+Open data
-Basic information
Entry | Database: PDB / ID: 1n6g | ||||||
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Title | The structure of immature Dengue-2 prM particles | ||||||
Components | major envelope protein E | ||||||
Keywords | VIRUS / FLAVIVIRUS / FLAVIVIRIDAE / DENGUE immature VIRUS / prM particle / Icosahedral virus | ||||||
Function / homology | Function and homology information flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity ...flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / double-stranded RNA binding / viral capsid / nucleoside-triphosphate phosphatase / 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 perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / 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: 16 Å | ||||||
Authors | Zhang, Y. / Corver, J. / Chipman, P.R. / Zhang, W. / Pletnev, S.V. / Sedlak, D. / Baker, T.S. / Strauss, J.H. / Kuhn, R.J. / Rossmann, M.G. | ||||||
Citation | Journal: EMBO J / Year: 2003 Title: Structures of immature flavivirus particles. Authors: Ying Zhang / Jeroen Corver / Paul R Chipman / Wei Zhang / Sergei V Pletnev / Dagmar Sedlak / Timothy S Baker / James H Strauss / Richard J Kuhn / Michael G Rossmann / Abstract: Structures of prM-containing dengue and yellow fever virus particles were determined to 16 and 25 A resolution, respectively, by cryoelectron microscopy and image reconstruction techniques. The ...Structures of prM-containing dengue and yellow fever virus particles were determined to 16 and 25 A resolution, respectively, by cryoelectron microscopy and image reconstruction techniques. The closely similar structures show 60 icosahedrally organized trimeric spikes on the particle surface. Each spike consists of three prM:E heterodimers, where E is an envelope glycoprotein and prM is the precursor to the membrane protein M. The pre-peptide components of the prM proteins in each spike cover the fusion peptides at the distal ends of the E glycoproteins in a manner similar to the organization of the glycoproteins in the alphavirus spikes. Each heterodimer is associated with an E and a prM transmembrane density. These transmembrane densities represent either an EE or prMprM antiparallel coiled coil by which each protein spans the membrane twice, leaving the C-terminus of each protein on the exterior of the viral membrane, consistent with the predicted membrane-spanning domains of the unprocessed polyprotein. | ||||||
History |
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Remark 999 | SEQUENCE AUTHORS PROVIDED COORDINATES FOR ALPHA CARBONS ONLY. THE SEQRES RECORDS ARE FROM TICK-BORN ...SEQUENCE AUTHORS PROVIDED COORDINATES FOR ALPHA CARBONS ONLY. THE SEQRES RECORDS ARE FROM TICK-BORN ENCEPHALITIS VIRUS BECAUSE THE FITTING MODEL OF MAJOR ENVELOPE PROTEIN E (1SVB) WAS USED IN THIS STUDY. |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 1n6g.cif.gz | 48.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n6g.ent.gz | 29.2 KB | Display | PDB format |
PDBx/mmJSON format | 1n6g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n6g_validation.pdf.gz | 279.5 KB | Display | wwPDB validaton report |
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Full document | 1n6g_full_validation.pdf.gz | 279 KB | Display | |
Data in XML | 1n6g_validation.xml.gz | 880 B | Display | |
Data in CIF | 1n6g_validation.cif.gz | 11.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n6/1n6g ftp://data.pdbj.org/pub/pdb/validation_reports/n6/1n6g | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 43231.145 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: P14336 |
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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-2 immature particle / Type: COMPLEX Details: The samples were produced by adding ammonium cloride to the medium in the late infection stage |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Crystal grow | *PLUS Method: electron microscopy / Details: electron microscopy |
-Electron microscopy imaging
Microscopy | Model: FEI/PHILIPS CM300FEG/T |
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Electron gun | Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 33000 X / Nominal defocus max: 3640 nm / Nominal defocus min: 1662 nm / Cs: 2 mm |
Specimen holder | Temperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 15 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] | ||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||
3D reconstruction | Method: COMMON-LINES AND POLAR-FOURIER-TRANSFORM ((FULLER ET AL. 1996,J.STRUC.BIOL. 116, 48-55 BAKER ANDCHENG, 1996, J.STRUC.BIOL. 116, 120-130) Resolution: 16 Å / Nominal pixel size: 4.24 Å / Symmetry type: POINT | ||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL Details: METHOD--The atomic structure of TBEV-E monomer was first fitted in one position in one asymmetry unit, then the densities at all pixels covered by the first fitted monomer was set to zero. ...Details: METHOD--The atomic structure of TBEV-E monomer was first fitted in one position in one asymmetry unit, then the densities at all pixels covered by the first fitted monomer was set to zero. After that, the second monomer was fitted into the left densities. The densities coresponding to the second monomer was again set to zero, then the third monomer was fitted. | ||||||||||||||||
Atomic model building | PDB-ID: 1SVB Accession code: 1SVB / Source name: PDB / Type: experimental model | ||||||||||||||||
Refinement step | Cycle: LAST
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