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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 Å resolution / Particle / Single particle)
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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 4, 2008 / Release: Apr 8, 2008
RevisionDateData content typeGroupProviderType
1.0Apr 8, 2008Structure modelrepositoryInitial release
1.1Jul 13, 2011Structure modelVersion format compliance

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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)159,4986
Polyers159,4986
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)9,569,869360
Polyers9,569,869360
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)797,48930
Polyers797,48930
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)956,98736
Polyers956,98736
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
#5


  • 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: 43904.410 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: 9261.531 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)
  • pore formation by virus in membrane of host cell (GO: 0039707)
  • protein oligomerization (GO: 0051259)
  • 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 experimentAggregation state: PARTICLE / Reconstruction method: SINGLE PARTICLE

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Sample preparation

ComponentName: DENGUE-2 IMMATURE PARTICLE
Details: THE SAMPLES WERE PRODUCED BY ADDING AMMONIUM CHLORIDE TO THE MEDIA IN THE LATE INFECTION STAGE
Type: VIRUS
Details of the virusVirus host category: VERTEBRATES / Virus isolate: STRAIN / Virus type: VIRION
EM virus natural hostOrganism: Aedes aegypti / Strain: C6/36
Buffer solutionDetails: 12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA / pH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE

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Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM300FEG/T / Date: Apr 4, 2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 / Calibrated magnification: 33000 / Nominal defocus max: 364 nm / Nominal defocus min: 1662 nm / Cs: 2 mm
Specimen holderTemperature: 1 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategory
1EMFitMODEL FITTING
2SPIDERRECONSTRUCTION
3XMIPPRECONSTRUCTION
SymmetryPoint symmetry: I
3D reconstructionResolution: 12.5 Å / Number of particles: 2741 / Symmetry type: POINT
Atomic model buildingDetails: METHOD--SEE PRIMARY CITATION REFINEMENT PROTOCOL--RIGID BODY
Ref protocol: RIGID BODY FIT / Ref space: REAL
Target criteria: USE PROGRAM EMFIT, SEARCH FOR POSTION WHERE ATOMS OCCUPY MOST EM DENSITY PEAKS
Atomic model building
IDPDB-ID 3D fitting ID
11TG81
23C5X1
Number of atoms included #LASTProtein: 1413 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1413

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