[English] 日本語
Yorodumi
- PDB-3j6s: Cryo-EM structure of Dengue virus serotype 3 at 28 degrees C -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 3j6s
TitleCryo-EM structure of Dengue virus serotype 3 at 28 degrees C
Components
  • envelope proteinViral envelope
  • membrane protein
KeywordsVIRUS / Dengue virus
Function / homologyFlavivirus capsid protein C / Envelope glycoprotein M, flavivirus / Flavivirus glycoprotein, central and dimerisation domain superfamily / 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 ...Flavivirus capsid protein C / Envelope glycoprotein M, flavivirus / Flavivirus glycoprotein, central and dimerisation domain superfamily / 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 / RNA-directed RNA polymerase, flavivirus / Flaviviral glycoprotein E, dimerisation domain / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS2A / Flavivirus glycoprotein central and dimerisation domain / Flavivirus non-structural protein NS1 / 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 capsid protein C superfamily / Peptidase S1, PA clan / DEAD box, Flavivirus / Flavivirus non-structural protein NS4A / 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 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 / host cell mitochondrion / suppression by virus of host TYK2 activity / flavivirin / suppression by virus of host STAT2 activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / suppression by virus of host innate immune response / host cell endoplasmic reticulum / suppression by virus of host MAVS activity / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA (guanine-N7-)-methyltransferase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / ATP-dependent helicase activity / host cell membrane / suppression by virus of host type I interferon-mediated signaling pathway / pore formation by virus in membrane of host cell / integral to membrane of host cell / RNA helicase activity / double-stranded RNA binding / RNA helicase / nucleoside-triphosphate phosphatase / viral capsid / RNA-directed RNA polymerase / induction by virus of host autophagy / ion channel activity / protein complex oligomerization / clathrin-dependent endocytosis of virus by host cell / viral RNA genome replication / fusion of virus membrane with host endosome membrane / RNA-directed 5'-3' RNA polymerase activity / viral envelope / protein dimerization activity / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / serine-type endopeptidase activity / integral component of membrane / extracellular region / ATP binding / metal ion binding / Genome polyprotein / Genome polyprotein
Function and homology information
Specimen sourceDengue virus 3
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 6 Å resolution
AuthorsFibriansah, G. / Tan, J.L. / Smith, S.A. / de Alwis, R. / Ng, T.-S. / Kostyuchenko, V.A. / Kukkaro, P. / de Silva, A.M. / Crowe Jr., J.E. / Lok, S.-M.
CitationJournal: Nat Commun / Year: 2015
Title: A highly potent human antibody neutralizes dengue virus serotype 3 by binding across three surface proteins.
Authors: Guntur Fibriansah / Joanne L Tan / Scott A Smith / Ruklanthi de Alwis / Thiam-Seng Ng / Victor A Kostyuchenko / Ramesh S Jadi / Petra Kukkaro / Aravinda M de Silva / James E Crowe / Shee-Mei Lok
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 24, 2014 / Release: Mar 4, 2015
RevisionDateData content typeGroupCategoryItemProviderType
1.0Mar 4, 2015Structure modelrepositoryInitial release
1.1Jul 18, 2018Structure modelData collectionem_software_em_software.image_processing_id

-
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
  • Simplified surface model + fitted atomic model
  • EMDB-5933
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-5933
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: envelope protein
B: membrane protein
C: envelope protein
D: membrane protein
E: envelope protein
F: membrane protein


Theoretical massNumber of molelcules
Total (without water)186,0916
Polyers186,0916
Non-polymers00
Water0
1
A: envelope protein
B: membrane protein
C: envelope protein
D: membrane protein
E: envelope protein
F: membrane protein
x 60


Theoretical massNumber of molelcules
Total (without water)11,165,458360
Polyers11,165,458360
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: envelope protein
B: membrane protein
C: envelope protein
D: membrane protein
E: envelope protein
F: membrane protein
x 5


  • icosahedral pentamer
  • 930 kDa, 30 polymers
Theoretical massNumber of molelcules
Total (without water)930,45530
Polyers930,45530
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: envelope protein
B: membrane protein
C: envelope protein
D: membrane protein
E: envelope protein
F: membrane protein
x 6


  • icosahedral 23 hexamer
  • 1.12 MDa, 36 polymers
Theoretical massNumber of molelcules
Total (without water)1,116,54636
Polyers1,116,54636
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 envelope protein / Viral envelope / Coordinate model: Cα atoms only


Mass: 53682.484 Da / Num. of mol.: 3 / Fragment: UNP residues 281-773 / Source: (gene. exp.) Dengue virus 3 / Strain: D3/SG/05K863DK1/2005 / Cell line (production host): C6/36 / Production host: Aedes albopictus (Asian tiger mosquito) / References: UniProt: Q6DLV0, UniProt: A9LID6*PLUS
#2: Protein/peptide membrane protein / / Coordinate model: Cα atoms only


Mass: 8347.836 Da / Num. of mol.: 3 / Fragment: UNP residues 206-280 / Source: (gene. exp.) Dengue virus 3 / Strain: D3/SG/05K863DK1/2005 / Cell line (production host): C6/36 / Production host: Aedes albopictus (Asian tiger mosquito) / References: UniProt: Q6DLV0, UniProt: A9LID6*PLUS

-
Experimental details

-
Experiment

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

-
Sample preparation

ComponentName: Dengue virus serotype 3 / Type: VIRUS
Details of virusEmpty: NO / Enveloped: YES / Virus host category: VERTEBRATES / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionName: 10 mM Tris-HCl, pH 8.0, 120 mM NaCl, 1 mM EDTA / Details: 10 mM Tris-HCl, pH 8.0, 120 mM NaCl, 1 mM EDTA / pH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: ultra-thin carbon-coated lacey carbon grid
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temp: 100 K / Humidity: 100 %
Details: Blotted with filter paper for 2 seconds prior to snap freezing in liquid ethane (FEI VITROBOT MARK IV)
Method: Blotted with filter paper for 2 seconds prior to snap freezing

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TITAN KRIOS / Date: Oct 27, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 75000 / Nominal defocus max: 3500 nm / Nominal defocus min: 1100 nm / Cs: 2.7 mm / Camera length: 0 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 100 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 20.4 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)
Image scansNumber digital images: 836
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

-
Processing

EM software
IDNameVersionCategory
1Cootmodel fitting
2MDFFmodel fitting
3NAMDmodel fitting
4UCSF Chimeramodel fitting
5EMAN13D reconstruction
6EMAN23D reconstruction
7MPSA3D reconstruction
CTF correctionDetails: each particle
SymmetryPoint symmetry: I
3D reconstructionMethod: Cross-common lines / Resolution: 6 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 6800 / Nominal pixel size: 1.16 / Actual pixel size: 1.16
Details: (Single particle details: Particles were manually selected.) (Single particle--Applied symmetry: I)
Symmetry type: POINT
Atomic model buildingDetails: REFINEMENT PROTOCOL--flexible DETAILS--Initially fitted in Chimera, model rebuilt in Coot, refined in NAMD/MDFF
Ref protocol: FLEXIBLE FIT / Ref space: REAL / Target criteria: real space correlation
Atomic model building
IDPDB-IDPdb chain ID 3D fitting ID
13J27A1
23J27B1
Number of atoms included #LASTProtein: 1695 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1695

+
About Yorodumi

-
News

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.: Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links: EMDB at PDBe / Contact to PDBj

-
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

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