[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
Components
  • Envelope protein M
  • Major envelope protein E
KeywordsVIRUS / FLAVIVIRUS / FLAVIVIRIDAE / DENGUE VIRUS / GLYCOPROTEIN E FROM TICK-BORNE ENCEPHALITIS VIRUS / MEMBRANE PROTEIN M / CRYO-EM / Icosahedral virus / Virus
Function / homologyFlavivirus non-structural protein NS1 / RNA-directed RNA polymerase, flavivirus / S-adenosyl-L-methionine-dependent methyltransferase / P-loop containing nucleoside triphosphate hydrolase / Flavivirus glycoprotein E, immunoglobulin-like domain / mRNA cap 0/1 methyltransferase / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Immunoglobulin E-set / Genome polyprotein, Flavivirus / Helicase superfamily 1/2, ATP-binding domain ...Flavivirus non-structural protein NS1 / RNA-directed RNA polymerase, flavivirus / S-adenosyl-L-methionine-dependent methyltransferase / P-loop containing nucleoside triphosphate hydrolase / Flavivirus glycoprotein E, immunoglobulin-like domain / mRNA cap 0/1 methyltransferase / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Immunoglobulin E-set / Genome polyprotein, Flavivirus / Helicase superfamily 1/2, ATP-binding domain / Flaviviral glycoprotein E, central domain, subdomain 2 / Flaviviral glycoprotein E, central domain, subdomain 1 / Envelope glycoprotein M, flavivirus / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS2A / Flavivirus capsid protein C / Flavivirus glycoprotein central and dimerisation domain / Flavivirus non-structural protein NS4B / Helicase, C-terminal / Flavivirus NS3, petidase S7 / Flavivirus polyprotein propeptide / Ribosomal RNA methyltransferase FtsJ domain / RNA-directed RNA polymerase, catalytic domain / Flavivirus glycoprotein, central and dimerisation domain superfamily / Peptidase S1, PA clan / DEAD box, Flavivirus / Flaviviral glycoprotein E, dimerisation domain / 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 envelope glycoprotein M / Flavivirus capsid protein C / Flavivirus non-structural protein NS2B / Flavivirus RNA-directed RNA polymerase / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus non-structural Protein NS1 / Flavivirus glycoprotein, central and dimerisation domains / Flavivirus polyprotein propeptide superfamily / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Envelope glycoprotein M superfamily, flavivirus / suppression by virus of host TYK2 activity / host cell mitochondrion / Flavivirin / mRNA (guanine-N7-)-methyltransferase / mRNA (nucleoside-2'-O-)-methyltransferase / suppression by virus of host STAT2 activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA (guanine-N7-)-methyltransferase activity / suppression by virus of host MAVS activity / host cell endoplasmic reticulum membrane / ATP-dependent helicase activity / host cell perinuclear region of cytoplasm / RNA helicase activity / pore formation by virus in membrane of host cell / integral to membrane of host cell / double-stranded RNA binding / suppression by virus of host type I interferon-mediated signaling pathway / RNA helicase / nucleoside-triphosphatase / viral capsid / RNA-directed RNA polymerase / ion channel activity / induction by virus of host autophagy / protein complex oligomerization / clathrin-dependent endocytosis of virus by host cell / fusion of virus membrane with host endosome membrane / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / viral envelope / protein dimerization activity / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / serine-type endopeptidase activity / regulation of transcription, DNA-templated / transcription, DNA-templated / integral component of membrane / extracellular region / ATP binding / metal ion binding / Genome polyprotein / Genome polyprotein / Genome polyprotein
Function and homology information
Specimen sourceDengue virus 2 Puerto Rico/PR159-S1/1969
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 9.5 Å resolution
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.
Citation
Journal: Nat. Struct. Biol. / Year: 2003
Title: Visualization of membrane protein domains by cryo-electron microscopy of dengue virus.
Authors: 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: Journal: Cell(Cambridge,Mass.) / Year: 2002
Title: Structure of Dengue Virus: Implications for Flaviviruses Organization, Maturation and Fusion
Authors: 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: 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.
#3: Journal: Nature / Year: 1995
Title: Virology. When it's better to lie low.
Authors: Kuhn, R.J. / Rossmann, M.G.
#4: Journal: Microbiol.Mol.Biol.Rev. / Year: 1999
Title: Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs
Authors: 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 typeGroupCategoryItemProviderType
1.0Nov 4, 2003Structure modelrepositoryInitial release
1.1Apr 29, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance
1.3Jul 18, 2018Structure modelData collectionem_image_scans / em_software_em_software.image_processing_id / _em_software.name
Remark 999SEQUENCE Only coordinates for CA atoms were submitted. The deposited sequence is based on the E ...SEQUENCE 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
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

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)188,3696
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

-
Components

#1: Protein/peptide Major envelope protein E / Coordinate model: Cα atoms only


Mass: 54401.758 Da / Num. of mol.: 3 / Source: (natural) Dengue virus 2 Puerto Rico/PR159-S1/1969 / Genus: Flavivirus / Species: Dengue virus / Strain: PR159/S1 / References: UniProt: P12823, UniProt: P14337*PLUS
#2: Protein/peptide Envelope protein M / / Coordinate model: Cα atoms only


Mass: 8387.841 Da / Num. of mol.: 3 / Source: (natural) Dengue virus 2 Puerto Rico/PR159-S1/1969 / Genus: Flavivirus / Species: Dengue virus / Strain: PR159/S1 / References: UniProt: P12823, UniProt: Q9WDA7*PLUS

-
Experimental details

-
Experiment

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

-
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
Method: electron microscopy / Details: Electron Microscopy

-
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 FIELDBright-field microscopy / 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

-
Processing

EM software
IDNameCategory
1EMfitmodel fitting
2EM3DR3D reconstruction
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

+
About Yorodumi

-
News

-
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
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

+
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

+
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

Read more

-
Yorodumi

Thousand views of thousand structures

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

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more