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- PDB-3c6r: Low pH Immature Dengue Virus -

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Basic information

Entry
Database: PDB / ID: 3c6r
TitleLow pH Immature Dengue Virus
DescriptorEnvelope protein, Peptide pr
KeywordsVIRUS / dengue / immature / prM / E / Capsid protein / Cleavage on pair of basic residues / Core protein / Endoplasmic reticulum / Envelope protein / Glycoprotein / Membrane / Secreted / Transmembrane / Virion / icosahedral virus / virus
Specimen sourceDengue virus type 2 / virus
MethodElectron microscopy (25 Å resolution / Particle / Single particle)
AuthorsYu, I. / Zhang, W. / Holdway, H.A. / Li, L. / Kostyuchenko, V.A. / Chipman, P.R. / Kuhn, R.J. / Rossmann, M.G. / Chen, J.
CitationScience, 2008, 319, 1834-1837

Science, 2008, 319, 1834-1837 StrPapers
Structure of the immature dengue virus at low pH primes proteolytic maturation.
I-Mei Yu / Wei Zhang / Heather A Holdaway / Long Li / Victor A Kostyuchenko / Paul R Chipman / Richard J Kuhn / Michael G Rossmann / Jue Chen

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Feb 5, 2008 / Release: Apr 22, 2008
RevisionDateData content typeGroupProviderType
1.0Apr 22, 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-5006
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Assembly

Deposited unit
A: Envelope protein
D: Peptide pr
B: Envelope protein
E: Peptide pr
C: Envelope protein
F: Peptide pr


Theoretical massNumber of molelcules
Total (without water)159,4986
Polyers159,4986
Non-polymers00
Water0
#1
A: Envelope protein
D: Peptide pr
B: Envelope protein
E: Peptide pr
C: Envelope protein
F: Peptide pr
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: Envelope protein
D: Peptide pr
B: Envelope protein
E: Peptide pr
C: Envelope protein
F: Peptide pr
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: Envelope protein
D: Peptide pr
B: Envelope protein
E: Peptide pr
C: Envelope protein
F: Peptide pr
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)Envelope protein / Coordinate model: Cα atoms only


Mass: 43904.410 Da / Num. of mol.: 3 / Source: (natural) Dengue virus type 2 / virus / References: UniProt: P18356

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)
  • virion attachment to host cell (GO: 0019062)
#2: Polypeptide(L)Peptide pr / Coordinate model: Cα atoms only


Mass: 9261.531 Da / Num. of mol.: 3 / Source: (natural) Dengue virus type 2 / virus / References: UniProt: P18356

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)
  • virion attachment to host cell (GO: 0019062)
Sequence detailsTHE AUTHORS STATE THAT THE SEQUENCE CONFLICTS ARE DUE TO STRAIN DIFFERENCES. THE PDB ENTRY USED TO FIT INTO THE MAP IS A MODEL GENERATED FROM TWO DIFFERENT STRUCTURES.

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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: immature Dengue virus / Type: VIRUS
Buffer solutionDetails: The virus was mixed in NTE buffer (10 mM Tris, 120 mM NaCl, and 1 mM EDTA at pH 8) with 50 mM MES, 120 mM NaCl at pH 5.6 to yield a final pH of 6
pH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM200FEG
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 / Nominal defocus max: 2900 nm / Nominal defocus min: 1400 nm
Image recordingElectron dose: 17 e/Å2 / Film or detector model: KODAK SO-163 FILM
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1EMFitMODEL FITTING
2EM3DRRECONSTRUCTION
CTF correctionDetails: Both amplitude and phase of CTF are corrected for each boxed particle.
SymmetryPoint symmetry: I
3D reconstructionMethod: Cross-correlation in real and reciprocal space for orientation determination; Fourier-Bessel method for reconstruction.
Resolution: 25 Å / Number of particles: 231 / Nominal pixel size: 2.8 / Actual pixel size: 2.7 / Magnification calibration: Grating Replica EM grid / Symmetry type: POINT
Atomic model buildingRef space: REAL
Number of atoms included #LASTProtein: 1422 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1422

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