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Yorodumi- PDB-1thd: COMPLEX ORGANIZATION OF DENGUE VIRUS E PROTEIN AS REVEALED BY 9.5... -
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-Basic information
Entry | Database: PDB / ID: 1thd | ||||||
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Title | COMPLEX ORGANIZATION OF DENGUE VIRUS E PROTEIN AS REVEALED BY 9.5 ANGSTROM CRYO-EM RECONSTRUCTION | ||||||
Components | Major envelope protein E | ||||||
Keywords | VIRUS / FLAVIVIRUS / FLAVIVIRIDAE / DENGUE VIRUS / GLYCOPROTEIN E / CRYO-EM / Icosahedral virus | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / : / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / : / nucleoside-triphosphate phosphatase / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Dengue virus 2 Puerto Rico/PR159-S1/1969 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.5 Å | ||||||
Authors | Zhang, Y. / Zhang, W. / Ogata, S. / Clements, D. / Strauss, J.H. / Baker, T.S. / Kuhn, R.J. / Rossmann, M.G. | ||||||
Citation | Journal: Structure / Year: 2004 Title: Conformational changes of the flavivirus E glycoprotein. Authors: Ying Zhang / Wei Zhang / Steven Ogata / David Clements / James H Strauss / Timothy S Baker / Richard J Kuhn / Michael G Rossmann / Abstract: Dengue virus, a member of the Flaviviridae family, has a surface composed of 180 copies each of the envelope (E) glycoprotein and the membrane (M) protein. The crystal structure of an N-terminal ...Dengue virus, a member of the Flaviviridae family, has a surface composed of 180 copies each of the envelope (E) glycoprotein and the membrane (M) protein. The crystal structure of an N-terminal fragment of E has been determined and compared with a previously described structure. The primary difference between these structures is a 10 degrees rotation about a hinge relating the fusion domain DII to domains DI and DIII. These two rigid body components were used for independent fitting of E into the cryo-electron microscopy maps of both immature and mature dengue viruses. The fitted E structures in these two particles showed a difference of 27 degrees between the two components. Comparison of the E structure in its postfusion state with that in the immature and mature virions shows a rotation approximately around the same hinge. Flexibility of E is apparently a functional requirement for assembly and infection of flaviviruses. #1: 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 / Abstract: Improved technology for reconstructing cryo-electron microscopy (cryo-EM) images has now made it possible to determine secondary structural features of membrane proteins in enveloped viruses. The ...Improved technology for reconstructing cryo-electron microscopy (cryo-EM) images has now made it possible to determine secondary structural features of membrane proteins in enveloped viruses. The structure of mature dengue virus particles was determined to a resolution of 9.5 A by cryo-EM and image reconstruction techniques, establishing the secondary structural disposition of the 180 envelope (E) and 180 membrane (M) proteins in the lipid envelope. The alpha-helical 'stem' regions of the E molecules, as well as part of the N-terminal section of the M proteins, are buried in the outer leaflet of the viral membrane. The 'anchor' regions of E and the M proteins each form antiparallel E-E and M-M transmembrane alpha-helices, leaving their C termini on the exterior of the viral membrane, consistent with the predicted topology of the unprocessed polyprotein. This is one of only a few determinations of the disposition of transmembrane proteins in situ and shows that the nucleocapsid core and envelope proteins do not have a direct interaction in the mature virus. | ||||||
History |
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Remark 999 | SEQUENCE AUTHORS SUBMITTED COORDINATES FOR CA ATOMS ONLY. |
-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
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PDBx/mmCIF format | 1thd.cif.gz | 49.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1thd.ent.gz | 29.9 KB | Display | PDB format |
PDBx/mmJSON format | 1thd.json.gz | Tree view | PDBx/mmJSON format | |
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-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/th/1thd ftp://data.pdbj.org/pub/pdb/validation_reports/th/1thd | HTTPS FTP |
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-Related structure data
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-Assembly
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Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 43863.398 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Dengue virus 2 Puerto Rico/PR159-S1/1969 / Genus: Flavivirus / Species: Dengue virus / Strain: PR159-S1 / References: UniProt: P12823 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: DENGUE VIRUS / Type: VIRUS |
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Buffer solution | Name: 50 mM TRIS, 75 mM NACL, 1 mM EDTA / pH: 7.6 / Details: 50 mM TRIS, 75 mM NACL, 1 mM EDTA |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Details: SAMPLES WERE PREPARED AS THIN LAYERS OF VITREOUS ICE AND MAINTAINED AT LIQUID NITROGEN TEMPERATURE IN THE ELECTRON MICROSCOPE |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM200T / Date: Jun 27, 2000 |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 50000 X / Nominal defocus max: 4800 nm / Nominal defocus min: 800 nm / Cs: 2 mm |
Specimen holder | Temperature: 87 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 27 e/Å2 / Film or detector model: KODAK SO-163 FILM |
-Processing
EM software |
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CTF correction | Details: EACH VIRAL IMAGE WAS CTF CORRECTED BEFORE RECONSTRUCTION, BASED ON THE FOLLOWING EQUATION: F(CORR)=F(OBS)/[|CTF|+WIENER*(1-|CTF|)] | ||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Method: FOURIER-BESSEL METHOD / Resolution: 9.5 Å / Nominal pixel size: 2.8 Å 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 ...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.STRUCT.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 building | Protocol: OTHER / Details: METHOD--please see citation | ||||||||||||
Atomic model building | PDB-ID: 1TG8 Accession code: 1TG8 / Source name: PDB / Type: experimental model | ||||||||||||
Refinement step | Cycle: LAST
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