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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
Components
  • Envelope proteinViral envelope
  • 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
Function / homologyFlaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein M / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus polyprotein propeptide superfamily / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Envelope glycoprotein M superfamily, flavivirus / Flaviviral glycoprotein E, dimerisation domain / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain ...Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein M / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus polyprotein propeptide superfamily / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Envelope glycoprotein M superfamily, flavivirus / Flaviviral glycoprotein E, dimerisation domain / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Immunoglobulin E-set / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus polyprotein propeptide / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Envelope glycoprotein M, flavivirus / Flavivirus polyprotein propeptide / host cell endoplasmic reticulum membrane / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral nucleocapsid / viral envelope / protein dimerization activity / virion attachment to host cell / virion membrane / integral component of membrane / extracellular region / Genome polyprotein
Function and homology information
Specimen sourceDengue virus type 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 25 Å resolution
AuthorsYu, I. / Zhang, W. / Holdway, H.A. / Li, L. / Kostyuchenko, V.A. / Chipman, P.R. / Kuhn, R.J. / Rossmann, M.G. / Chen, J.
CitationJournal: Science / Year: 2008
Title: Structure of the immature dengue virus at low pH primes proteolytic maturation.
Authors: 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

Movie
  • 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
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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: Protein/peptide Envelope protein / Viral envelope / Coordinate model: Cα atoms only


Mass: 43904.410 Da / Num. of mol.: 3 / Source: (natural) Dengue virus type 2 / Strain: Thailand/PUO-218/1980 / References: UniProt: P18356
#2: Protein/peptide Peptide pr / Coordinate model: Cα atoms only


Mass: 9261.531 Da / Num. of mol.: 3 / Source: (natural) Dengue virus type 2 / Strain: Thailand/PUO-218/1980 / References: UniProt: P18356
Sequence detailsTHE AUTHORS STATE THAT THE SEQUENCE CONFLICTS ARE DUE TO STRAIN DIFFERENCES. THE PDB ENTRY USED TO ...THE 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 reconstruction

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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 FIELDBright-field microscopy / 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
2EM3DR3D reconstruction
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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