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- PDB-1k4r: Structure of Dengue Virus -

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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 / Virus
Function / homologyDEAD box, Flavivirus / Genome polyprotein, Flavivirus / Helicase, C-terminal / Flavivirus NS3, petidase S7 / Flavivirus polyprotein propeptide / Ribosomal RNA methyltransferase FtsJ domain / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus glycoprotein central and dimerisation domain ...DEAD box, Flavivirus / Genome polyprotein, Flavivirus / Helicase, C-terminal / Flavivirus NS3, petidase S7 / Flavivirus polyprotein propeptide / Ribosomal RNA methyltransferase FtsJ domain / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus glycoprotein central and dimerisation domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Helicase superfamily 1/2, ATP-binding domain / Immunoglobulin E-set / Flavivirus non-structural protein NS1 / Flavivirus envelope glycoprotein E, Stem/Anchor domain / mRNA cap 0/1 methyltransferase / Flavivirus glycoprotein E, immunoglobulin-like domain / P-loop containing nucleoside triphosphate hydrolase / S-adenosyl-L-methionine-dependent methyltransferase / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flavivirus capsid protein C superfamily / Flaviviral glycoprotein E, dimerisation domain / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus polyprotein propeptide superfamily / Flavivirus non-structural protein NS4B / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS2A / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus NS3 protease (NS3pro) domain profile. / Flavivirus NS2B domain profile. / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / RdRp of positive ssRNA viruses catalytic domain profile. / Flavivirus DEAD domain / Flavivirus glycoprotein, immunoglobulin-like domain / FtsJ-like methyltransferase / Flavivirus polyprotein propeptide / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS2A / Flavivirus capsid protein C / Flavivirus non-structural protein NS2B / Flavivirus RNA-directed RNA polymerase / RNA-directed RNA polymerase, flavivirus / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus glycoprotein, central and dimerisation domains / suppression by virus of host STAT2 activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA (guanine-N7-)-methyltransferase activity / host cell endoplasmic reticulum membrane / ATP-dependent helicase activity / RNA helicase activity / double-stranded RNA binding / suppression by virus of host type I interferon-mediated signaling pathway / viral capsid / induction by virus of host autophagy / fusion of virus membrane with host endosome membrane / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / protein dimerization activity / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / serine-type endopeptidase activity / integral component of membrane / extracellular region / ATP binding / metal ion binding / Genome polyprotein
Function and homology information
Specimen sourceChimeric Tick-borne encephalitis virus/Dengue virus 4
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 24 Å resolution
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.
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 S Baker / James H Strauss
#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.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Oct 8, 2001 / Release: Mar 13, 2002
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 13, 2002Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Jul 18, 2018Structure modelData collectionem_software_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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Structure viewerMolecule:
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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: Protein/peptide 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
Genus: Flavivirus / References: UniProt: C3V005

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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: 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
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 FIELDBright-field microscopy / 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
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
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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