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- PDB-1k4r: Structure of Dengue Virus -

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Entry
Database: PDB / ID: 1k4r
TitleStructure of Dengue Virus
DescriptorMAJOR ENVELOPE PROTEIN E
KeywordsVIRUS / Flavivirus / Flaviviridae / Dengue virus / glycoprotein E from tick-borne encephalitis virus / Icosahedral virus / Virus
Specimen sourceChimeric Tick-borne encephalitis virus/Dengue virus 4 / virus
MethodElectron microscopy (24 Å resolution / Particle / Single particle)
AuthorsKuhn, 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.
CitationCell, 2002, 108, 717-725

primary. Cell, 2002, 108, 717-725 Yorodumi Papers
Structure of dengue virus: implications for flavivirus organization, maturation, and fusion.
Richard J Kuhn / Wei Zhang / Michael G Rossmann / Sergei V Pletnev / Jeroen Corver / Edith Lenches / Christopher T Jones / Suchetana Mukhopadhyay / Paul R Chipman / Ellen G Strauss / Timothy S Baker / James H Strauss

#1. Nature, 1995, 375, 275-276
Virology. When It's Better to Lie Low
Kuhn, R.J. / Rossmann, M.G.

#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.

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 8, 2001 / Release: Mar 13, 2002
RevisionDateData content typeGroupProviderType
1.0Mar 13, 2002Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
Remark 2RESOLUTION. 24.00 ANGSTROM.

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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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Assembly

Deposited unit
A: MAJOR ENVELOPE PROTEIN E
B: MAJOR ENVELOPE PROTEIN E
C: MAJOR ENVELOPE PROTEIN E


Theoretical massNumber of molelcules
Total (without water)129,6933
Polyers129,6933
Non-polymers00
Water0
#1
A: MAJOR ENVELOPE PROTEIN E
B: MAJOR ENVELOPE PROTEIN E
C: MAJOR ENVELOPE PROTEIN E
x 60


Theoretical massNumber of molelcules
Total (without water)7,781,606180
Polyers7,781,606180
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
x 5


  • icosahedral pentamer
  • 648 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)648,46715
Polyers648,46715
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
#4
A: MAJOR ENVELOPE PROTEIN E
B: MAJOR ENVELOPE PROTEIN E
C: MAJOR ENVELOPE PROTEIN E
x 6


  • icosahedral 23 hexamer
  • 778 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)778,16118
Polyers778,16118
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: 43231.145 Da / Num. of mol.: 3 / Fragment: UNP residues 284-678
Source: (natural) Chimeric Tick-borne encephalitis virus/Dengue virus 4 / virus
References: UniProt: C3V005

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 STAT1 activity (GO: 0039563)
  • suppression by virus of host STAT2 activity (GO: 0039564)
  • 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 MAJOR ENVELOPE PROTEIN E / Type: VIRUS
Details: SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT NEAR LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE.
Details of virusEmpty: NO / Enveloped: YES / Virus host category: VERTEBRATES / Virus isolate: SPECIES / Virus type: VIRION
Natural hostOrganism: Primates
Buffer solutionpH: 7.6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: sample conc. l2.0E10 PFU/ML
VitrificationDetails: LIQUID NITROGEN TEMPERATURE 50MM TRIS-HCL, 75MM NACL, 1MM EDTA
Crystal grow
*PLUS
Temp unit: K / Method: cryo-electron microscopy

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Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM200T
Electron gunElectron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 / Nominal defocus max: 192 nm / Nominal defocus min: 79 nm / Cs: 2 mm
Specimen holderTemperature: 100 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 25.5 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 25
ReflectionD resolution high: 24 Å

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Processing

Software
NameClassification
emfitmodel building
EMFITphasing
EM software
IDNameCategoryDetails
1EMFitMODEL FITTINGCLIMB procedure
2OTHERRECONSTRUCTION
CTF correctionDetails: EACH VIRAL IMAGE WAS CTF CORRECTED BEFORE RECONSTRUCTION, BASED ON THE FOLLOWING EQUATION: F(CORR)=F(OBS)/[|CTF|+WIENER]
SymmetryPoint symmetry: I
3D reconstructionMethod: COMMON-LINES AND POLAR-FOURIER-TRANSFORM (FULLER ET AL. 1996, J.STRUC.BIOL. 116, 48-55 BAKER AND CHENG, 1996, J.STRUC.BIOL. 116, 120-130) SOFTWARE USED, PURDUE PROGRAMS
Resolution: 24 Å / Number of particles: 526 / Nominal pixel size: 2.8 / Actual pixel size: 2.9 / Symmetry type: POINT
Atomic model buildingDetails: METHOD--IN THE FIRST STEP THE CRYSTAL STRUCTURE OF TBEV-E CRYSTALLOGRAPHIC DIMER (REY ET.AL., 1995 NATURELONDON) 375, 291-298) WAS ROTATED ABOUT AND TRANSLATEDAROUND AN ICOSAHEDRAL TWO FOLD AXES TO FIND THE BEST FIT. AFTER THAT THE DENSITIES AT ALL PIXELS COVERED BY THE FIRST FITTED DIMER WERE SET TO ZERO. THE SECOND DIMER WAS THAN PLACED ON A RADIAL AXIS PASSING THROUGH A POINT NEAR THE QUASI-TWOFOLD AXIS.
Ref protocol: RIGID BODY FIT / Ref space: REAL
Atomic model buildingPDB-ID: 1SVB
RefineDetails: Molecules of glycoprotein E of Tick-borne encephalitis virus were solved by using cryo-EM map of Dengue virus
Least-squares processHighest resolution: 24 Å
Refine hist #LASTHighest resolution: 24 Å
Number of atoms included #LASTProtein: 9084 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 9084

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