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- EMDB-5422: cryo-EM reconstruction of immature dengue virus -

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Basic information

Entry
Database: EMDB / ID: EMD-5422
Titlecryo-EM reconstruction of immature dengue virus
Map dataReconstruction of immature dengue viral particles
Sample
  • Sample: immature dengue particle
  • Virus: Dengue virus 2
Keywordsimmature dengue flavivirus cryo-EM
Function / homology
Function and homology information


flavivirin / serine-type peptidase activity / nucleoside-triphosphate phosphatase / double-stranded RNA binding / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / RNA helicase ...flavivirin / serine-type peptidase activity / nucleoside-triphosphate phosphatase / double-stranded RNA binding / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / RNA helicase activity / host cell endoplasmic reticulum membrane / protein dimerization activity / RNA helicase / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane
Similarity search - Function
Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Flaviviral glycoprotein E, central domain, subdomain 1 ...Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesDengue virus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 12.5 Å
AuthorsZhang Y / Zhang W / Ogata S / Clements D / Strauss JH / Baker TS / Kuhn RJ / Rossmann MG
CitationJournal: Structure / Year: 2004
Title: Conformational changes of the flavivirus E glycoprotein.
Authors: Ying Zhang / Wei Zhang / Steven Ogata / David Clements / James H Strauss / Timothy S Baker / Richard J Kuhn / Michael G Rossmann /
Abstract: Dengue virus, a member of the Flaviviridae family, has a surface composed of 180 copies each of the envelope (E) glycoprotein and the membrane (M) protein. The crystal structure of an N-terminal ...Dengue virus, a member of the Flaviviridae family, has a surface composed of 180 copies each of the envelope (E) glycoprotein and the membrane (M) protein. The crystal structure of an N-terminal fragment of E has been determined and compared with a previously described structure. The primary difference between these structures is a 10 degrees rotation about a hinge relating the fusion domain DII to domains DI and DIII. These two rigid body components were used for independent fitting of E into the cryo-electron microscopy maps of both immature and mature dengue viruses. The fitted E structures in these two particles showed a difference of 27 degrees between the two components. Comparison of the E structure in its postfusion state with that in the immature and mature virions shows a rotation approximately around the same hinge. Flexibility of E is apparently a functional requirement for assembly and infection of flaviviruses.
History
DepositionMay 14, 2012-
Header (metadata) releaseMay 16, 2012-
Map releaseMay 16, 2012-
UpdateOct 12, 2016-
Current statusOct 12, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-1tge
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5422_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5422.map.gz / Format: CCP4 / Size: 51 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of immature dengue viral particles
Voxel sizeX=Y=Z: 2.12 Å
Density
Contour LevelBy EMDB: 1.25 / Movie #1: 1
Minimum - Maximum-3.10537338 - 5.79204464
Average (Standard dev.)-0.02588803 (±1.00161886)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-150-1500
Dimensions301301151
Spacing301301151
CellA: 638.12 Å / B: 638.12 Å / C: 320.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.122.122.12
M x/y/z301301151
origin x/y/z0.0000.0000.000
length x/y/z638.120638.120320.120
α/β/γ90.00090.00090.000
start NX/NY/NZ-150-1500
NX/NY/NZ301301151
MAP C/R/S213
start NC/NR/NS-150-1500
NC/NR/NS301301151
D min/max/mean-3.1055.792-0.026

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Supplemental data

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Sample components

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Entire : immature dengue particle

EntireName: immature dengue particle
Components
  • Sample: immature dengue particle
  • Virus: Dengue virus 2

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Supramolecule #1000: immature dengue particle

SupramoleculeName: immature dengue particle / type: sample / ID: 1000 / Oligomeric state: icosahedral / Number unique components: 3

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Supramolecule #1: Dengue virus 2

SupramoleculeName: Dengue virus 2 / type: virus / ID: 1 / Details: Dengue virus 2 strain PR159-S1 / NCBI-ID: 11060 / Sci species name: Dengue virus 2 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Aedes albopictus (Asian tiger mosquito) / synonym: INVERTEBRATES

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Purdue-manufactured, gravity-driven device. Vitrification carried out in hood.

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
DateFeb 1, 2003
Image recordingDigitization - Scanner: ZEISS SCAI

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 12.5 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 4099

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Atomic model buiding 1

Initial modelPDB ID:

3c6d

RefinementSpace: REAL
Output model

PDB-1tge:
The structure of immature Dengue virus at 12.5 angstrom

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