[English] 日本語
Yorodumi
- PDB-1p58: Complex Organization of Dengue Virus Membrane Proteins as Reveale... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

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
Specimen sourceDengue virus 2 Puerto Rico/PR159-S1/1969 / virus
MethodElectron microscopy (9.5 A resolution / Single particle / Vitreous ice (cryo EM))
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.

DateDeposition: Apr 25, 2003 / Release: Nov 4, 2003 / Last modification: Mar 2, 2011
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).

-
Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
  • Download
  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
  • Download
  • Deposited structure unit
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide

Downloads & links

-
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)188,3716
Polyers188,3716
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)11,302,239360
Polyers11,302,239360
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)941,85330
Polyers941,85330
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)1,130,22436
Polyers1,130,22436
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
PAU


  • idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1

-
Components

#1: Polypeptide(L)Major envelope protein E


Mass: 54402.305 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: 8387.914 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)

+
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

-
Sample preparation

Assembly of specimenName: DENGUE VIRUS / Aggregation state: PARTICLE
Details of the virusVirus host category: INVERTEBRATES / Virus host growth cell: mosquito C6/36 / Virus host species: Aedes aegypti / Virus isolate: STRAIN / Virus type: VIRION
Buffer solutionName: 50 mM TRIS, 75 mM NaCl, 1 mM EDTA
Sample preparationpH: 7.6 / Sample conc.: 20 mg/ml
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

-
Electron microscopy imaging

MicroscopyMicroscope model: FEI/PHILIPS CM200T / Date: Jun 27, 2000
Electron gunElectron source: SCHOTTKY FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 2700 e/A2 / Illumination mode: FLOOD BEAM LOW DOSE
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 48 nm / Nominal defocus min: 8 nm / Cs: 2 mm
Specimen holderTemperature: 87 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
CameraType: KODAK SO163 FILM

-
Processing

Image selectionSoftware name: EMFIT / Number of particles: 1691
EM single particle entitySymmetry type: ICOSAHEDRAL
3D reconstructionMethod: FOURIER-BESSEL METHOD / Resolution: 9.5 A / Nominal pixel size: 2.8 A/pix
CTF correction method: each viral image was CTF corrected before reconstruction, based on the following equation: F(corr)=F(obs)/[|CTF|+wiener*(1-|CTF|)]
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).
Atomic model buildingSoftware name: EMFIT / Ref space: REAL
Atomic model buildingPDB-ID: 1SVB and 1JCH
Number of atoms included #LASTProtein: 1635 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1635

+
About Yorodumi

-
News

-
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

-
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

+
Mar 3, 2016. Presentation (PDF format) at IPR seminar on Feb 19.

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more