PDB-1k4r: Structure of Dengue Virus

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 1k4r
Title	Structure of Dengue Virus
Descriptor	MAJOR ENVELOPE PROTEIN E
Keywords	Virus, Flavivirus, Flaviviridae, Dengue virus, glycoprotein E from tick-borne encephalitis virus, Icosahedral virus
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-1p58 PDB-1svb
Similar strucutres (beta)	Diagram PDB-1thd PDB-3j05 PDB-3j0b PDB-2y83 List of similar structure data about Omokage system

Article
Citation - primary
Article	Cell(Cambridge,Mass.), Vol. 108, Page: 717 - 725, Year: 2002,
Title	Structure of dengue virus: implications for flavivirus organization, maturation, and fusion.
Authors	Kuhn, R.J., Zhang, W., Rossmann, M.G., Pletnev, S.V., Corver, J., Lenches, E., Jones, C.T., Mukhopadhyay, S., Chipman, P.R., Strauss, E.G., Baker, T.S., Strauss, J.H.
Links	DOI: 10.1016/S0092-8674(02)00660-8
Citation - 1
Article	Nature, Vol. 375, Page: 275 - 276, Year: 1995,
Title	Virology. When It's Better to Lie Low
Authors	Kuhn, R.J., Rossmann, M.G.
Citation - 2
Article	Nature, Vol. 375, Page: 291 - 298, Year: 1995,
Title	The Envelope Glycoprotein from Tick-borne Encephalitis Virus at 2 A Resolution
Authors	Rey, F.A., Heinz, F.X., Mandl, C., Kunz, C., Harrison, S.C.

Components
ID 1 : MAJOR ENVELOPE PROTEIN E
Image
Description	MAJOR ENVELOPE PROTEIN E
Type	polypeptide(L)
Fragment	UNP residues 284-678
Formula weight	43231.574 Da
Number of molecules	3
ID	1
Source	Method: Isolated from a natural source Genus: Flavivirus NCBI taxonomy: ID:638787 Organism scientific: Chimeric Tick-borne encephalitis virus/Dengue virus 4
Links	UniProt: C3V005, Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Details	SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE.
Name	DENGUE VIRUS MAJOR ENVELOPE PROTEIN E
Entity assembly
Assembly-ID	1
Name	DENGUE VIRUS MAJOR ENVELOPE PROTEIN E
Virus entity
Virus type	VIRION
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE (CRYO EM)
Sample preparation
pH	7.6
Sample support
Details	sample conc. l2.0E10 PFU/ML
Vitrification
Details	LIQUID NITROGEN TEMPERATURE 50MM TRIS-HCL, 75MM NACL, 1MM EDTA
Experiment
Method	ELECTRON MICROSCOPY

Processing
Reflection
Ordinal	1
D resolution high	24
2D projection selection
Number of particles	526
Software name	EMFIT
Single particle entity
Symmetry type	ICOSAHEDRAL
3D reconstruction
Actual pixel size	2.9 A/pix
CTF correction method	EACH VIRAL IMAGE WAS CTF CORRECTED BEFORE RECONSTRUCTION, BASED ON THE FOLLOWING EQUATION: F(CORR)=F(OBS)/[\|CTF\|+WIENER]
Method	COMMON-LINES AND POLAR-FOURIER-TRANSFORM (FULLER ET AL. 1996, J.STRUC.BIOL. 116, 48-55 BAKER AND CHENG, 1996, J.STRUC.BIOL. 116, 120-130) SOFTWARE USED, PURDUE PROGRAMS
Nominal pixel size	2.8 A/pix
Resolution	24 A
3D fitting
Method	IN THE FIRST STEP THE CRYSTAL STRUCTURE OF TBEV-E CRYSTALLOGRAPHIC DIMER (REY ET.AL., 1995 NATURELONDON) 375, 291-298) WAS ROTATED ABOUT AND TRANSLATEDAROUND AN ICOSAHEDRAL TWO FOLD AXES TO FIND THE BEST FIT. AFTER THAT THE DENSITIES AT ALL PIXELS COVERED BY THE FIRST FITTED DIMER WERE SET TO ZERO. THE SECOND DIMER WAS THAN PLACED ON A RADIAL AXIS PASSING THROUGH A POINT NEAR THE QUASI-TWOFOLD AXIS.
Refinement Space	REAL
Software name	CLIMB
3D fitting list
3D fitting id	1
Computing
Structure solution	EMFIT
Refine
Refine id	ELECTRON MICROSCOPY
Details	Molecules of glycoprotein E of Tick-borne encephalitis virus were solved by using cryo-EM map of Dengue virus
Ls d res high	24 A
Refine hist
Cycle id	LAST
Refine id	ELECTRON MICROSCOPY
D res high	24
Total atoms	9084
Protein atoms	9084
Software
Ordinal	1
Classification	model building
Name	emfit

PDB format

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Header only

mmCIF format

mmCIF

XML format

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No-atom

Ext-atom

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.5 MB .webm (WebM/VP8 format), 4.9 MB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 2.7 MB .webm (WebM/VP8 format), 3.7 MB

movie #3

	.mp4 (H.264/MPEG-4 AVC format), 3 MB .webm (WebM/VP8 format), 3.9 MB

movie #4

	.mp4 (H.264/MPEG-4 AVC format), 2.5 MB .webm (WebM/VP8 format), 3.5 MB