infection stage.
Name	Yellow fever immature virus
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE (CRYO EM)

Electron Microscopy

Processing
2D projection selection
Software name	EMFIT
Single particle entity
Symmetry type	ICOSAHEDRAL
3D fitting
Refinement Space	REAL
Software name	EMFIT
Refine hist
Total atoms	1185
Protein atoms	1185

PDB format

All

pdb1na4.ent (uncompressed file)

Header only

mmCIF format

mmCIF

XML format

All

No-atom

1na4-noatom.xml.gz

Ext-atom

1na4-extatom.xml.gz

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.6 MB .webm (WebM/VP8 format), 5 MB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 2.9 MB .webm (WebM/VP8 format), 3.8 MB

movie #3

	.mp4 (H.264/MPEG-4 AVC format), 2.8 MB .webm (WebM/VP8 format), 3.8 MB

movie #4

	.mp4 (H.264/MPEG-4 AVC format), 2.5 MB .webm (WebM/VP8 format), 3.4 MB