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- EMDB-2485: Near-atomic resolution cryo-EM structure of Dengue serotype 4 virus -

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Basic information

Entry
Database: EMDB / ID: 2485
TitleNear-atomic resolution cryo-EM structure of Dengue serotype 4 virus
Map dataMature dengue virus serotype 4 icosahedral reconstruction
SampleMature Dengue virus serotype 4:
virus
Keywordsflavivirus / virus / dengue virus serotype 4 / cryo-EM / dengue virus
Function / homologyDEAD box, Flavivirus / Helicase superfamily 1/2, ATP-binding domain / Flavivirus non-structural protein NS1 / Flavivirus non-structural protein NS4B / Helicase, C-terminal / Flavivirus NS3, petidase S7 / Flavivirus polyprotein propeptide / Ribosomal RNA methyltransferase FtsJ domain / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan ...DEAD box, Flavivirus / Helicase superfamily 1/2, ATP-binding domain / Flavivirus non-structural protein NS1 / Flavivirus non-structural protein NS4B / Helicase, C-terminal / Flavivirus NS3, petidase S7 / Flavivirus polyprotein propeptide / Ribosomal RNA methyltransferase FtsJ domain / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus glycoprotein central and dimerisation domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS2A / Immunoglobulin E-set / Flavivirus envelope glycoprotein E, Stem/Anchor domain / mRNA cap 0/1 methyltransferase / Flavivirus glycoprotein E, immunoglobulin-like domain / P-loop containing nucleoside triphosphate hydrolase / S-adenosyl-L-methionine-dependent methyltransferase / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flavivirus capsid protein C superfamily / Flaviviral glycoprotein E, dimerisation domain / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus polyprotein propeptide superfamily / Flavivirus capsid protein C / Flavivirus non-structural protein NS2B / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS4A / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus NS3 protease (NS3pro) domain profile. / Flavivirus NS2B domain profile. / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / RdRp of positive ssRNA viruses catalytic domain profile. / Flavivirus DEAD domain / Flavivirus glycoprotein, immunoglobulin-like domain / FtsJ-like methyltransferase / Flavivirus non-structural protein NS4A / Flavivirus polyprotein propeptide / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS2A / Flavivirus envelope glycoprotein M / Flavivirus capsid protein C / Flavivirus non-structural protein NS2B / Flavivirus RNA-directed RNA polymerase / Envelope glycoprotein M, flavivirus / RNA-directed RNA polymerase, flavivirus / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domains / suppression by virus of host STAT2 activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA (guanine-N7-)-methyltransferase activity / host cell endoplasmic reticulum membrane / ATP-dependent helicase activity / viral life cycle / RNA helicase activity / double-stranded RNA binding / suppression by virus of host type I interferon-mediated signaling pathway / viral capsid / induction by virus of host autophagy / fusion of virus membrane with host endosome membrane / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / viral envelope / protein dimerization activity / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / serine-type endopeptidase activity / integral component of membrane / extracellular region / ATP binding / metal ion binding / Premembrane protein / Genome polyprotein
Function and homology information
SourceDengue virus 4
Methodsingle particle reconstruction / cryo EM / 4.1 Å resolution
AuthorsKostyuchenko VA / Chew PL / Ng TS / Lok SM
CitationJournal: J. Virol. / Year: 2014
Title: Near-atomic resolution cryo-electron microscopic structure of dengue serotype 4 virus.
Authors: Victor A Kostyuchenko / Pau Ling Chew / Thiam-Seng Ng / Shee-Mei Lok
Validation ReportPDB-ID: 4cbf

SummaryFull reportAbout validation report
DateDeposition: Oct 14, 2013 / Header (metadata) release: Oct 23, 2013 / Map release: Nov 6, 2013 / Last update: Feb 17, 2016

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Structure visualization

Movie
  • 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
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  • Surface view with fitted model
  • Atomic models: : PDB-4cbf
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-4cbf
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_2485.map.gz (map file in CCP4 format, 1024001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
640 pix
0.8 Å/pix.
= 512. Å
640 pix
0.8 Å/pix.
= 512. Å
640 pix
0.8 Å/pix.
= 512. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8 Å
Density
Contour Level:2.5 (by author), 2.5 (movie #1):
Minimum - Maximum-10.29256344 - 9.6550312
Average (Standard dev.)-0.11775072 (1.00091231)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions640640640
Origin-320-320-320
Limit319319319
Spacing640640640
CellA=B=C: 512 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.80.80.8
M x/y/z640640640
origin x/y/z0.0000.0000.000
length x/y/z512.000512.000512.000
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS-320-320-320
NC/NR/NS640640640
D min/max/mean-10.2939.655-0.118

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Supplemental data

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Sample components

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Entire Mature Dengue virus serotype 4

EntireName: Mature Dengue virus serotype 4 / Number of components: 1

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Component #1: virus, Dengue virus 4

VirusName: Dengue virus 4 / Class: VIRION / Empty: No / Enveloped: Yes / Isolate: SEROTYPE
SpeciesSpecies: Dengue virus 4 / Serotype: 4
Source (engineered)Expression System: Drosophila melanogaster (fruit fly) / Cell of expression system: c6/36
Source (natural)Host Species: Homo sapiens (human) / Host category: VERTEBRATES
Shell #1Name of element: glycoprotein shell / Diameter: 480 Å / T number(triangulation number): 1

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 12 mM Tris, 120 mM NaCl, 1 mM EDTA / pH: 8
Support filmthin carbon film
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Method: Blot for 2 seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Apr 14, 2012
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 18 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 125000 X (nominal), 129629 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected at 250,000 times magnification
Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 0.5 - 3.5 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 100 K
CameraDetector: FEI FALCON I (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 716 / Sampling size: 14 microns / Bit depth: 16

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 16602
Details: particles selected in EMAN2 boxer swarm mode, CTF estimated with ctffind3
3D reconstructionAlgorithm: Cross-common lines / Software: MPSA, EMAN, EMAN2 / CTF correction: each particle / Resolution: 4.1 Å / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: CHIMERA, Coot, CNS / Refinement protocol: flexible / Target criteria: real space correlation / Refinement space: REAL
Details: Initially fitted in Chimera, model rebuilt in Coot, refined in CNS
Input PDB model: 3j27
Chain ID: A, B, C, D, E, F
Output model

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