+Open data
-Basic information
Entry | Database: PDB / ID: 1uzg | |||||||||
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Title | CRYSTAL STRUCTURE OF THE DENGUE TYPE 3 VIRUS ENVELOPE PROTEIN | |||||||||
Components | MAJOR ENVELOPE PROTEIN E | |||||||||
Keywords | VIRAL PROTEIN / MEMBRANE FUSION / FLAVIVIRUS / FUSION LOOP / CLASS 2 FUSION PROTEIN / GLYCOPROTEIN / ENVELOPE PROTEIN | |||||||||
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 / structural molecule activity / virion attachment to host cell / virion membrane / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | DENGUE VIRUS TYPE 3 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | |||||||||
Authors | Modis, Y. / Harrison, S.C. | |||||||||
Citation | Journal: J.Virol. / Year: 2005 Title: Variable Surface Epitopes in the Crystal Structure of Dengue Virus Type 3 Envelope Glycoprotein Authors: Modis, Y. / Ogata, S. / Clements, D. / Harrison, S.C. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 2003 Title: A Ligand-Binding Pocket in the Dengue Virus Envelope Glycoprotein Authors: Modis, Y. / Ogata, S. / Clements, D. / Harrison, S.C. | |||||||||
History |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | |||||||||
Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1uzg.cif.gz | 170.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1uzg.ent.gz | 134.5 KB | Display | PDB format |
PDBx/mmJSON format | 1uzg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uz/1uzg ftp://data.pdbj.org/pub/pdb/validation_reports/uz/1uzg | HTTPS FTP |
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-Related structure data
Related structure data | 1oanS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Refine code: 5
NCS ensembles :
NCS oper: (Code: given Matrix: (-0.90052, -0.43253, 0.04449), Vector: Details | THE VIRION OF THIS VIRUS IS A NUCLEOCAPSID COVERED BY ALIPOPROTEIN ENVELOPE CONSISTING OF A LIPID MEMBRANE AND 2ENVELOPE GLYCOPROTEINS, M AND E. THE NUCLEOCAPSID IS ACOMPLEX OF PROTEIN C AND MRNA. | |
-Components
-Protein / Non-polymers , 2 types, 16 molecules AB
#1: Protein | Mass: 43170.398 Da / Num. of mol.: 2 / Fragment: SOLUBLE ECTODOMAIN, RESIDUES 281-672 Source method: isolated from a genetically manipulated source Source: (gene. exp.) DENGUE VIRUS TYPE 3 / Cell line: DROSOPHILA SCHNEIDER 2 / Plasmid: PMTT / Cell line (production host): SCHNEIDER 2 / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: P27915 #6: Water | ChemComp-HOH / | |
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-Sugars , 4 types, 4 molecules
#2: Polysaccharide | beta-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#4: Polysaccharide | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Sugar | ChemComp-NAG / |
-Details
Compound details | CATALYTIC ACTIVITY: SELECTIVE HYDROLYSIS OF XAA-XAA-|-XBB BONDS IN WHICH EACH OF THE XAA CAN BE ...CATALYTIC ACTIVITY: SELECTIVE HYDROLYSIS |
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Sequence details | RESIDUES 100-108 FORM THE GLYCINE-RICH, HYDROPHOBIC FUSION LOOP (ALLISON ET AL., J.VIROL. 75, 4268- ...RESIDUES 100-108 FORM THE GLYCINE-RICH, HYDROPHOBI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.737 Å3/Da / Density % sol: 55.1 % |
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Crystal grow | pH: 8.5 / Details: 15% PEG 8K, 0.2 M LICL2, 0.1 M TRIS/HCL, PH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.91 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 15, 2003 / Details: RH-COATED SI MIRRORS |
Radiation | Monochromator: SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 3.6→21 Å / Num. obs: 12090 / % possible obs: 91.8 % / Redundancy: 5 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 12.3 |
Reflection shell | Resolution: 3.6→3.73 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2.6 / % possible all: 81.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1OAN Resolution: 3.5→20.99 Å / Cor.coef. Fo:Fc: 0.861 / Cor.coef. Fo:Fc free: 0.867 / SU B: 52.79 / SU ML: 0.827 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.862 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 75.13 Å2
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Refinement step | Cycle: LAST / Resolution: 3.5→20.99 Å
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Refine LS restraints |
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