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- PDB-1p58: Complex Organization of Dengue Virus Membrane Proteins as Reveale... -

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Entry
Database: PDB / ID: 1p58
TitleComplex Organization of Dengue Virus Membrane Proteins as Revealed by 9.5 Angstrom Cryo-EM reconstruction
DescriptorMajor envelope protein E/Envelope glycoprotein M
KeywordsVIRUS / FLAVIVIRUS / FLAVIVIRIDAE / DENGUE VIRUS / GLYCOPROTEIN E FROM TICK-BORNE ENCEPHALITIS VIRUS / MEMBRANE PROTEIN M / CRYO-EM / Icosahedral virus / Virus
Specimen sourceDengue virus 2 Puerto Rico/PR159-S1/1969 / virus
MethodElectron microscopy (9.5 Å resolution / Particle / Single particle)
AuthorsZhang, W. / Chipman, P.R. / Corver, J. / Johnson, P.R. / Zhang, Y. / Mukhopadhyay, S. / Baker, T.S. / Strauss, J.H. / Rossmann, M.G. / Kuhn, R.J.
CitationNat. Struct. Biol., 2003, 10, 907-912

primary. Nat. Struct. Biol., 2003, 10, 907-912 StrPapers
Visualization of membrane protein domains by cryo-electron microscopy of dengue virus.
Wei Zhang / Paul R Chipman / Jeroen Corver / Peter R Johnson / Ying Zhang / Suchetana Mukhopadhyay / Timothy S Baker / James H Strauss / Michael G Rossmann / Richard J Kuhn

#1. Cell(Cambridge,Mass.), 2002, 108, 717-725
Structure of Dengue Virus: Implications for Flaviviruses Organization, Maturation and Fusion
Kuhn, R.J. / Zhang, W. / Rossmann, M.G. / Pletnev, S.V. / Corver, J. / Lenches, E. / Jones, C.T. / Mukhopadhyay, S. / Chipman, P.R. / Strauss, E.G. / Baker, T.S. / Strauss, J.H.

#2. Nature, 1995, 375, 291-298
The envelope glycoprotein from tick-borne encephalitis virus at 2 A resolution
Rey, F.A. / Heinz, F.X. / Mandl, C. / Kunz, C. / Harrison, S.C.

#3. Nature, 1995, 375, 275-276
Virology. When it's better to lie low.
Kuhn, R.J. / Rossmann, M.G.

#4. Microbiol.Mol.Biol.Rev., 1999, 63, 862-922
Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs
Baker, T.S. / Olson, N.H. / Fuller, S.D.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 25, 2003 / Release: Nov 4, 2003
RevisionDateData content typeGroupProviderType
1.0Nov 4, 2003Structure modelrepositoryInitial release
1.1Apr 29, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
Remark 999SEQUENCE Only coordinates for CA atoms were submitted. The deposited sequence is based on the E protein of dengue 2 virus S1 strain supplied by Hawaii Biotechnology Group, Inc. (Aiea, Hawaii).

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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
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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Assembly

Deposited unit
A: Major envelope protein E
B: Major envelope protein E
C: Major envelope protein E
D: Envelope protein M
E: Envelope protein M
F: Envelope protein M


Theoretical massNumber of molelcules
Total (without water)188,3696
Polyers188,3696
Non-polymers00
Water0
#1
A: Major envelope protein E
B: Major envelope protein E
C: Major envelope protein E
D: Envelope protein M
E: Envelope protein M
F: Envelope protein M
x 60


Theoretical massNumber of molelcules
Total (without water)11,302,128360
Polyers11,302,128360
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: Major envelope protein E
B: Major envelope protein E
C: Major envelope protein E
D: Envelope protein M
E: Envelope protein M
F: Envelope protein M
x 5


  • icosahedral pentamer
  • 942 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)941,84430
Polyers941,84430
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#4
A: Major envelope protein E
B: Major envelope protein E
C: Major envelope protein E
D: Envelope protein M
E: Envelope protein M
F: Envelope protein M
x 6


  • icosahedral 23 hexamer
  • 1.13 MDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)1,130,21336
Polyers1,130,21336
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)Major envelope protein E


Mass: 54401.758 Da / Num. of mol.: 3
Source: (natural) Dengue virus 2 Puerto Rico/PR159-S1/1969 / virus
References: UniProt: P12823

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)
#2: Polypeptide(L)Envelope protein M


Mass: 8387.841 Da / Num. of mol.: 3
Source: (natural) Dengue virus 2 Puerto Rico/PR159-S1/1969 / virus
References: UniProt: P12823

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)

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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 VIRUS / Type: VIRUS
Details of virusVirus host category: INVERTEBRATES / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Aedes aegypti / Strain: C6/36
Buffer solutionName: 50 mM TRIS, 75 mM NaCl, 1 mM EDTA / Details: 50 mM TRIS, 75 mM NaCl, 1 mM EDTA / pH: 7.6
SpecimenConc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: Concentration is given in PFU/ML
VitrificationDetails: SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE
Crystal grow
*PLUS
Temp unit: K / Method: electron microscopy / Details: Electron Microscopy

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Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM200T / Date: Jun 27, 2000
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 / Nominal defocus max: 48 nm / Nominal defocus min: 8 nm / Cs: 2 mm
Specimen holderTemperature: 87 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 27 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategory
1EMFitMODEL FITTING
2EM3DRRECONSTRUCTION
CTF correctionDetails: each viral image was CTF corrected before reconstruction, based on the following equation: F(corr)=F(obs)/[|CTF|+wiener*(1-|CTF|)]
SymmetryPoint symmetry: I
3D reconstructionMethod: FOURIER-BESSEL METHOD / Resolution: 9.5 Å / Number of particles: 1691 / Nominal pixel size: 2.8
Details: THE RECONSTRUCTION WAS COMPUTED FROM 1691 DENGUE VIRUS IMAGES THAT WERE SELECTED FROM 78 MICROGRAPHS. ORIENTATIONS WERE DETERMINED BY THE MODEL-BASED POLAR-FOURIER TRANSFORM METHOD (BAKER AND CHENG, 1996, J.STRUC.BIOL. 116,120-130) AND REFINED BY THE MODEL-BASED FOURIER TRANSFORM REFINEMENT PROCEDURE(http://bond.cs.ucf.edu/ComputationalBiology/Projects/POR/Home.html).
Symmetry type: POINT
Atomic model buildingRef space: REAL
Atomic model building
IDPDB-ID 3D fitting ID
11SVB1
21JCH1
Number of atoms included #LASTProtein: 1635 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1635

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