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Yorodumi- PDB-7qre: Structure of the hetero-tetramer complex between precursor membra... -
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-Basic information
Entry | Database: PDB / ID: 7qre | ||||||||||||
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Title | Structure of the hetero-tetramer complex between precursor membrane protein fragment (pr) and envelope protein (E) from tick-borne encephalitis virus | ||||||||||||
Components |
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Keywords | VIRAL PROTEIN / class II fusion envelope protein / precursor membrane protein / chaperone / flavivirus maturation / trans-golgi acid pH | ||||||||||||
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 / viral capsid / double-stranded RNA binding / 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 / viral capsid / double-stranded RNA binding / 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 innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / induction by virus of host autophagy / serine-type endopeptidase activity / RNA-directed RNA polymerase / 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 / 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 | Tick-borne encephalitis virus | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å | ||||||||||||
Authors | Vaney, M.C. / Dellarole, M. / Rey, F.A. | ||||||||||||
Funding support | France, 3items
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Citation | Journal: Nat Commun / Year: 2022 Title: Evolution and activation mechanism of the flavivirus class II membrane-fusion machinery. Authors: Vaney, M.C. / Dellarole, M. / Duquerroy, S. / Medits, I. / Tsouchnikas, G. / Rouvinski, A. / England, P. / Stiasny, K. / Heinz, F.X. / Rey, F.A. #1: Journal: Nature / Year: 1995 Title: The envelope glycoprotein from tick-borne encephalitis virus at 2 A resolution. Authors: Rey, F.A. / Heinz, F.X. / Mandl, C. / Kunz, C. / Harrison, S.C. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qre.cif.gz | 206 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qre.ent.gz | 164.6 KB | Display | PDB format |
PDBx/mmJSON format | 7qre.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qre_validation.pdf.gz | 468.9 KB | Display | wwPDB validaton report |
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Full document | 7qre_full_validation.pdf.gz | 473.6 KB | Display | |
Data in XML | 7qre_validation.xml.gz | 18.4 KB | Display | |
Data in CIF | 7qre_validation.cif.gz | 25.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qr/7qre ftp://data.pdbj.org/pub/pdb/validation_reports/qr/7qre | HTTPS FTP |
-Related structure data
Related structure data | 7qrfC 7qrgC 1svbS 3c5xS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 13703.804 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: For purification, at the C-terminal of pr (chain D), an enterokinase site with a dstrep-tag sequence is added: GPFEDDDDKAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK. Source: (gene. exp.) Tick-borne encephalitis virus (WESTERN SUBTYPE) Strain: Neudoerfl / Plasmid: PT389 / Cell (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P14336 | ||||||
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#2: Protein | Mass: 47639.652 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: For purification, at the C-terminal of E (chain A), an enterokinase site with a dstrep-tag sequence is added: GPFEDDDDKAGWSHPQFEKGGGSGGGSGGGSWSHPQFEK Source: (gene. exp.) Tick-borne encephalitis virus (WESTERN SUBTYPE) Strain: Neudoerfl / Plasmid: PT389 / Cell (production host): SCHNEIDER 2 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: P14336 | ||||||
#3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.01 Å3/Da / Density % sol: 59.19 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 4.6 Details: 0.2M (NH4)SO4, 0.1M Na acetate pH 4.6, 28% (v/v) PEG MME 550, 2.8% (v/v) tert-Butanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 1.07197 Å | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 18, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.07197 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.7→49.56 Å / Num. obs: 21401 / % possible obs: 100 % / Redundancy: 32.9 % / Biso Wilson estimate: 101.65 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.244 / Rpim(I) all: 0.043 / Rrim(I) all: 0.248 / Net I/σ(I): 13.8 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1SVB, 3C5X Resolution: 2.7→49.54 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.921 / SU R Cruickshank DPI: 0.386 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.403 / SU Rfree Blow DPI: 0.28 / SU Rfree Cruickshank DPI: 0.28
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Displacement parameters | Biso max: 178.58 Å2 / Biso mean: 85.14 Å2 / Biso min: 33.51 Å2
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Refine analyze | Luzzati coordinate error obs: 0.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.7→49.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.83 Å / Rfactor Rfree error: 0 / Total num. of bins used: 11
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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