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Yorodumi- PDB-3c6e: Crystal structure of the precursor membrane protein- envelope pro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c6e | |||||||||
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Title | Crystal structure of the precursor membrane protein- envelope protein heterodimer from the dengue 2 virus at neutral pH | |||||||||
Components |
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Keywords | VIRAL PROTEIN / beta barrel / prM-E protein complex structure / Helicase / Hydrolase / Nucleotide-binding / RNA replication / Transmembrane | |||||||||
Function / homology | Function and homology information : / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity ...: / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / protein complex oligomerization / monoatomic ion channel activity / 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 / protein dimerization activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / induction by virus of host autophagy / serine-type endopeptidase activity / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / structural molecule activity / virion membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Dengue virus 2 Thailand/16681/84 Dengue virus | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | |||||||||
Authors | Li, L. | |||||||||
Citation | Journal: Science / Year: 2008 Title: The flavivirus precursor membrane-envelope protein complex: structure and maturation. Authors: Long Li / Shee-Mei Lok / I-Mei Yu / Ying Zhang / Richard J Kuhn / Jue Chen / Michael G Rossmann / Abstract: Many viruses go through a maturation step in the final stages of assembly before being transmitted to another host. The maturation process of flaviviruses is directed by the proteolytic cleavage of ...Many viruses go through a maturation step in the final stages of assembly before being transmitted to another host. The maturation process of flaviviruses is directed by the proteolytic cleavage of the precursor membrane protein (prM), turning inert virus into infectious particles. We have determined the 2.2 angstrom resolution crystal structure of a recombinant protein in which the dengue virus prM is linked to the envelope glycoprotein E. The structure represents the prM-E heterodimer and fits well into the cryo-electron microscopy density of immature virus at neutral pH. The pr peptide beta-barrel structure covers the fusion loop in E, preventing fusion with host cell membranes. The structure provides a basis for identifying the stages of its pH-directed conformational metamorphosis during maturation, ending with release of pr when budding from the host. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c6e.cif.gz | 113.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c6e.ent.gz | 84.3 KB | Display | PDB format |
PDBx/mmJSON format | 3c6e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3c6e_validation.pdf.gz | 769.9 KB | Display | wwPDB validaton report |
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Full document | 3c6e_full_validation.pdf.gz | 790.3 KB | Display | |
Data in XML | 3c6e_validation.xml.gz | 22.5 KB | Display | |
Data in CIF | 3c6e_validation.cif.gz | 30.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c6/3c6e ftp://data.pdbj.org/pub/pdb/validation_reports/c6/3c6e | HTTPS FTP |
-Related structure data
Related structure data | 3c5xC 3c6dC 1tg8S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 2 types, 2 molecules AC
#1: Protein | Mass: 44801.410 Da / Num. of mol.: 1 / Fragment: UNP residues 281-674 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus 2 Thailand/16681/84 / Genus: Flavivirus / Species: Dengue virus / Strain: 16681 / Plasmid: pMT/BiP/prM-TEV-E / Genus (production host): Drosophila / Production host: Drosophila (fruit flies) / Strain (production host): S2 cells / References: UniProt: O09234, UniProt: O11875*PLUS |
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#2: Protein | Mass: 14870.891 Da / Num. of mol.: 1 / Fragment: UNP residues 115-244 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Dengue virus / Genus: Flavivirus / Strain: 2 / Plasmid: pMT/BiP/prM-TEV-E / Genus (production host): Drosophila / Production host: Drosophila (fruit flies) / Strain (production host): S2 cells / References: UniProt: O09234, UniProt: Q3BCY3*PLUS |
-Sugars , 3 types, 3 molecules
#3: Polysaccharide | alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#4: Sugar | ChemComp-NDG / |
#5: Sugar | ChemComp-NAG / |
-Non-polymers , 1 types, 45 molecules
#6: Water | ChemComp-HOH / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.52 Å3/Da / Density % sol: 65.03 % |
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Crystal grow | Temperature: 293 K / Method: evaporation / pH: 7 Details: 10-12% PEG 3350, 0.1M HEPES, pH7.0, EVAPORATION, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2006 |
Radiation | Monochromator: Si(111) Double Crystal Monochrometer / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. all: 26645 / Num. obs: 26645 / % possible obs: 99.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 70.8 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 4.3 / Num. unique all: 2617 / Rsym value: 0.28 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1TG8 Resolution: 2.6→50 Å / Isotropic thermal model: anisotropic / Cross valid method: R free / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.69 Å
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