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- PDB-1k4r: Structure of Dengue Virus -

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Basic information

Entry
Database: PDB / ID: 1k4r
TitleStructure of Dengue Virus
ComponentsMAJOR ENVELOPE PROTEIN E
KeywordsVIRUS / Flavivirus / Flaviviridae / Dengue virus / glycoprotein E from tick-borne encephalitis virus / Icosahedral virus
Function / homology
Function and homology information


flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / membrane => GO:0016020 ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / membrane => GO:0016020 / protein dimerization activity / RNA helicase / induction by virus of host autophagy / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / structural molecule activity / virion attachment to host cell / endoplasmic reticulum membrane / virion membrane / extracellular region / ATP binding / metal ion binding / nucleus
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesChimeric Tick-borne encephalitis virus/Dengue virus 4
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 24 Å
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. ...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.
Citation
Journal: Cell / Year: 2002
Title: Structure of dengue virus: implications for flavivirus organization, maturation, and fusion.
Authors: 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 ...Authors: 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 /
Abstract: The first structure of a flavivirus has been determined by using a combination of cryoelectron microscopy and fitting of the known structure of glycoprotein E into the electron density map. The virus ...The first structure of a flavivirus has been determined by using a combination of cryoelectron microscopy and fitting of the known structure of glycoprotein E into the electron density map. The virus core, within a lipid bilayer, has a less-ordered structure than the external, icosahedral scaffold of 90 glycoprotein E dimers. The three E monomers per icosahedral asymmetric unit do not have quasiequivalent symmetric environments. Difference maps indicate the location of the small membrane protein M relative to the overlaying scaffold of E dimers. The structure suggests that flaviviruses, and by analogy also alphaviruses, employ a fusion mechanism in which the distal beta barrels of domain II of the glycoprotein E are inserted into the cellular membrane.
#1: Journal: Nature / Year: 1995
Title: Virology. When It's Better to Lie Low
Authors: Kuhn, R.J. / Rossmann, M.G.
#2: Journal: Nature / Year: 1995
Title: The Envelope Glycoprotein from Tick-borne Encephalitis Virus at 2 A Resolution
Authors: Rey, F.A. / Heinz, F.X. / Mandl, C. / Kunz, C. / Harrison, S.C.
History
DepositionOct 8, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 13, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
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
Polymers129,6933
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
Polymers7,781,606180
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
Polymers648,46715
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
Polymers778,16118
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
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

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Components

#1: Protein MAJOR ENVELOPE PROTEIN E


Mass: 43231.145 Da / Num. of mol.: 3 / Fragment: UNP residues 284-678 / Source method: isolated from a natural source
Source: (natural) Chimeric Tick-borne encephalitis virus/Dengue virus 4
Genus: Flavivirus / References: UniProt: C3V005

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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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 / Host category: VERTEBRATES / Isolate: SPECIES / 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
Method: cryo-electron microscopy

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200T
Electron gunElectron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Nominal defocus max: 1920 nm / Nominal defocus min: 790 nm / Cs: 2 mm
Specimen holderTemperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 25.5 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 25
ReflectionHighest resolution: 24 Å

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Processing

Software
NameClassification
emfitmodel building
EMFITphasing
EM software
IDNameCategoryDetails
1EMfitmodel fittingCLIMB procedure
2OTHER3D reconstruction
CTF correctionDetails: EACH VIRAL IMAGE WAS CTF CORRECTED BEFORE RECONSTRUCTION, BASED ON THE FOLLOWING EQUATION: F(CORR)=F(OBS)/[|CTF|+WIENER]
SymmetryPoint symmetry: I (icosahedral)
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 / Num. of particles: 526 / Nominal pixel size: 2.8 Å / Actual pixel size: 2.9 Å / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Details: 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 ...Details: 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.
Atomic model buildingPDB-ID: 1SVB
RefinementHighest resolution: 24 Å
Details: Molecules of glycoprotein E of Tick-borne encephalitis virus were solved by using cryo-EM map of Dengue virus
Refinement stepCycle: LAST / Highest resolution: 24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9084 0 0 0 9084

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