PDB-1p58: Complex Organization of Dengue Virus Membrane Proteins ...

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 1p58
Title	Complex Organization of Dengue Virus Membrane Proteins as Revealed by 9.5 Angstrom Cryo-EM reconstruction
Descriptor	Major envelope protein E/Envelope glycoprotein M
Keywords	Virus, FLAVIVIRUS, FLAVIVIRIDAE, DENGUE VIRUS, GLYCOPROTEIN E FROM TICK-BORNE ENCEPHALITIS VIRUS, MEMBRANE PROTEIN M, CRYO-EM, Icosahedral virus
Authors	Zhang, W., Chipman, P.R., Corver, J., Johnson, P.R., Zhang, Y., Mukhopadhyay, S., Baker, T.S., Strauss, J.H., Rossmann, M.G., Kuhn, R.J.
Date	Deposition: 2003-04-25, Release: 2003-11-04
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-1jch PDB-1k4r PDB-1svb PDB-1thd
Similar strucutres (beta)	Diagram PDB-3iya PDB-4azx PDB-4a7n EMDB-1872 PDB-3c6r List of similar structure data about Omokage system

Article
Citation - primary
Article	Nat. Struct. Biol., Vol. 10, Issue 11, Page 907-12, Year 2003
Title	Visualization of membrane protein domains by cryo-electron microscopy of dengue virus.
Authors	Wei Zhang, Paul R Chipman, Jeroen Corver, Peter R Johnson, Ying Zhang, Suchetana Mukhopadhyay, Timothy S Baker, James H Strauss, Michael G Rossmann, Richard J Kuhn Department of Biological Sciences, Lilly Hall, 915 W. State Street, Purdue University, West Lafayette, Indiana 47907, USA.
Keywords	Cryoelectron Microscopy, Dengue Virus (metabolism), Nucleocapsid (metabolism), Protein Structure, Secondary, Protein Structure, Tertiary, Viral Matrix Proteins (metabolism)
Links	PubMed: 14528291, DOI: 10.1038/nsb990
Citation - 1
Article	Cell(Cambridge,Mass.), Vol. 108, Page: 717 - 725, Year: 2002,
Title	Structure of Dengue Virus: Implications for Flaviviruses 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.
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.
Citation - 3
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 - 4
Article	Microbiol.Mol.Biol.Rev., Vol. 63, Page: 862 - 922, Year: 1999,
Title	Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs
Authors	Baker, T.S., Olson, N.H., Fuller, S.D.

Components
ID 1 : Major envelope protein E
Image
Description	Major envelope protein E
Type	polypeptide(L)
Formula weight	54402.305 Da
Number of molecules	3
ID	1
Source	Method: Isolated from a natural source Genus: Flavivirus NCBI taxonomy: ID:11066 Organism scientific: Dengue virus 2 Puerto Rico/PR159-S1/1969 Species: Dengue virus Strain: PR159/S1
Links	UniProt: P12823, Sequence view
ID 2 : Envelope protein M
Image
Description	Envelope protein M
Type	polypeptide(L)
Formula weight	8387.914 Da
Number of molecules	3
ID	2
Source	Method: Isolated from a natural source Genus: Flavivirus NCBI taxonomy: ID:11066 Organism scientific: Dengue virus 2 Puerto Rico/PR159-S1/1969 Species: Dengue virus Strain: PR159/S1
Links	UniProt: P12823, Sequence view

Sample
Assembly
Aggregation state	PARTICLE
Name	DENGUE VIRUS
Entity assembly
Assembly-ID	1
Virus entity
Ictvdb id	00.026.0.01.013
Virus host category	INVERTEBRATES
Virus host growth cell	mosquito C6/36
Virus host species	Aedes aegypti
Virus isolate	STRAIN
Virus type	VIRION
Buffer
Name	50 mM TRIS, 75 mM NaCl, 1 mM EDTA
Experiment
Reconstruction method	SINGLE PARTICLE
Specimen type	VITREOUS ICE (CRYO EM)
Sample preparation
pH	7.6
Sample concentration	20 mg/ml
Sample support
Details	Concentration is given in PFU/ML
Vitrification
Details	SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE
Experiment
Method	ELECTRON MICROSCOPY

Electron Microscopy
Imaging
Microscope	Model: FEI/PHILIPS CM200T
Date	2000-06-27
Electron gun
Electron source	SCHOTTKY FIELD EMISSION GUN
Accelerating voltage	200 kV
Electron dose	2700 e/A**2
Illumination mode	FLOOD BEAM LOW DOSE
Lens
Mode	BRIGHT FIELD
Magnification	Nominal: 50000 X
Cs	Nominal: 2.0 mm
Nominal defocus	Max: 4800.0 nm, Min: 800.0 nm
Specimen holder
Tilt angle	Min: 0.0 degrees, Max: 0.0 degrees
Temperature	87 Kelvin
Detector
Type	KODAK SO163 FILM

Processing
2D projection selection
Number of particles	1691
Software name	EMFIT
Single particle entity
Symmetry type	ICOSAHEDRAL
3D reconstruction
CTF correction method	each viral image was CTF corrected before reconstruction, based on the following equation: F(corr)=F(obs)/[\|CTF\|+wiener*(1-\|CTF\|)]
Details	THE RECONSTRUCTION WAS COMPUTED FROM 1691 DENGUE VIRUS IMAGES THAT WERE SELECTED FROM 78 MICROGRAPHS. ORIENTATIONS WERE DETERMINED BY THE MODEL-BASED POLAR-FOURIER TRANSFORM METHOD (BAKER AND CHENG, 1996, J.STRUC.BIOL. 116,120-130) AND REFINED BY THE MODEL-BASED FOURIER TRANSFORM REFINEMENT PROCEDURE(http://bond.cs.ucf.edu/ComputationalBiology/Projects/POR/Home.html).
Method	FOURIER-BESSEL METHOD
Nominal pixel size	2.8 A/pix
Resolution	9.5 A
3D fitting
Refinement Space	REAL
Software name	EMFIT
3D fitting list
3D fitting id	1
PDB entry ID	1SVB and 1JCH PDB-1svb PDB-1jch
Refine hist
Cycle id	LAST
Refine id	ELECTRON MICROSCOPY
Total atoms	1635
Protein atoms	1635

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1p58.cif.gz

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Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.7 MB .webm (WebM/VP8 format), 5.3 MB

movie #2

	.mp4 (H.264/MPEG-4 AVC format), 2.9 MB .webm (WebM/VP8 format), 3.9 MB

movie #3

	.mp4 (H.264/MPEG-4 AVC format), 3.3 MB .webm (WebM/VP8 format), 4.2 MB

movie #4

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