PDB-3c6r: Low pH Immature Dengue Virus

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 3c6r
Title	Low pH Immature Dengue Virus
Descriptor	Envelope protein Peptide pr
Keywords	VIRUS, dengue, immature, prM, E, Capsid protein, Cleavage on pair of basic residues, Core protein, Endoplasmic reticulum, Envelope protein, Glycoprotein, Membrane, Secreted, Transmembrane, Virion, icosahedral virus, virus
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Sequence details	THE AUTHORS STATE THAT THE SEQUENCE CONFLICTS ARE DUE TO STRAIN DIFFERENCES. THE PDB ENTRY USED TO FIT INTO THE MAP IS A MODEL GENERATED FROM TWO DIFFERENT STRUCTURES.
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 #5: Superimposing with simplified surface model of EM map, EMDB-5006, Made by Jmol #6: Superimposing with EM 3D map: EMDB-5006, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-5006 Fit Fit: target map of fitting
Similar strucutres (beta)	Diagram PDB-3iya PDB-3j0b PDB-3j05 PDB-2b6b EMDB-1872 List of similar structure data about Omokage system

Article
Citation - primary
Article	Science, Vol. 319, Page: 1834 - 1837, Year: 2008,
Title	Structure of the immature dengue virus at low pH primes proteolytic maturation
Authors	Yu, I.M., Zhang, W., Holdaway, H.A., Li, L., Kostyuchenko, V.A., Chipman, P.R., Kuhn, R.J., Rossmann, M.G., Chen, J.
Links	DOI: 10.1126/science.1153264

Components
ID 1 : Envelope protein
Image
Description	Envelope protein
Type	polypeptide(L)
Formula weight	43904.797 Da
Number of molecules	3
ID	1
Source	Method: Isolated from a natural source Organism scientific: Dengue virus type 2 Strain: Thailand/PUO-218/1980
Links	UniProt: P18356, Sequence view
ID 2 : Peptide pr
Image
Description	Peptide pr
Type	polypeptide(L)
Formula weight	9261.574 Da
Number of molecules	3
ID	2
Source	Method: Isolated from a natural source Organism scientific: Dengue virus type 2 Strain: Thailand/PUO-218/1980
Links	UniProt: P18356, Sequence view

Processing
2D projection selection
Software name	EMfit
Single particle entity
Symmetry type	ICOSAHEDRAL
3D reconstruction
Actual pixel size	2.7 A/pix
CTF correction method	Both amplitude and phase of CTF are corrected for each boxed particle.
Magnification calibration	Grating Replica EM grid
Method	Cross-correlation in real and reciprocal space for orientation determination; Fourier-Bessel method for reconstruction.
Nominal pixel size	2.8 A/pix
Resolution	25 A
3D fitting
Refinement Space	REAL
Software name	EMfit
Refine hist
Cycle id	LAST
Refine id	ELECTRON MICROSCOPY
Total atoms	1422
Protein atoms	1422

PDB format

All

Header only

mmCIF format

mmCIF

XML format

All

No-atom

Ext-atom

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.7 MB .webm (WebM/VP8 format), 5.2 MB

movie #2

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

movie #3

	.mp4 (H.264/MPEG-4 AVC format), 3.1 MB .webm (WebM/VP8 format), 4.1 MB

movie #4

	.mp4 (H.264/MPEG-4 AVC format), 2.7 MB .webm (WebM/VP8 format), 3.6 MB

movie #5

	.mp4 (H.264/MPEG-4 AVC format), 3.9 MB .webm (WebM/VP8 format), 5.6 MB

movie #6

	.mp4 (H.264/MPEG-4 AVC format), 3.6 MB .webm (WebM/VP8 format), 4.8 MB