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- PDB-3c6d: The pseudo-atomic structure of dengue immature virus -

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Basic information

Entry
Database: PDB / ID: 3c6d
TitleThe pseudo-atomic structure of dengue immature virus
DescriptorPolyprotein, prM
KeywordsVIRUS / icosahedral virion / Helicase / Hydrolase / Nucleotide-binding / RNA replication / Transmembrane / ATP-binding / Capsid protein / Cleavage on pair of basic residues / Endoplasmic reticulum / Envelope protein / Glycoprotein / Metal-binding / Multifunctional enzyme / Nucleotidyltransferase / Nucleus / Phosphoprotein / Protease / Ribonucleoprotein / RNA-binding / RNA-directed RNA polymerase / Secreted / Serine protease / Transcription / Transcription regulation / Transferase / Viral nucleoprotein / icosahedral virus
Specimen sourceDengue virus 2 Thailand/16681/84 / virus
Dengue virus 2 / virus
MethodElectron microscopy (12.5 A resolution / Single particle / Vitreous ice (cryo EM))
AuthorsLi, L.
CitationScience, 2008, 319, 1830-1834

Science, 2008, 319, 1830-1834 StrPapers
The flavivirus precursor membrane-envelope protein complex: structure and maturation.
Long Li / Shee-Mei Lok / I-Mei Yu / Ying Zhang / Richard J Kuhn / Jue Chen / Michael G Rossmann

DateDeposition: Feb 4, 2008 / Release: Apr 8, 2008 / Last modification: Feb 2, 2010

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-5102
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Assembly

Deposited unit
A: Polyprotein
B: Polyprotein
C: Polyprotein
D: prM
E: prM
F: prM


Theoretical massNumber of molelcules
Total (without water)159,4996
Polyers159,4996
Non-polymers00
Water0
#1
A: Polyprotein
B: Polyprotein
C: Polyprotein
D: prM
E: prM
F: prM
x 60


Theoretical massNumber of molelcules
Total (without water)9,569,947360
Polyers9,569,947360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
#2


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
#3
A: Polyprotein
B: Polyprotein
C: Polyprotein
D: prM
E: prM
F: prM
x 5


  • icosahedral pentamer
  • 797 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)797,49630
Polyers797,49630
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#4
A: Polyprotein
B: Polyprotein
C: Polyprotein
D: prM
E: prM
F: prM
x 6


  • icosahedral 23 hexamer
  • 957 kDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)956,99536
Polyers956,99536
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
PAU


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

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Components

#1: Polypeptide(L)Polyprotein


Mass: 43904.797 Da / Num. of mol.: 3 / Source: (natural) Dengue virus 2 Thailand/16681/84 / virus / References: UniProt: O11875

Cellular component

Molecular function

Biological process

#2: Polypeptide(L)prM


Mass: 9261.574 Da / Num. of mol.: 3 / Source: (natural) Dengue virus 2 / virus / References: UniProt: P14337

Cellular component

Molecular function

Biological process

  • clathrin-dependent endocytosis of virus by host cell (GO: 0075512)
  • fusion of virus membrane with host endosome membrane (GO: 0039654)
  • induction by virus of host autophagy (GO: 0039520)
  • regulation of transcription, DNA-templated (GO: 0006355)
  • suppression by virus of host STAT2 activity (GO: 0039564)
  • suppression by virus of host TYK2 activity (GO: 0039574)
  • suppression by virus of host type I interferon-mediated signaling pathway (GO: 0039502)
  • transcription, DNA-templated (GO: 0006351)
  • viral RNA genome replication (GO: 0039694)
  • virion attachment to host cell (GO: 0019062)
Sequence detailsTHE AUTHOR STATES THAT THE DIFFERENCES BETWEEN THE SEQUENCE AND THE SEQUENCE IN THE DATABASE REFERENCE ARE DUE TO THE DIFFERENCES BETWEEN VIRUS STRAINS.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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Sample preparation

Assembly of specimenName: DENGUE-2 IMMATURE PARTICLE / Aggregation state: PARTICLE
Details: THE SAMPLES WERE PRODUCED BY ADDING AMMONIUM CHLORIDE TO THE MEDIA IN THE LATE INFECTION STAGE
Details of the virusVirus host category: VERTEBRATES / Virus host growth cell: C6/36 / Virus host species: homo sapiens / Virus isolate: STRAIN / Virus type: immature virion

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Electron microscopy imaging

MicroscopyMicroscope model: PHILLIPS CM300
Electron gunElectron source: FIELD EMISSION GUN
Electron lensMode: BRIGHT FIELD / Calibrated magnification: 33000 X / Nominal defocus max: 364 nm / Nominal defocus min: 1662 nm / Cs: 2 mm
Specimen holderTemperature: 1 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

Image selectionSoftware name: EMFIT
EM single particle entitySymmetry type: ICOSAHEDRAL
3D reconstructionResolution: 12.5 A
Atomic model buildingMethod: SEE PRIMARY CITATION / Ref protocol: RIGID BODY / Ref space: REAL
Target criteria: USE PROGRAM EMFIT, SEARCH FOR POSTION WHERE ATOMS OCCUPY MOST EM DENSITY PEAKS
Atomic model buildingPDB-ID: 1TG8, 3C5X
Number of atoms included #LASTProtein: 1413 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1413

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